Starting phenix.real_space_refine on Sun Aug 24 13:40:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bbe_15954/08_2025/8bbe_15954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bbe_15954/08_2025/8bbe_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/cci-nas-00/data/ceres_data/8bbe_15954/08_2025/8bbe_15954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bbe_15954/08_2025/8bbe_15954.map" model { file = "/net/cci-nas-00/data/ceres_data/8bbe_15954/08_2025/8bbe_15954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bbe_15954/08_2025/8bbe_15954.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 119 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20181 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1563 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "C" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4032 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 493} Chain breaks: 1 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: 3.94, per 1000 atoms: 0.20 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 - 3.00 Amino acid : True - 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: 1.34 Conformation dependent library (CDL) restraints added in 891.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.70 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: 4.27 Time building geometry restraints manager: 1.89 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: 0.00 - 2.13: 21481 2.13 - 4.26: 5704 4.26 - 6.39: 564 6.39 - 8.52: 34 8.52 - 10.65: 4 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 3.040 nonbonded pdb=" OD1 ASP E 808 " pdb=" OH TYR E 823 " model vdw 2.556 3.040 nonbonded pdb=" OD2 ASP C 9 " pdb=" OH TYR C 38 " model vdw 2.560 3.040 nonbonded pdb=" OE2 GLU E1059 " pdb=" OH TYR E1068 " model vdw 2.571 3.040 nonbonded pdb=" OG SER C 322 " pdb=" OD2 ASP C 342 " model vdw 2.571 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 12.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.600 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.160 ------------------------------------------------------------------------------- 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= 0.763 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.15), residues: 2495 helix: -0.90 (0.13), residues: 1074 sheet: -0.28 (0.23), residues: 450 loop : -0.81 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 453 TYR 0.318 0.024 TYR C 61 PHE 0.108 0.014 PHE E 751 TRP 0.152 0.025 TRP C 259 HIS 0.012 0.003 HIS E1054 Details of bonding type rmsd covalent geometry : bond 0.01261 (20583) covalent geometry : angle 1.79960 (27787) hydrogen bonds : bond 0.15566 ( 1071) hydrogen bonds : angle 7.05683 ( 3102) *********************** 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 to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 0.805 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: symmetry clash revert: symmetry clash REVERT: D 974 HIS cc_start: 0.5842 (m-70) cc_final: 0.5615 (m-70) REVERT: E 267 VAL cc_start: 0.7525 (t) cc_final: 0.7205 (m) REVERT: E 784 LEU cc_start: 0.8465 (tp) cc_final: 0.8141 (tt) REVERT: E 910 MET cc_start: 0.1506 (mmp) cc_final: 0.1249 (mmm) REVERT: E 937 TYR cc_start: 0.5249 (m-10) cc_final: 0.4927 (m-10) REVERT: E 1067 ILE cc_start: 0.7545 (mt) cc_final: 0.7276 (mm) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.1459 time to fit residues: 79.5234 Evaluate side-chains 197 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 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 196 ASN ** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1082 ASN D1156 HIS D1226 HIS D1253 ASN E 342 ASN E 637 ASN E 717 GLN E 923 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.091497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.072091 restraints weight = 84756.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.073917 restraints weight = 43267.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.075145 restraints weight = 26209.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.075342 restraints weight = 22861.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.075365 restraints weight = 17719.856| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20583 Z= 0.172 Angle : 0.721 11.682 27787 Z= 0.385 Chirality : 0.047 0.192 3047 Planarity : 0.004 0.047 3552 Dihedral : 6.020 30.368 2746 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.96 % Allowed : 8.17 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.16), residues: 2495 helix: 0.74 (0.15), residues: 1062 sheet: -0.20 (0.21), residues: 527 loop : -0.48 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 691 TYR 0.050 0.002 TYR C 61 PHE 0.021 0.002 PHE E 609 TRP 0.035 0.002 TRP D1258 HIS 0.013 0.002 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00372 (20583) covalent geometry : angle 0.72149 (27787) hydrogen bonds : bond 0.04766 ( 1071) hydrogen bonds : angle 5.29190 ( 3102) *********************** 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 230 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.741 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: C 84 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7340 (mm) REVERT: C 247 LEU cc_start: 0.8670 (pt) cc_final: 0.8412 (mt) REVERT: D 1163 MET cc_start: 0.8747 (mtm) cc_final: 0.8478 (ttm) REVERT: D 1168 MET cc_start: 0.7327 (mmm) cc_final: 0.7102 (mmm) REVERT: E 99 MET cc_start: 0.8341 (ptp) cc_final: 0.7932 (ptp) REVERT: E 910 MET cc_start: 0.1972 (mmp) cc_final: 0.1384 (mmm) REVERT: E 985 MET cc_start: 0.7941 (ptt) cc_final: 0.7565 (ptt) outliers start: 21 outliers final: 8 residues processed: 220 average time/residue: 0.1461 time to fit residues: 49.5701 Evaluate side-chains 169 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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: 249 random chunks: chunk 26 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 168 optimal weight: 0.1980 chunk 121 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 701 HIS ** D 977 GLN ** 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 188 ASN E 263 HIS ** E1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1169 HIS F 178 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.086902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.066319 restraints weight = 86013.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.068289 restraints weight = 42251.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.069476 restraints weight = 26455.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.070316 restraints weight = 19394.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.070848 restraints weight = 15594.618| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 20583 Z= 0.290 Angle : 0.778 10.138 27787 Z= 0.412 Chirality : 0.050 0.409 3047 Planarity : 0.005 0.050 3552 Dihedral : 5.868 32.061 2746 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.70 % Allowed : 10.55 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.16), residues: 2495 helix: 0.76 (0.15), residues: 1058 sheet: -0.60 (0.22), residues: 530 loop : -0.74 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 863 TYR 0.038 0.003 TYR C 61 PHE 0.027 0.003 PHE C 307 TRP 0.025 0.002 TRP E 98 HIS 0.009 0.002 HIS E1054 Details of bonding type rmsd covalent geometry : bond 0.00656 (20583) covalent geometry : angle 0.77809 (27787) hydrogen bonds : bond 0.04836 ( 1071) hydrogen bonds : angle 5.46651 ( 3102) *********************** 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 202 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.814 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: C 84 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7441 (mm) REVERT: C 247 LEU cc_start: 0.8650 (pt) cc_final: 0.8252 (mt) REVERT: D 804 TRP cc_start: 0.8783 (m100) cc_final: 0.8316 (m100) REVERT: D 1011 MET cc_start: 0.4472 (ttp) cc_final: 0.4260 (mmt) REVERT: D 1092 GLU cc_start: 0.3881 (OUTLIER) cc_final: 0.3302 (pm20) REVERT: D 1168 MET cc_start: 0.8090 (mmm) cc_final: 0.7635 (mmm) REVERT: D 1256 MET cc_start: 0.9081 (mmt) cc_final: 0.8838 (mmp) REVERT: E 99 MET cc_start: 0.8385 (ptp) cc_final: 0.7279 (ptp) REVERT: E 239 MET cc_start: 0.7917 (mmm) cc_final: 0.7489 (mmp) REVERT: E 254 MET cc_start: 0.7106 (ptt) cc_final: 0.6881 (ptm) REVERT: E 985 MET cc_start: 0.7669 (ptt) cc_final: 0.7403 (ptt) REVERT: E 1103 GLN cc_start: 0.9412 (tp40) cc_final: 0.9201 (tm-30) REVERT: E 1130 MET cc_start: 0.7161 (mtp) cc_final: 0.6903 (ptm) outliers start: 37 outliers final: 19 residues processed: 194 average time/residue: 0.1517 time to fit residues: 46.1701 Evaluate side-chains 158 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 1092 GLU Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1306 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 427 ILE 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 784 LEU Chi-restraints excluded: chain E residue 893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 771 ASN ** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1037 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.089595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.068912 restraints weight = 85210.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.070937 restraints weight = 50325.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.071938 restraints weight = 27807.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.072352 restraints weight = 22854.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.072469 restraints weight = 19628.487| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20583 Z= 0.154 Angle : 0.637 9.334 27787 Z= 0.337 Chirality : 0.045 0.244 3047 Planarity : 0.004 0.044 3552 Dihedral : 5.374 28.041 2746 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.28 % Allowed : 12.16 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.17), residues: 2495 helix: 0.92 (0.15), residues: 1070 sheet: -0.59 (0.21), residues: 559 loop : -0.61 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1263 TYR 0.023 0.002 TYR E1041 PHE 0.022 0.002 PHE C 608 TRP 0.021 0.002 TRP E 98 HIS 0.005 0.001 HIS E1054 Details of bonding type rmsd covalent geometry : bond 0.00339 (20583) covalent geometry : angle 0.63724 (27787) hydrogen bonds : bond 0.04084 ( 1071) hydrogen bonds : angle 5.08948 ( 3102) *********************** 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 184 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 247 LEU cc_start: 0.8693 (pt) cc_final: 0.8281 (mt) REVERT: D 694 MET cc_start: 0.6908 (mtt) cc_final: 0.6599 (mmt) REVERT: D 804 TRP cc_start: 0.8794 (m100) cc_final: 0.8286 (m100) REVERT: D 1092 GLU cc_start: 0.3894 (OUTLIER) cc_final: 0.3429 (pm20) REVERT: D 1168 MET cc_start: 0.8131 (mmm) cc_final: 0.7669 (mmm) REVERT: D 1236 TYR cc_start: 0.6860 (m-80) cc_final: 0.6565 (m-80) REVERT: D 1256 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8817 (mmp) REVERT: E 99 MET cc_start: 0.8595 (ptp) cc_final: 0.7415 (ptp) REVERT: E 254 MET cc_start: 0.7015 (ptt) cc_final: 0.6733 (ptm) REVERT: E 712 LEU cc_start: 0.7583 (mp) cc_final: 0.7349 (mm) REVERT: E 985 MET cc_start: 0.7784 (ptt) cc_final: 0.7564 (ptt) REVERT: E 1103 GLN cc_start: 0.9300 (tp40) cc_final: 0.9072 (tm-30) outliers start: 28 outliers final: 12 residues processed: 177 average time/residue: 0.1456 time to fit residues: 41.2958 Evaluate side-chains 150 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 119 TRP Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 893 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 160 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 139 optimal weight: 0.5980 chunk 135 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN E 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.089192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.068487 restraints weight = 84616.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.071173 restraints weight = 46678.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.071940 restraints weight = 24365.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.072511 restraints weight = 18860.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.072609 restraints weight = 16797.655| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20583 Z= 0.146 Angle : 0.600 8.141 27787 Z= 0.318 Chirality : 0.044 0.226 3047 Planarity : 0.004 0.043 3552 Dihedral : 5.114 29.995 2746 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.65 % Allowed : 11.70 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.17), residues: 2495 helix: 1.04 (0.15), residues: 1080 sheet: -0.56 (0.21), residues: 559 loop : -0.66 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG D 926 TYR 0.023 0.001 TYR E1041 PHE 0.017 0.002 PHE C 68 TRP 0.019 0.001 TRP E 98 HIS 0.007 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00325 (20583) covalent geometry : angle 0.59997 (27787) hydrogen bonds : bond 0.03860 ( 1071) hydrogen bonds : angle 4.90667 ( 3102) *********************** 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 180 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7235 (mm) REVERT: C 247 LEU cc_start: 0.8620 (pt) cc_final: 0.8160 (mt) REVERT: C 608 PHE cc_start: 0.6826 (p90) cc_final: 0.6344 (p90) REVERT: D 802 LEU cc_start: 0.9246 (mp) cc_final: 0.8801 (mp) REVERT: D 804 TRP cc_start: 0.8832 (m100) cc_final: 0.8256 (m100) REVERT: D 1092 GLU cc_start: 0.4166 (OUTLIER) cc_final: 0.3718 (pm20) REVERT: D 1131 MET cc_start: 0.1689 (OUTLIER) cc_final: 0.0742 (ptm) REVERT: D 1168 MET cc_start: 0.8234 (mmm) cc_final: 0.7737 (mmm) REVERT: D 1192 ASP cc_start: 0.4766 (m-30) cc_final: 0.3908 (t0) REVERT: D 1236 TYR cc_start: 0.6873 (m-80) cc_final: 0.6624 (m-80) REVERT: D 1256 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8728 (mmp) REVERT: E 99 MET cc_start: 0.8453 (ptp) cc_final: 0.7298 (ptp) REVERT: E 254 MET cc_start: 0.7069 (ptt) cc_final: 0.6786 (ptm) REVERT: E 438 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8120 (tptt) REVERT: E 712 LEU cc_start: 0.7698 (mp) cc_final: 0.7417 (mm) REVERT: E 796 ASP cc_start: 0.7983 (m-30) cc_final: 0.7471 (p0) REVERT: E 1103 GLN cc_start: 0.9298 (tp40) cc_final: 0.9086 (tm-30) REVERT: E 1130 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6502 (ptt) outliers start: 36 outliers final: 23 residues processed: 170 average time/residue: 0.1341 time to fit residues: 37.2998 Evaluate side-chains 166 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 119 TRP Chi-restraints excluded: chain C residue 169 ILE 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 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1306 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 TRP 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 784 LEU Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain E residue 1130 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 118 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 239 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1082 ASN D1296 HIS E 928 ASN E 980 GLN ** E1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.087430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.067919 restraints weight = 86723.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.069631 restraints weight = 42482.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.070986 restraints weight = 26543.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.071107 restraints weight = 22727.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.071171 restraints weight = 17653.071| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20583 Z= 0.170 Angle : 0.614 7.923 27787 Z= 0.325 Chirality : 0.044 0.180 3047 Planarity : 0.004 0.045 3552 Dihedral : 5.087 32.861 2746 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.02 % Allowed : 12.11 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.17), residues: 2495 helix: 0.98 (0.15), residues: 1089 sheet: -0.47 (0.22), residues: 535 loop : -0.84 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 926 TYR 0.020 0.002 TYR E1041 PHE 0.016 0.002 PHE C 68 TRP 0.019 0.001 TRP E 98 HIS 0.004 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00381 (20583) covalent geometry : angle 0.61364 (27787) hydrogen bonds : bond 0.03918 ( 1071) hydrogen bonds : angle 4.92502 ( 3102) *********************** 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 to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7314 (mm) REVERT: C 115 ASP cc_start: 0.6407 (OUTLIER) cc_final: 0.6042 (p0) REVERT: C 247 LEU cc_start: 0.8706 (pt) cc_final: 0.8199 (mt) REVERT: D 694 MET cc_start: 0.7066 (mtt) cc_final: 0.6756 (mmt) REVERT: D 802 LEU cc_start: 0.9243 (mp) cc_final: 0.8769 (mp) REVERT: D 804 TRP cc_start: 0.8767 (m100) cc_final: 0.8164 (m100) REVERT: D 1092 GLU cc_start: 0.4133 (OUTLIER) cc_final: 0.3736 (pm20) REVERT: D 1131 MET cc_start: 0.1835 (OUTLIER) cc_final: 0.0871 (ptm) REVERT: D 1168 MET cc_start: 0.8361 (mmm) cc_final: 0.7944 (mmm) REVERT: D 1192 ASP cc_start: 0.4972 (m-30) cc_final: 0.4001 (t0) REVERT: D 1256 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8837 (mmp) REVERT: E 99 MET cc_start: 0.8484 (ptp) cc_final: 0.7313 (ptp) REVERT: E 254 MET cc_start: 0.7058 (ptt) cc_final: 0.6792 (ptm) REVERT: E 438 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8175 (tptt) REVERT: E 611 MET cc_start: 0.6069 (ttp) cc_final: 0.4416 (tmm) REVERT: E 712 LEU cc_start: 0.7751 (mp) cc_final: 0.7474 (mm) REVERT: E 1103 GLN cc_start: 0.9265 (tp40) cc_final: 0.9050 (tm-30) REVERT: E 1130 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6478 (ptt) outliers start: 44 outliers final: 26 residues processed: 176 average time/residue: 0.1326 time to fit residues: 39.1197 Evaluate side-chains 171 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 115 ASP Chi-restraints excluded: chain C residue 169 ILE 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 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 956 MET Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1306 ILE 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 784 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain E residue 1130 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 36 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 GLN ** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E1054 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.085594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.066230 restraints weight = 87392.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.067827 restraints weight = 41482.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.069013 restraints weight = 27280.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.069150 restraints weight = 22543.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.069248 restraints weight = 18293.134| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20583 Z= 0.232 Angle : 0.678 11.941 27787 Z= 0.356 Chirality : 0.046 0.282 3047 Planarity : 0.004 0.046 3552 Dihedral : 5.299 37.098 2746 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.34 % Allowed : 12.48 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.17), residues: 2495 helix: 0.86 (0.15), residues: 1088 sheet: -0.61 (0.22), residues: 530 loop : -1.09 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 863 TYR 0.018 0.002 TYR E1041 PHE 0.027 0.002 PHE C 608 TRP 0.057 0.002 TRP F 174 HIS 0.006 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00525 (20583) covalent geometry : angle 0.67754 (27787) hydrogen bonds : bond 0.04201 ( 1071) hydrogen bonds : angle 5.13386 ( 3102) *********************** 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 193 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7611 (mm) REVERT: C 101 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7113 (m-10) REVERT: C 115 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6276 (p0) REVERT: C 193 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8169 (t80) REVERT: C 247 LEU cc_start: 0.8702 (pt) cc_final: 0.8132 (mt) REVERT: D 802 LEU cc_start: 0.9261 (mp) cc_final: 0.8745 (mp) REVERT: D 804 TRP cc_start: 0.8767 (m100) cc_final: 0.8150 (m100) REVERT: D 974 HIS cc_start: 0.8393 (m170) cc_final: 0.8082 (m170) REVERT: D 1092 GLU cc_start: 0.4197 (OUTLIER) cc_final: 0.3779 (pm20) REVERT: D 1131 MET cc_start: 0.1949 (OUTLIER) cc_final: 0.0925 (ptm) REVERT: D 1163 MET cc_start: 0.8807 (tpp) cc_final: 0.8345 (tpp) REVERT: D 1168 MET cc_start: 0.8473 (mmm) cc_final: 0.8086 (mmm) REVERT: D 1192 ASP cc_start: 0.4969 (m-30) cc_final: 0.4013 (t70) REVERT: D 1256 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8850 (mmp) REVERT: E 99 MET cc_start: 0.8515 (ptp) cc_final: 0.7387 (ptp) REVERT: E 239 MET cc_start: 0.8139 (mmm) cc_final: 0.7706 (mmm) REVERT: E 1103 GLN cc_start: 0.9270 (tp40) cc_final: 0.9021 (tm-30) REVERT: E 1130 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6270 (ptt) REVERT: F 130 MET cc_start: 0.6768 (mpp) cc_final: 0.6537 (mpp) outliers start: 51 outliers final: 32 residues processed: 181 average time/residue: 0.1298 time to fit residues: 39.3017 Evaluate side-chains 174 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 101 TYR 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 193 PHE 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 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 956 MET Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1256 MET 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 331 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 742 MET Chi-restraints excluded: chain E residue 784 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain E residue 1130 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 232 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.086978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.067714 restraints weight = 86850.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.069546 restraints weight = 40874.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.070660 restraints weight = 26022.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.070813 restraints weight = 22450.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.070871 restraints weight = 18177.701| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20583 Z= 0.146 Angle : 0.614 11.746 27787 Z= 0.320 Chirality : 0.045 0.263 3047 Planarity : 0.004 0.046 3552 Dihedral : 5.082 39.335 2746 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.17), residues: 2495 helix: 0.97 (0.15), residues: 1090 sheet: -0.59 (0.21), residues: 538 loop : -0.97 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 863 TYR 0.022 0.001 TYR D1167 PHE 0.019 0.002 PHE D 687 TRP 0.022 0.001 TRP F 174 HIS 0.005 0.001 HIS D1226 Details of bonding type rmsd covalent geometry : bond 0.00327 (20583) covalent geometry : angle 0.61436 (27787) hydrogen bonds : bond 0.03834 ( 1071) hydrogen bonds : angle 4.95744 ( 3102) *********************** 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 183 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7405 (mm) REVERT: C 115 ASP cc_start: 0.6462 (OUTLIER) cc_final: 0.6127 (p0) REVERT: C 247 LEU cc_start: 0.8635 (pt) cc_final: 0.8083 (mt) REVERT: C 725 MET cc_start: 0.7799 (ppp) cc_final: 0.7462 (ppp) REVERT: D 802 LEU cc_start: 0.9236 (mp) cc_final: 0.8735 (mp) REVERT: D 804 TRP cc_start: 0.8812 (m100) cc_final: 0.8234 (m100) REVERT: D 919 LYS cc_start: 0.8347 (tppt) cc_final: 0.8116 (mtpt) REVERT: D 921 MET cc_start: 0.4601 (ppp) cc_final: 0.4200 (ppp) REVERT: D 1092 GLU cc_start: 0.4329 (OUTLIER) cc_final: 0.3841 (pm20) REVERT: D 1131 MET cc_start: 0.1888 (ptt) cc_final: 0.0892 (ptm) REVERT: D 1163 MET cc_start: 0.8814 (tpp) cc_final: 0.8377 (tpp) REVERT: D 1168 MET cc_start: 0.8478 (mmm) cc_final: 0.7974 (mmm) REVERT: D 1192 ASP cc_start: 0.4831 (m-30) cc_final: 0.3476 (t0) REVERT: D 1215 MET cc_start: 0.8395 (pmm) cc_final: 0.8126 (pmm) REVERT: D 1256 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8829 (mmp) REVERT: E 99 MET cc_start: 0.8505 (ptp) cc_final: 0.7420 (ptp) REVERT: E 239 MET cc_start: 0.8076 (mmm) cc_final: 0.7681 (mmm) REVERT: E 438 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8139 (tptt) REVERT: E 611 MET cc_start: 0.5925 (ttp) cc_final: 0.4252 (tmm) REVERT: E 712 LEU cc_start: 0.7888 (mp) cc_final: 0.7667 (mm) REVERT: E 1103 GLN cc_start: 0.9252 (tp40) cc_final: 0.9043 (tm-30) REVERT: E 1130 MET cc_start: 0.6459 (ptm) cc_final: 0.6223 (ptt) REVERT: F 130 MET cc_start: 0.6699 (mpp) cc_final: 0.6438 (mpp) REVERT: F 174 TRP cc_start: 0.7873 (m100) cc_final: 0.7643 (m100) outliers start: 39 outliers final: 28 residues processed: 172 average time/residue: 0.1233 time to fit residues: 34.9838 Evaluate side-chains 166 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 115 ASP Chi-restraints excluded: chain C residue 119 TRP Chi-restraints excluded: chain C residue 169 ILE 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 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 956 MET Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1306 ILE 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 331 ILE 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 742 MET Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain E residue 1139 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 144 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 50 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 ASN ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E1177 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.087135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.067992 restraints weight = 86792.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.070004 restraints weight = 42807.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.070397 restraints weight = 25939.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.070647 restraints weight = 23785.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.070941 restraints weight = 19661.132| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20583 Z= 0.144 Angle : 0.614 11.605 27787 Z= 0.319 Chirality : 0.045 0.257 3047 Planarity : 0.003 0.045 3552 Dihedral : 4.961 38.484 2746 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.83 % Allowed : 13.62 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.17), residues: 2495 helix: 1.00 (0.15), residues: 1088 sheet: -0.60 (0.21), residues: 543 loop : -0.96 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 926 TYR 0.020 0.001 TYR E1041 PHE 0.026 0.002 PHE C 608 TRP 0.019 0.001 TRP E 98 HIS 0.004 0.001 HIS D1226 Details of bonding type rmsd covalent geometry : bond 0.00318 (20583) covalent geometry : angle 0.61380 (27787) hydrogen bonds : bond 0.03803 ( 1071) hydrogen bonds : angle 4.90984 ( 3102) *********************** 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 181 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7378 (mm) REVERT: C 115 ASP cc_start: 0.6364 (OUTLIER) cc_final: 0.6069 (p0) REVERT: C 247 LEU cc_start: 0.8764 (pt) cc_final: 0.8175 (mt) REVERT: C 725 MET cc_start: 0.7797 (ppp) cc_final: 0.7470 (ppp) REVERT: D 719 MET cc_start: 0.1578 (mpp) cc_final: 0.1312 (ptp) REVERT: D 733 MET cc_start: 0.8475 (mmm) cc_final: 0.7966 (ppp) REVERT: D 802 LEU cc_start: 0.9250 (mp) cc_final: 0.8754 (mp) REVERT: D 804 TRP cc_start: 0.8824 (m100) cc_final: 0.8267 (m100) REVERT: D 921 MET cc_start: 0.4241 (ppp) cc_final: 0.3842 (ppp) REVERT: D 1072 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7238 (p0) REVERT: D 1092 GLU cc_start: 0.4448 (OUTLIER) cc_final: 0.3966 (pm20) REVERT: D 1131 MET cc_start: 0.2079 (ptt) cc_final: 0.1052 (ptm) REVERT: D 1163 MET cc_start: 0.8753 (tpp) cc_final: 0.7844 (tpp) REVERT: D 1168 MET cc_start: 0.8484 (mmm) cc_final: 0.8027 (mmm) REVERT: D 1192 ASP cc_start: 0.4759 (m-30) cc_final: 0.3835 (t70) REVERT: D 1215 MET cc_start: 0.8403 (pmm) cc_final: 0.8107 (pmm) REVERT: D 1256 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8785 (mmp) REVERT: E 99 MET cc_start: 0.8600 (ptp) cc_final: 0.7464 (ptp) REVERT: E 239 MET cc_start: 0.8064 (mmm) cc_final: 0.7630 (mmm) REVERT: E 438 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8161 (tptt) REVERT: E 490 MET cc_start: 0.8348 (ttm) cc_final: 0.7907 (mpp) REVERT: E 611 MET cc_start: 0.5802 (ttp) cc_final: 0.4173 (tmm) REVERT: E 712 LEU cc_start: 0.7871 (mp) cc_final: 0.7662 (mm) REVERT: E 788 LYS cc_start: 0.8333 (mttp) cc_final: 0.8127 (mtmm) REVERT: E 1103 GLN cc_start: 0.9233 (tp40) cc_final: 0.9014 (tm-30) REVERT: E 1130 MET cc_start: 0.6376 (ptm) cc_final: 0.6148 (ptt) REVERT: F 174 TRP cc_start: 0.7811 (m100) cc_final: 0.7590 (m100) outliers start: 40 outliers final: 30 residues processed: 173 average time/residue: 0.1252 time to fit residues: 36.1911 Evaluate side-chains 171 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 115 ASP Chi-restraints excluded: chain C residue 119 TRP Chi-restraints excluded: chain C residue 169 ILE 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 607 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 956 MET Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1072 ASN Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1194 GLU Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1306 ILE 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 442 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 742 MET Chi-restraints excluded: chain E residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 151 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 ASN E 928 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.087344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.068355 restraints weight = 88116.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.069917 restraints weight = 42063.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.070835 restraints weight = 27231.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.071005 restraints weight = 25008.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.071480 restraints weight = 19794.565| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 20583 Z= 0.185 Angle : 0.768 59.191 27787 Z= 0.432 Chirality : 0.046 0.360 3047 Planarity : 0.004 0.045 3552 Dihedral : 4.953 38.495 2746 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 1.88 % Allowed : 13.85 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.17), residues: 2495 helix: 0.99 (0.15), residues: 1087 sheet: -0.62 (0.21), residues: 544 loop : -0.95 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 863 TYR 0.019 0.001 TYR E1041 PHE 0.020 0.002 PHE D 687 TRP 0.019 0.001 TRP E 98 HIS 0.006 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00401 (20583) covalent geometry : angle 0.76823 (27787) hydrogen bonds : bond 0.03807 ( 1071) hydrogen bonds : angle 4.92080 ( 3102) ********************** 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 178 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7379 (mm) REVERT: C 115 ASP cc_start: 0.6368 (OUTLIER) cc_final: 0.6075 (p0) REVERT: C 247 LEU cc_start: 0.8744 (pt) cc_final: 0.8158 (mt) REVERT: C 725 MET cc_start: 0.7801 (ppp) cc_final: 0.7478 (ppp) REVERT: D 719 MET cc_start: 0.1631 (mpp) cc_final: 0.1352 (ptp) REVERT: D 733 MET cc_start: 0.8442 (mmm) cc_final: 0.7943 (ppp) REVERT: D 802 LEU cc_start: 0.9251 (mp) cc_final: 0.8747 (mp) REVERT: D 804 TRP cc_start: 0.8798 (m100) cc_final: 0.8240 (m100) REVERT: D 921 MET cc_start: 0.4203 (ppp) cc_final: 0.3837 (ppp) REVERT: D 1072 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6901 (p0) REVERT: D 1092 GLU cc_start: 0.4443 (OUTLIER) cc_final: 0.3966 (pm20) REVERT: D 1131 MET cc_start: 0.2102 (OUTLIER) cc_final: 0.1073 (ptm) REVERT: D 1163 MET cc_start: 0.8729 (tpp) cc_final: 0.7818 (tpp) REVERT: D 1168 MET cc_start: 0.8481 (mmm) cc_final: 0.8021 (mmm) REVERT: D 1192 ASP cc_start: 0.4783 (m-30) cc_final: 0.3843 (t70) REVERT: D 1215 MET cc_start: 0.8410 (pmm) cc_final: 0.8109 (pmm) REVERT: D 1256 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8787 (mmp) REVERT: E 99 MET cc_start: 0.8586 (ptp) cc_final: 0.7453 (ptp) REVERT: E 239 MET cc_start: 0.8073 (mmm) cc_final: 0.7632 (mmm) REVERT: E 438 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8160 (tptt) REVERT: E 490 MET cc_start: 0.8331 (ttm) cc_final: 0.7907 (mpp) REVERT: E 611 MET cc_start: 0.5774 (ttp) cc_final: 0.4126 (tmm) REVERT: E 788 LYS cc_start: 0.8330 (mttp) cc_final: 0.8125 (mtmm) REVERT: E 1103 GLN cc_start: 0.9221 (tp40) cc_final: 0.9002 (tm-30) REVERT: E 1130 MET cc_start: 0.6320 (ptm) cc_final: 0.6115 (ptt) REVERT: F 174 TRP cc_start: 0.7789 (m100) cc_final: 0.7589 (m100) outliers start: 41 outliers final: 32 residues processed: 169 average time/residue: 0.1144 time to fit residues: 32.4120 Evaluate side-chains 172 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 115 ASP Chi-restraints excluded: chain C residue 119 TRP Chi-restraints excluded: chain C residue 169 ILE 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 607 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 956 MET Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1072 ASN Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1194 GLU Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1306 ILE 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 331 ILE Chi-restraints excluded: chain E residue 442 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 742 MET Chi-restraints excluded: chain E residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 247 optimal weight: 9.9990 chunk 199 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.088602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.067678 restraints weight = 87212.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.069741 restraints weight = 43688.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.071079 restraints weight = 27556.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.071957 restraints weight = 20012.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.072517 restraints weight = 16046.097| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.316 20583 Z= 0.208 Angle : 0.749 46.504 27787 Z= 0.468 Chirality : 0.046 0.489 3047 Planarity : 0.004 0.094 3552 Dihedral : 4.953 38.495 2746 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 1.70 % Allowed : 14.08 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.17), residues: 2495 helix: 0.99 (0.15), residues: 1087 sheet: -0.62 (0.21), residues: 544 loop : -0.95 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 863 TYR 0.019 0.001 TYR E1041 PHE 0.020 0.002 PHE D 687 TRP 0.019 0.001 TRP E 98 HIS 0.006 0.001 HIS C 376 Details of bonding type rmsd covalent geometry : bond 0.00448 (20583) covalent geometry : angle 0.74902 (27787) hydrogen bonds : bond 0.03807 ( 1071) hydrogen bonds : angle 4.92080 ( 3102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3483.42 seconds wall clock time: 61 minutes 24.25 seconds (3684.25 seconds total)