Starting phenix.real_space_refine on Wed Apr 10 18:13:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bbe_15954/04_2024/8bbe_15954.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bbe_15954/04_2024/8bbe_15954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bbe_15954/04_2024/8bbe_15954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bbe_15954/04_2024/8bbe_15954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bbe_15954/04_2024/8bbe_15954.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bbe_15954/04_2024/8bbe_15954.pdb" } resolution = 3.5 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= 0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 137 5.16 5 C 12840 2.51 5 N 3438 2.21 5 O 3766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 2": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ARG 250": "NH1" <-> "NH2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 277": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 398": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C ARG 425": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 474": "NH1" <-> "NH2" Residue "C ARG 485": "NH1" <-> "NH2" Residue "C ARG 518": "NH1" <-> "NH2" Residue "C ARG 526": "NH1" <-> "NH2" Residue "C ARG 587": "NH1" <-> "NH2" Residue "C ARG 627": "NH1" <-> "NH2" Residue "C ARG 647": "NH1" <-> "NH2" Residue "C ARG 668": "NH1" <-> "NH2" Residue "C ARG 673": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 687": "NH1" <-> "NH2" Residue "C ARG 715": "NH1" <-> "NH2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D ARG 691": "NH1" <-> "NH2" Residue "D ARG 702": "NH1" <-> "NH2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D ARG 718": "NH1" <-> "NH2" Residue "D ARG 723": "NH1" <-> "NH2" Residue "D ARG 832": "NH1" <-> "NH2" Residue "D ARG 858": "NH1" <-> "NH2" Residue "D ARG 863": "NH1" <-> "NH2" Residue "D ARG 867": "NH1" <-> "NH2" Residue "D ARG 898": "NH1" <-> "NH2" Residue "D ARG 908": "NH1" <-> "NH2" Residue "D ARG 926": "NH1" <-> "NH2" Residue "D ARG 939": "NH1" <-> "NH2" Residue "D ARG 964": "NH1" <-> "NH2" Residue "D ARG 981": "NH1" <-> "NH2" Residue "D ARG 991": "NH1" <-> "NH2" Residue "D ARG 997": "NH1" <-> "NH2" Residue "D ARG 998": "NH1" <-> "NH2" Residue "D ARG 1007": "NH1" <-> "NH2" Residue "D ARG 1015": "NH1" <-> "NH2" Residue "D ARG 1018": "NH1" <-> "NH2" Residue "D ARG 1044": "NH1" <-> "NH2" Residue "D ARG 1050": "NH1" <-> "NH2" Residue "D ARG 1053": "NH1" <-> "NH2" Residue "D ARG 1102": "NH1" <-> "NH2" Residue "D ARG 1123": "NH1" <-> "NH2" Residue "D ARG 1175": "NH1" <-> "NH2" Residue "D ARG 1177": "NH1" <-> "NH2" Residue "D ARG 1182": "NH1" <-> "NH2" Residue "D ARG 1222": "NH1" <-> "NH2" Residue "D ARG 1225": "NH1" <-> "NH2" Residue "D ARG 1228": "NH1" <-> "NH2" Residue "D ARG 1263": "NH1" <-> "NH2" Residue "D ARG 1281": "NH1" <-> "NH2" Residue "D ARG 1303": "NH1" <-> "NH2" Residue "D ARG 1311": "NH1" <-> "NH2" Residue "D ARG 1315": "NH1" <-> "NH2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E ARG 119": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 350": "NH1" <-> "NH2" Residue "E ARG 353": "NH1" <-> "NH2" Residue "E ARG 455": "NH1" <-> "NH2" Residue "E ARG 472": "NH1" <-> "NH2" Residue "E ARG 476": "NH1" <-> "NH2" Residue "E ARG 478": "NH1" <-> "NH2" Residue "E ARG 504": "NH1" <-> "NH2" Residue "E ARG 521": "NH1" <-> "NH2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E ARG 545": "NH1" <-> "NH2" Residue "E ARG 557": "NH1" <-> "NH2" Residue "E ARG 575": "NH1" <-> "NH2" Residue "E ARG 593": "NH1" <-> "NH2" Residue "E ARG 594": "NH1" <-> "NH2" Residue "E ARG 616": "NH1" <-> "NH2" Residue "E ARG 621": "NH1" <-> "NH2" Residue "E ARG 669": "NH1" <-> "NH2" Residue "E ARG 672": "NH1" <-> "NH2" Residue "E ARG 675": "NH1" <-> "NH2" Residue "E ARG 697": "NH1" <-> "NH2" Residue "E ARG 700": "NH1" <-> "NH2" Residue "E ARG 721": "NH1" <-> "NH2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "E ARG 753": "NH1" <-> "NH2" Residue "E ARG 759": "NH1" <-> "NH2" Residue "E ARG 766": "NH1" <-> "NH2" Residue "E ARG 767": "NH1" <-> "NH2" Residue "E ARG 774": "NH1" <-> "NH2" Residue "E ARG 782": "NH1" <-> "NH2" Residue "E ARG 813": "NH1" <-> "NH2" Residue "E ARG 827": "NH1" <-> "NH2" Residue "E ARG 831": "NH1" <-> "NH2" Residue "E ARG 868": "NH1" <-> "NH2" Residue "E ARG 919": "NH1" <-> "NH2" Residue "E ARG 938": "NH1" <-> "NH2" Residue "E ARG 966": "NH1" <-> "NH2" Residue "E ARG 1018": "NH1" <-> "NH2" Residue "E ARG 1025": "NH1" <-> "NH2" Residue "E ARG 1038": "NH1" <-> "NH2" Residue "E ARG 1079": "NH1" <-> "NH2" Residue "E ARG 1122": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F ARG 168": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20181 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 5595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5595 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 685} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 5253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5253 Classifications: {'peptide': 648} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 627} Chain: "E" Number of atoms: 8863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8863 Classifications: {'peptide': 1112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1078} Chain breaks: 4 Chain: "F" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 470 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Time building chain proxies: 10.67, per 1000 atoms: 0.53 Number of scatterers: 20181 At special positions: 0 Unit cell: (92.829, 134.442, 196.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 137 16.00 O 3766 8.00 N 3438 7.00 C 12840 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: 7.68 Conformation dependent library (CDL) restraints added in 3.3 seconds 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4762 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 32 sheets defined 46.0% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 188 through 193 removed outlier: 3.939A pdb=" N SER C 192 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 617 through 627 removed outlier: 3.644A pdb=" N ARG C 627 " --> pdb=" O GLN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 4.224A pdb=" N GLN C 635 " --> pdb=" O LYS C 631 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 656 Processing helix chain 'C' and resid 658 through 670 removed outlier: 3.611A pdb=" N LYS C 664 " --> pdb=" O GLU C 660 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 686 Processing helix chain 'C' and resid 691 through 703 Processing helix chain 'C' and resid 705 through 716 Processing helix chain 'C' and resid 718 through 729 removed outlier: 3.837A pdb=" N ALA C 722 " --> pdb=" O HIS C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'D' and resid 670 through 679 Processing helix chain 'D' and resid 686 through 701 Processing helix chain 'D' and resid 704 through 719 Processing helix chain 'D' and resid 721 through 735 Processing helix chain 'D' and resid 737 through 750 Processing helix chain 'D' and resid 755 through 769 Processing helix chain 'D' and resid 771 through 785 Processing helix chain 'D' and resid 790 through 802 Processing helix chain 'D' and resid 804 through 815 Processing helix chain 'D' and resid 823 through 844 removed outlier: 3.834A pdb=" N LYS D 843 " --> pdb=" O LYS D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 872 removed outlier: 4.930A pdb=" N MET D 870 " --> pdb=" O LYS D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 897 Processing helix chain 'D' and resid 899 through 914 Processing helix chain 'D' and resid 917 through 931 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 951 through 965 Processing helix chain 'D' and resid 967 through 982 Processing helix chain 'D' and resid 985 through 1000 Processing helix chain 'D' and resid 1001 through 1004 Processing helix chain 'D' and resid 1005 through 1016 removed outlier: 3.711A pdb=" N PHE D1009 " --> pdb=" O VAL D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1021 Processing helix chain 'D' and resid 1022 through 1037 Processing helix chain 'D' and resid 1038 through 1050 Processing helix chain 'D' and resid 1054 through 1069 Processing helix chain 'D' and resid 1077 through 1082 removed outlier: 4.007A pdb=" N ASN D1082 " --> pdb=" O GLU D1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1089 Processing helix chain 'D' and resid 1090 through 1111 removed outlier: 4.292A pdb=" N LYS D1106 " --> pdb=" O ARG D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1115 through 1133 Processing helix chain 'D' and resid 1135 through 1153 Processing helix chain 'D' and resid 1156 through 1170 Processing helix chain 'D' and resid 1172 through 1185 removed outlier: 3.626A pdb=" N ASN D1178 " --> pdb=" O PRO D1174 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D1179 " --> pdb=" O ARG D1175 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D1183 " --> pdb=" O GLN D1179 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1210 Processing helix chain 'D' and resid 1212 through 1227 removed outlier: 3.807A pdb=" N ALA D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1244 Processing helix chain 'D' and resid 1246 through 1261 Processing helix chain 'D' and resid 1265 through 1279 Processing helix chain 'D' and resid 1281 through 1296 Processing helix chain 'D' and resid 1301 through 1315 removed outlier: 3.571A pdb=" N ASP D1308 " --> pdb=" O LYS D1304 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG D1315 " --> pdb=" O ARG D1311 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 15 Processing helix chain 'E' and resid 195 through 199 Processing helix chain 'E' and resid 473 through 475 No H-bonds generated for 'chain 'E' and resid 473 through 475' Processing helix chain 'E' and resid 495 through 501 removed outlier: 3.855A pdb=" N ILE E 500 " --> pdb=" O SER E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 652 Processing helix chain 'E' and resid 659 through 661 No H-bonds generated for 'chain 'E' and resid 659 through 661' Processing helix chain 'E' and resid 668 through 681 Processing helix chain 'E' and resid 682 through 693 removed outlier: 3.986A pdb=" N SER E 687 " --> pdb=" O ILE E 683 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN E 688 " --> pdb=" O LYS E 684 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE E 689 " --> pdb=" O ASP E 685 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE E 690 " --> pdb=" O ALA E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 695 through 709 removed outlier: 3.525A pdb=" N ARG E 700 " --> pdb=" O PRO E 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 711 through 722 Processing helix chain 'E' and resid 724 through 735 Processing helix chain 'E' and resid 739 through 751 removed outlier: 3.530A pdb=" N TYR E 750 " --> pdb=" O GLU E 746 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE E 751 " --> pdb=" O VAL E 747 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 764 Processing helix chain 'E' and resid 766 through 778 Processing helix chain 'E' and resid 779 through 790 Processing helix chain 'E' and resid 795 through 813 removed outlier: 3.539A pdb=" N ARG E 813 " --> pdb=" O TYR E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 815 through 824 removed outlier: 3.905A pdb=" N GLN E 821 " --> pdb=" O LEU E 817 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR E 822 " --> pdb=" O ASN E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 828 through 839 removed outlier: 4.524A pdb=" N GLU E 834 " --> pdb=" O GLU E 830 " (cutoff:3.500A) Processing helix chain 'E' and resid 841 through 852 removed outlier: 3.529A pdb=" N SER E 851 " --> pdb=" O ASN E 847 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 852 " --> pdb=" O LEU E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 858 through 870 Processing helix chain 'E' and resid 871 through 882 Processing helix chain 'E' and resid 884 through 895 removed outlier: 3.848A pdb=" N ALA E 888 " --> pdb=" O GLN E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 904 removed outlier: 3.747A pdb=" N LEU E 904 " --> pdb=" O LYS E 900 " (cutoff:3.500A) Processing helix chain 'E' and resid 908 through 927 removed outlier: 3.527A pdb=" N GLU E 912 " --> pdb=" O HIS E 908 " (cutoff:3.500A) Processing helix chain 'E' and resid 929 through 940 Processing helix chain 'E' and resid 942 through 960 Processing helix chain 'E' and resid 963 through 985 Processing helix chain 'E' and resid 986 through 986 No H-bonds generated for 'chain 'E' and resid 986 through 986' Processing helix chain 'E' and resid 1018 through 1022 removed outlier: 3.979A pdb=" N ASN E1022 " --> pdb=" O PHE E1019 " (cutoff:3.500A) Processing helix chain 'E' and resid 1024 through 1042 Processing helix chain 'E' and resid 1044 through 1055 Processing helix chain 'E' and resid 1056 through 1059 removed outlier: 4.114A pdb=" N GLU E1059 " --> pdb=" O LYS E1056 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1056 through 1059' Processing helix chain 'E' and resid 1063 through 1079 removed outlier: 3.573A pdb=" N ILE E1067 " --> pdb=" O PRO E1063 " (cutoff:3.500A) Processing helix chain 'E' and resid 1080 through 1093 Processing helix chain 'E' and resid 1098 through 1116 Processing helix chain 'E' and resid 1126 through 1131 Processing helix chain 'E' and resid 1165 through 1170 Processing helix chain 'F' and resid 131 through 141 removed outlier: 3.533A pdb=" N ASN F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS F 141 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 163 through 168 Processing helix chain 'F' and resid 175 through 186 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 10 removed outlier: 5.619A pdb=" N LEU C 5 " --> pdb=" O GLN C 349 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN C 349 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR C 344 " --> pdb=" O CYS C 340 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 326 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 20 removed outlier: 4.008A pdb=" N ASP C 17 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN C 47 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASP C 39 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU C 45 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 61 removed outlier: 3.550A pdb=" N CYS C 58 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 88 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 96 through 101 removed outlier: 4.309A pdb=" N CYS C 98 " --> pdb=" O CYS C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 135 through 140 removed outlier: 4.016A pdb=" N ILE C 155 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE C 156 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS C 168 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C 158 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.733A pdb=" N SER C 181 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 263 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS C 275 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE C 265 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 283 through 288 removed outlier: 4.433A pdb=" N ILE C 286 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU C 296 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR C 288 " --> pdb=" O TYR C 294 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR C 294 " --> pdb=" O TYR C 288 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C 304 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR C 316 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 306 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AA9, first strand: chain 'C' and resid 393 through 397 removed outlier: 6.156A pdb=" N GLU C 413 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL C 426 " --> pdb=" O GLU C 413 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 438 through 441 removed outlier: 3.516A pdb=" N LEU C 438 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 454 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU C 466 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS C 456 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 478 removed outlier: 4.189A pdb=" N GLN C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 497 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 519 through 522 removed outlier: 3.659A pdb=" N CYS C 519 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS C 538 " --> pdb=" O GLN C 551 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN C 551 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL C 540 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 557 through 560 removed outlier: 3.513A pdb=" N SER C 557 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 593 through 598 removed outlier: 5.885A pdb=" N VAL C 594 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU C 605 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 596 " --> pdb=" O PHE C 603 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 2 through 10 removed outlier: 6.714A pdb=" N PHE E 328 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS E 8 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE E 326 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 17 through 22 removed outlier: 3.926A pdb=" N LEU E 38 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET E 63 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 80 removed outlier: 4.235A pdb=" N LYS E 85 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N MET E 99 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLU E 107 " --> pdb=" O MET E 99 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR E 101 " --> pdb=" O TRP E 105 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TRP E 105 " --> pdb=" O TYR E 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 118 through 123 removed outlier: 6.852A pdb=" N VAL E 141 " --> pdb=" O ILE E 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 162 through 164 removed outlier: 6.424A pdb=" N ASP E 184 " --> pdb=" O PHE E 189 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE E 189 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 207 through 212 removed outlier: 4.023A pdb=" N ARG E 235 " --> pdb=" O PHE E 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 255 through 261 removed outlier: 5.204A pdb=" N VAL E 256 " --> pdb=" O PHE E 273 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE E 273 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN E 284 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY E 297 " --> pdb=" O PHE E 288 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 337 through 340 removed outlier: 4.218A pdb=" N ARG E 350 " --> pdb=" O GLU E 355 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU E 355 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 376 through 382 removed outlier: 6.783A pdb=" N ALA E 389 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE E 379 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE E 387 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR E 381 " --> pdb=" O PHE E 385 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE E 385 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE E 410 " --> pdb=" O TYR E 426 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR E 426 " --> pdb=" O PHE E 410 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU E 412 " --> pdb=" O PRO E 424 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU E 414 " --> pdb=" O LEU E 422 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 433 through 436 Processing sheet with id=AC7, first strand: chain 'E' and resid 507 through 512 removed outlier: 3.543A pdb=" N ALA E 509 " --> pdb=" O GLY E 520 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR E 525 " --> pdb=" O ARG E 521 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER E 530 " --> pdb=" O LEU E 536 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU E 536 " --> pdb=" O SER E 530 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 546 through 551 removed outlier: 4.250A pdb=" N VAL E 566 " --> pdb=" O ASP E 562 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N LEU E 572 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N LEU E 588 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA E 574 " --> pdb=" O GLY E 586 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 546 through 551 removed outlier: 4.250A pdb=" N VAL E 566 " --> pdb=" O ASP E 562 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG E 593 " --> pdb=" O LEU E 567 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 599 through 601 Processing sheet with id=AD2, first strand: chain 'E' and resid 616 through 617 Processing sheet with id=AD3, first strand: chain 'E' and resid 634 through 639 removed outlier: 5.750A pdb=" N ILE E 635 " --> pdb=" O VAL E 646 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL E 646 " --> pdb=" O ILE E 635 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 1153 through 1154 Processing sheet with id=AD5, first strand: chain 'F' and resid 147 through 148 1080 hydrogen bonds defined for protein. 3102 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: 9.12 Time building geometry restraints manager: 8.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5178 1.33 - 1.46: 3776 1.46 - 1.58: 11424 1.58 - 1.70: 0 1.70 - 1.82: 205 Bond restraints: 20583 Sorted by residual: bond pdb=" CA PRO C 482 " pdb=" C PRO C 482 " ideal model delta sigma weight residual 1.517 1.541 -0.024 6.70e-03 2.23e+04 1.29e+01 bond pdb=" CZ ARG C 474 " pdb=" NH2 ARG C 474 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.24e+01 bond pdb=" CZ ARG E1122 " pdb=" NH2 ARG E1122 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.12e+01 bond pdb=" CZ ARG D 997 " pdb=" NH2 ARG D 997 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.09e+01 bond pdb=" CZ ARG C 189 " pdb=" NH2 ARG C 189 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.07e+01 ... (remaining 20578 not shown) Histogram of bond angle deviations from ideal: 96.59 - 104.43: 230 104.43 - 112.26: 8641 112.26 - 120.09: 10376 120.09 - 127.92: 8364 127.92 - 135.75: 176 Bond angle restraints: 27787 Sorted by residual: angle pdb=" CA PHE E 620 " pdb=" CB PHE E 620 " pdb=" CG PHE E 620 " ideal model delta sigma weight residual 113.80 120.93 -7.13 1.00e+00 1.00e+00 5.09e+01 angle pdb=" C ASP D1004 " pdb=" N VAL D1005 " pdb=" CA VAL D1005 " ideal model delta sigma weight residual 120.24 124.23 -3.99 6.30e-01 2.52e+00 4.00e+01 angle pdb=" C TYR C 61 " pdb=" CA TYR C 61 " pdb=" CB TYR C 61 " ideal model delta sigma weight residual 109.65 120.30 -10.65 1.75e+00 3.27e-01 3.70e+01 angle pdb=" C VAL C 669 " pdb=" N GLN C 670 " pdb=" CA GLN C 670 " ideal model delta sigma weight residual 122.07 130.57 -8.50 1.43e+00 4.89e-01 3.53e+01 angle pdb=" C LYS D 788 " pdb=" N ASN D 789 " pdb=" CA ASN D 789 " ideal model delta sigma weight residual 120.82 129.68 -8.86 1.50e+00 4.44e-01 3.49e+01 ... (remaining 27782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11543 17.99 - 35.99: 750 35.99 - 53.98: 107 53.98 - 71.98: 36 71.98 - 89.97: 18 Dihedral angle restraints: 12454 sinusoidal: 5066 harmonic: 7388 Sorted by residual: dihedral pdb=" CA LEU D1314 " pdb=" C LEU D1314 " pdb=" N ARG D1315 " pdb=" CA ARG D1315 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA ALA D1049 " pdb=" C ALA D1049 " pdb=" N ARG D1050 " pdb=" CA ARG D1050 " ideal model delta harmonic sigma weight residual 180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA SER C 458 " pdb=" C SER C 458 " pdb=" N PHE C 459 " pdb=" CA PHE C 459 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 12451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2263 0.104 - 0.209: 680 0.209 - 0.313: 88 0.313 - 0.417: 12 0.417 - 0.522: 4 Chirality restraints: 3047 Sorted by residual: chirality pdb=" CA GLU C 122 " pdb=" N GLU C 122 " pdb=" C GLU C 122 " pdb=" CB GLU C 122 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" CA LYS E1159 " pdb=" N LYS E1159 " pdb=" C LYS E1159 " pdb=" CB LYS E1159 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA PHE C 116 " pdb=" N PHE C 116 " pdb=" C PHE C 116 " pdb=" CB PHE C 116 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 ... (remaining 3044 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 61 " 0.318 2.00e-02 2.50e+03 1.60e-01 5.14e+02 pdb=" CG TYR C 61 " -0.205 2.00e-02 2.50e+03 pdb=" CD1 TYR C 61 " -0.088 2.00e-02 2.50e+03 pdb=" CD2 TYR C 61 " -0.143 2.00e-02 2.50e+03 pdb=" CE1 TYR C 61 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR C 61 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR C 61 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR C 61 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 259 " 0.152 2.00e-02 2.50e+03 8.30e-02 1.72e+02 pdb=" CG TRP C 259 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP C 259 " -0.081 2.00e-02 2.50e+03 pdb=" CD2 TRP C 259 " -0.042 2.00e-02 2.50e+03 pdb=" NE1 TRP C 259 " -0.065 2.00e-02 2.50e+03 pdb=" CE2 TRP C 259 " 0.023 2.00e-02 2.50e+03 pdb=" CE3 TRP C 259 " -0.103 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 259 " 0.116 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 259 " -0.063 2.00e-02 2.50e+03 pdb=" CH2 TRP C 259 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 90 " 0.155 2.00e-02 2.50e+03 9.11e-02 1.66e+02 pdb=" CG TYR C 90 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR C 90 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 TYR C 90 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 TYR C 90 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR C 90 " -0.069 2.00e-02 2.50e+03 pdb=" CZ TYR C 90 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 90 " 0.147 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 10245 3.02 - 3.49: 20747 3.49 - 3.96: 33676 3.96 - 4.43: 37042 4.43 - 4.90: 61969 Nonbonded interactions: 163679 Sorted by model distance: nonbonded pdb=" OH TYR E 450 " pdb=" OE1 GLU E 477 " model vdw 2.550 2.440 nonbonded pdb=" OD1 ASP E 808 " pdb=" OH TYR E 823 " model vdw 2.556 2.440 nonbonded pdb=" OD2 ASP C 9 " pdb=" OH TYR C 38 " model vdw 2.560 2.440 nonbonded pdb=" OE2 GLU E1059 " pdb=" OH TYR E1068 " model vdw 2.571 2.440 nonbonded pdb=" OG SER C 322 " pdb=" OD2 ASP C 342 " model vdw 2.571 2.440 ... (remaining 163674 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.130 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: 0.020 Extract box with map and model: 27.210 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 55.100 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 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 : 0.013 0.046 20583 Z= 0.815 Angle : 1.800 10.651 27787 Z= 1.212 Chirality : 0.096 0.522 3047 Planarity : 0.015 0.207 3552 Dihedral : 13.293 89.971 7692 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 0.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.05 % Allowed : 2.02 % Favored : 97.94 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 1.43 % 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: -1.28 (0.15), residues: 2495 helix: -0.90 (0.13), residues: 1074 sheet: -0.33 (0.23), residues: 463 loop : -0.80 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.152 0.025 TRP C 259 HIS 0.012 0.003 HIS E1054 PHE 0.108 0.014 PHE E 751 TYR 0.318 0.024 TYR C 61 ARG 0.013 0.001 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 974 HIS cc_start: 0.5842 (m-70) cc_final: 0.5585 (m-70) REVERT: E 910 MET cc_start: 0.1506 (mmp) cc_final: 0.1248 (mmm) REVERT: E 937 TYR cc_start: 0.5249 (m-10) cc_final: 0.4921 (m-10) REVERT: E 1067 ILE cc_start: 0.7545 (mt) cc_final: 0.7280 (mm) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.3814 time to fit residues: 205.8273 Evaluate side-chains 194 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 0.5980 chunk 189 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 ASN C 196 ASN C 280 ASN C 556 ASN ** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1156 HIS D1226 HIS D1227 ASN D1253 ASN E 342 ASN E 637 ASN E 717 GLN ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 923 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20583 Z= 0.234 Angle : 0.702 12.358 27787 Z= 0.373 Chirality : 0.047 0.203 3047 Planarity : 0.004 0.039 3552 Dihedral : 5.974 31.890 2746 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.24 % Allowed : 8.39 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.06 (0.17), residues: 2495 helix: 0.76 (0.15), residues: 1059 sheet: -0.24 (0.21), residues: 554 loop : -0.49 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D1258 HIS 0.010 0.001 HIS E 923 PHE 0.021 0.002 PHE C 68 TYR 0.044 0.002 TYR C 61 ARG 0.007 0.001 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 213 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7313 (mm) REVERT: E 99 MET cc_start: 0.6665 (ptp) cc_final: 0.6437 (ptp) REVERT: E 910 MET cc_start: 0.1428 (mmp) cc_final: 0.0807 (mmm) REVERT: F 160 VAL cc_start: 0.5193 (t) cc_final: 0.4991 (m) outliers start: 27 outliers final: 9 residues processed: 230 average time/residue: 0.3708 time to fit residues: 131.3983 Evaluate side-chains 171 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 119 TRP Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain E residue 500 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 893 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 182 optimal weight: 0.0870 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN C 320 GLN D 701 HIS D 977 GLN ** D1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 ASN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20583 Z= 0.275 Angle : 0.666 11.100 27787 Z= 0.354 Chirality : 0.046 0.312 3047 Planarity : 0.004 0.045 3552 Dihedral : 5.472 29.610 2746 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.38 % Allowed : 10.05 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.22 (0.17), residues: 2495 helix: 1.04 (0.15), residues: 1058 sheet: -0.29 (0.21), residues: 557 loop : -0.50 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 98 HIS 0.009 0.001 HIS E1054 PHE 0.033 0.002 PHE D 712 TYR 0.038 0.002 TYR E1041 ARG 0.016 0.001 ARG D 863 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7346 (mm) REVERT: D 694 MET cc_start: 0.6330 (mtt) cc_final: 0.6126 (mtt) REVERT: E 99 MET cc_start: 0.6599 (ptp) cc_final: 0.6370 (ptp) REVERT: E 239 MET cc_start: 0.7327 (mmm) cc_final: 0.6600 (mmt) outliers start: 30 outliers final: 16 residues processed: 189 average time/residue: 0.3575 time to fit residues: 109.2951 Evaluate side-chains 164 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 119 TRP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain E residue 500 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 118 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 241 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 216 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 586 HIS C 703 GLN ** D1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 453 GLN E1169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20583 Z= 0.198 Angle : 0.590 13.409 27787 Z= 0.313 Chirality : 0.044 0.197 3047 Planarity : 0.003 0.041 3552 Dihedral : 5.095 26.115 2746 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.15 % Allowed : 11.19 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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 (0.17), residues: 2495 helix: 1.21 (0.16), residues: 1069 sheet: -0.29 (0.21), residues: 562 loop : -0.48 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 98 HIS 0.004 0.001 HIS E1054 PHE 0.021 0.002 PHE C 608 TYR 0.027 0.001 TYR E1041 ARG 0.010 0.000 ARG D 863 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7182 (mm) REVERT: C 247 LEU cc_start: 0.7410 (pt) cc_final: 0.7137 (mt) REVERT: D 1011 MET cc_start: 0.5669 (mmt) cc_final: 0.4987 (ttp) REVERT: D 1144 ASN cc_start: 0.6989 (m-40) cc_final: 0.6732 (m-40) REVERT: E 99 MET cc_start: 0.6455 (ptp) cc_final: 0.6237 (ptp) REVERT: F 130 MET cc_start: 0.7012 (mpp) cc_final: 0.5273 (tpt) outliers start: 25 outliers final: 16 residues processed: 181 average time/residue: 0.3193 time to fit residues: 92.5988 Evaluate side-chains 162 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 119 TRP Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1306 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain F residue 181 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 201 optimal weight: 0.8980 chunk 137 optimal weight: 0.0980 chunk 3 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 554 ASN ** D1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1296 HIS E 26 GLN E 84 GLN E 263 HIS ** E1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20583 Z= 0.352 Angle : 0.689 8.668 27787 Z= 0.365 Chirality : 0.046 0.200 3047 Planarity : 0.004 0.047 3552 Dihedral : 5.372 27.850 2746 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.06 % Allowed : 11.61 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -0.02 (0.17), residues: 2495 helix: 0.98 (0.15), residues: 1073 sheet: -0.50 (0.21), residues: 565 loop : -0.79 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 98 HIS 0.007 0.002 HIS C 52 PHE 0.021 0.003 PHE C 116 TYR 0.022 0.002 TYR C 365 ARG 0.017 0.001 ARG D 926 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 145 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7466 (mm) REVERT: C 247 LEU cc_start: 0.7440 (pt) cc_final: 0.7181 (mt) REVERT: C 641 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7356 (t) REVERT: E 99 MET cc_start: 0.6628 (ptp) cc_final: 0.6353 (ptp) outliers start: 45 outliers final: 26 residues processed: 180 average time/residue: 0.3162 time to fit residues: 92.5185 Evaluate side-chains 164 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1262 ASN Chi-restraints excluded: chain D residue 1306 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 TRP Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 893 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 241 optimal weight: 0.4980 chunk 200 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN D 771 ASN ** D1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 980 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20583 Z= 0.208 Angle : 0.593 8.302 27787 Z= 0.313 Chirality : 0.044 0.234 3047 Planarity : 0.003 0.045 3552 Dihedral : 5.062 28.665 2746 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.83 % Allowed : 11.83 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.13 (0.17), residues: 2495 helix: 1.12 (0.15), residues: 1086 sheet: -0.38 (0.21), residues: 559 loop : -0.81 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 98 HIS 0.004 0.001 HIS D1226 PHE 0.016 0.002 PHE C 68 TYR 0.022 0.001 TYR E1041 ARG 0.006 0.000 ARG D 863 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 641 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7330 (t) REVERT: D 1131 MET cc_start: 0.1074 (ptt) cc_final: 0.0531 (ptm) REVERT: D 1163 MET cc_start: 0.6989 (tpp) cc_final: 0.6711 (mmt) REVERT: E 611 MET cc_start: 0.5627 (ttp) cc_final: 0.4916 (tmm) outliers start: 40 outliers final: 26 residues processed: 180 average time/residue: 0.3011 time to fit residues: 89.2978 Evaluate side-chains 166 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 TRP Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1262 ASN Chi-restraints excluded: chain D residue 1306 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 TRP Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain F residue 181 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 233 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 240 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN ** D1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 20583 Z= 0.230 Angle : 0.604 8.252 27787 Z= 0.319 Chirality : 0.044 0.210 3047 Planarity : 0.003 0.045 3552 Dihedral : 4.964 28.986 2746 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.88 % Allowed : 12.75 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.15 (0.17), residues: 2495 helix: 1.15 (0.15), residues: 1086 sheet: -0.40 (0.21), residues: 564 loop : -0.82 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 98 HIS 0.006 0.001 HIS E1177 PHE 0.023 0.002 PHE D 687 TYR 0.020 0.001 TYR E1041 ARG 0.005 0.000 ARG D 863 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5753 (p0) REVERT: C 641 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7276 (t) REVERT: D 1131 MET cc_start: 0.1080 (ptt) cc_final: 0.0540 (ptm) outliers start: 41 outliers final: 29 residues processed: 170 average time/residue: 0.3031 time to fit residues: 84.2662 Evaluate side-chains 166 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 TRP Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1262 ASN Chi-restraints excluded: chain D residue 1306 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 TRP Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain F residue 130 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN ** D1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 453 GLN ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20583 Z= 0.223 Angle : 0.608 9.079 27787 Z= 0.320 Chirality : 0.044 0.199 3047 Planarity : 0.003 0.044 3552 Dihedral : 4.929 30.072 2746 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.65 % Allowed : 13.12 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.11 (0.17), residues: 2495 helix: 1.14 (0.15), residues: 1087 sheet: -0.35 (0.22), residues: 548 loop : -0.92 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 98 HIS 0.005 0.001 HIS E1177 PHE 0.021 0.002 PHE D 687 TYR 0.019 0.001 TYR E1041 ARG 0.007 0.000 ARG E 733 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7375 (mm) REVERT: C 115 ASP cc_start: 0.5987 (OUTLIER) cc_final: 0.5778 (p0) REVERT: D 1131 MET cc_start: 0.1155 (ptt) cc_final: 0.0590 (ptm) REVERT: D 1144 ASN cc_start: 0.7207 (m-40) cc_final: 0.6808 (m-40) REVERT: E 99 MET cc_start: 0.5913 (ptp) cc_final: 0.5704 (ptp) REVERT: E 611 MET cc_start: 0.5562 (ttp) cc_final: 0.4709 (tmm) REVERT: E 742 MET cc_start: 0.8451 (mmm) cc_final: 0.8181 (mmp) outliers start: 36 outliers final: 31 residues processed: 168 average time/residue: 0.3090 time to fit residues: 86.0963 Evaluate side-chains 167 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 TRP Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 456 CYS Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1262 ASN Chi-restraints excluded: chain D residue 1306 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 TRP Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain F residue 130 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 219 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 chunk 212 optimal weight: 0.3980 chunk 223 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20583 Z= 0.238 Angle : 0.630 10.746 27787 Z= 0.330 Chirality : 0.044 0.246 3047 Planarity : 0.003 0.044 3552 Dihedral : 4.944 31.955 2746 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.79 % Allowed : 13.21 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.05 (0.17), residues: 2495 helix: 1.11 (0.16), residues: 1085 sheet: -0.40 (0.22), residues: 551 loop : -0.94 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 804 HIS 0.005 0.001 HIS E1177 PHE 0.027 0.002 PHE D 687 TYR 0.019 0.001 TYR E1041 ARG 0.006 0.000 ARG E 733 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7426 (mm) REVERT: C 115 ASP cc_start: 0.6046 (OUTLIER) cc_final: 0.5816 (p0) REVERT: C 259 TRP cc_start: 0.8060 (OUTLIER) cc_final: 0.7845 (m-10) REVERT: D 719 MET cc_start: 0.0568 (mpp) cc_final: -0.0054 (ptp) REVERT: D 1131 MET cc_start: 0.1291 (ptt) cc_final: 0.0579 (ptm) REVERT: D 1144 ASN cc_start: 0.7236 (m-40) cc_final: 0.6815 (m-40) REVERT: E 611 MET cc_start: 0.5370 (ttp) cc_final: 0.4587 (tmm) REVERT: E 742 MET cc_start: 0.8442 (mmm) cc_final: 0.8232 (mmp) outliers start: 39 outliers final: 31 residues processed: 169 average time/residue: 0.2975 time to fit residues: 83.1145 Evaluate side-chains 168 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 TRP Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 259 TRP Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 456 CYS Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1262 ASN Chi-restraints excluded: chain D residue 1306 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 TRP Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain F residue 130 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 147 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 249 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20583 Z= 0.265 Angle : 0.647 9.895 27787 Z= 0.338 Chirality : 0.045 0.211 3047 Planarity : 0.004 0.044 3552 Dihedral : 5.035 34.556 2746 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.70 % Allowed : 13.35 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -0.03 (0.17), residues: 2495 helix: 1.08 (0.15), residues: 1086 sheet: -0.47 (0.21), residues: 565 loop : -1.03 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 804 HIS 0.006 0.001 HIS E1177 PHE 0.023 0.002 PHE D 687 TYR 0.018 0.002 TYR E1041 ARG 0.006 0.000 ARG E 733 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 133 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7431 (mm) REVERT: C 115 ASP cc_start: 0.6119 (OUTLIER) cc_final: 0.5897 (p0) REVERT: C 259 TRP cc_start: 0.8093 (OUTLIER) cc_final: 0.7828 (m-10) REVERT: D 719 MET cc_start: 0.0950 (mpp) cc_final: 0.0457 (ptp) REVERT: D 1144 ASN cc_start: 0.7345 (m-40) cc_final: 0.6977 (m-40) REVERT: E 611 MET cc_start: 0.5431 (ttp) cc_final: 0.4647 (tmm) outliers start: 37 outliers final: 31 residues processed: 164 average time/residue: 0.2929 time to fit residues: 80.4612 Evaluate side-chains 163 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 259 TRP Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 456 CYS Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1262 ASN Chi-restraints excluded: chain D residue 1306 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 TRP Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain F residue 130 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN C 588 GLN ** D1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.087074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.067685 restraints weight = 88037.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.069467 restraints weight = 45928.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.070001 restraints weight = 27095.502| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20583 Z= 0.224 Angle : 0.630 9.849 27787 Z= 0.327 Chirality : 0.044 0.224 3047 Planarity : 0.003 0.046 3552 Dihedral : 4.964 36.075 2746 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.65 % Allowed : 13.53 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.03 (0.17), residues: 2495 helix: 1.14 (0.16), residues: 1082 sheet: -0.40 (0.22), residues: 542 loop : -1.03 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 804 HIS 0.006 0.001 HIS E1177 PHE 0.022 0.002 PHE C 608 TYR 0.018 0.001 TYR E1041 ARG 0.005 0.000 ARG E 733 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3732.28 seconds wall clock time: 70 minutes 32.30 seconds (4232.30 seconds total)