Starting phenix.real_space_refine on Tue Jun 17 19:12:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bbe_15954/06_2025/8bbe_15954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bbe_15954/06_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_15954/06_2025/8bbe_15954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bbe_15954/06_2025/8bbe_15954.map" model { file = "/net/cci-nas-00/data/ceres_data/8bbe_15954/06_2025/8bbe_15954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bbe_15954/06_2025/8bbe_15954.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 137 5.16 5 C 12840 2.51 5 N 3438 2.21 5 O 3766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.78, per 1000 atoms: 0.68 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: 5.37 Conformation dependent library (CDL) restraints added in 2.9 seconds 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4762 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 32 sheets defined 46.0% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 188 through 193 removed outlier: 3.939A pdb=" N SER C 192 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 617 through 627 removed outlier: 3.644A pdb=" N ARG C 627 " --> pdb=" O GLN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 4.224A pdb=" N GLN C 635 " --> pdb=" O LYS C 631 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 656 Processing helix chain 'C' and resid 658 through 670 removed outlier: 3.611A pdb=" N LYS C 664 " --> pdb=" O GLU C 660 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 686 Processing helix chain 'C' and resid 691 through 703 Processing helix chain 'C' and resid 705 through 716 Processing helix chain 'C' and resid 718 through 729 removed outlier: 3.837A pdb=" N ALA C 722 " --> pdb=" O HIS C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'D' and resid 670 through 679 Processing helix chain 'D' and resid 686 through 701 Processing helix chain 'D' and resid 704 through 719 Processing helix chain 'D' and resid 721 through 735 Processing helix chain 'D' and resid 737 through 750 Processing helix chain 'D' and resid 755 through 769 Processing helix chain 'D' and resid 771 through 785 Processing helix chain 'D' and resid 790 through 802 Processing helix chain 'D' and resid 804 through 815 Processing helix chain 'D' and resid 823 through 844 removed outlier: 3.834A pdb=" N LYS D 843 " --> pdb=" O LYS D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 872 removed outlier: 4.930A pdb=" N MET D 870 " --> pdb=" O LYS D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 897 Processing helix chain 'D' and resid 899 through 914 Processing helix chain 'D' and resid 917 through 931 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 951 through 965 Processing helix chain 'D' and resid 967 through 982 Processing helix chain 'D' and resid 985 through 1000 Processing helix chain 'D' and resid 1001 through 1004 Processing helix chain 'D' and resid 1005 through 1016 removed outlier: 3.711A pdb=" N PHE D1009 " --> pdb=" O VAL D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1021 Processing helix chain 'D' and resid 1022 through 1037 Processing helix chain 'D' and resid 1038 through 1050 Processing helix chain 'D' and resid 1054 through 1069 Processing helix chain 'D' and resid 1077 through 1082 removed outlier: 4.007A pdb=" N ASN D1082 " --> pdb=" O GLU D1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1089 Processing helix chain 'D' and resid 1090 through 1111 removed outlier: 4.292A pdb=" N LYS D1106 " --> pdb=" O ARG D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1115 through 1133 Processing helix chain 'D' and resid 1135 through 1153 Processing helix chain 'D' and resid 1156 through 1170 Processing helix chain 'D' and resid 1172 through 1185 removed outlier: 3.626A pdb=" N ASN D1178 " --> pdb=" O PRO D1174 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D1179 " --> pdb=" O ARG D1175 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D1183 " --> pdb=" O GLN D1179 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1210 Processing helix chain 'D' and resid 1212 through 1227 removed outlier: 3.807A pdb=" N ALA D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1244 Processing helix chain 'D' and resid 1246 through 1261 Processing helix chain 'D' and resid 1265 through 1279 Processing helix chain 'D' and resid 1281 through 1296 Processing helix chain 'D' and resid 1301 through 1315 removed outlier: 3.571A pdb=" N ASP D1308 " --> pdb=" O LYS D1304 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG D1315 " --> pdb=" O ARG D1311 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 15 Processing helix chain 'E' and resid 195 through 199 Processing helix chain 'E' and resid 473 through 475 No H-bonds generated for 'chain 'E' and resid 473 through 475' Processing helix chain 'E' and resid 495 through 501 removed outlier: 3.855A pdb=" N ILE E 500 " --> pdb=" O SER E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 652 Processing helix chain 'E' and resid 659 through 661 No H-bonds generated for 'chain 'E' and resid 659 through 661' Processing helix chain 'E' and resid 668 through 681 Processing helix chain 'E' and resid 682 through 693 removed outlier: 3.986A pdb=" N SER E 687 " --> pdb=" O ILE E 683 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN E 688 " --> pdb=" O LYS E 684 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE E 689 " --> pdb=" O ASP E 685 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE E 690 " --> pdb=" O ALA E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 695 through 709 removed outlier: 3.525A pdb=" N ARG E 700 " --> pdb=" O PRO E 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 711 through 722 Processing helix chain 'E' and resid 724 through 735 Processing helix chain 'E' and resid 739 through 751 removed outlier: 3.530A pdb=" N TYR E 750 " --> pdb=" O GLU E 746 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE E 751 " --> pdb=" O VAL E 747 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 764 Processing helix chain 'E' and resid 766 through 778 Processing helix chain 'E' and resid 779 through 790 Processing helix chain 'E' and resid 795 through 813 removed outlier: 3.539A pdb=" N ARG E 813 " --> pdb=" O TYR E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 815 through 824 removed outlier: 3.905A pdb=" N GLN E 821 " --> pdb=" O LEU E 817 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR E 822 " --> pdb=" O ASN E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 828 through 839 removed outlier: 4.524A pdb=" N GLU E 834 " --> pdb=" O GLU E 830 " (cutoff:3.500A) Processing helix chain 'E' and resid 841 through 852 removed outlier: 3.529A pdb=" N SER E 851 " --> pdb=" O ASN E 847 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 852 " --> pdb=" O LEU E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 858 through 870 Processing helix chain 'E' and resid 871 through 882 Processing helix chain 'E' and resid 884 through 895 removed outlier: 3.848A pdb=" N ALA E 888 " --> pdb=" O GLN E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 904 removed outlier: 3.747A pdb=" N LEU E 904 " --> pdb=" O LYS E 900 " (cutoff:3.500A) Processing helix chain 'E' and resid 908 through 927 removed outlier: 3.527A pdb=" N GLU E 912 " --> pdb=" O HIS E 908 " (cutoff:3.500A) Processing helix chain 'E' and resid 929 through 940 Processing helix chain 'E' and resid 942 through 960 Processing helix chain 'E' and resid 963 through 985 Processing helix chain 'E' and resid 986 through 986 No H-bonds generated for 'chain 'E' and resid 986 through 986' Processing helix chain 'E' and resid 1018 through 1022 removed outlier: 3.979A pdb=" N ASN E1022 " --> pdb=" O PHE E1019 " (cutoff:3.500A) Processing helix chain 'E' and resid 1024 through 1042 Processing helix chain 'E' and resid 1044 through 1055 Processing helix chain 'E' and resid 1056 through 1059 removed outlier: 4.114A pdb=" N GLU E1059 " --> pdb=" O LYS E1056 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1056 through 1059' Processing helix chain 'E' and resid 1063 through 1079 removed outlier: 3.573A pdb=" N ILE E1067 " --> pdb=" O PRO E1063 " (cutoff:3.500A) Processing helix chain 'E' and resid 1080 through 1093 Processing helix chain 'E' and resid 1098 through 1116 Processing helix chain 'E' and resid 1126 through 1131 Processing helix chain 'E' and resid 1165 through 1170 Processing helix chain 'F' and resid 131 through 141 removed outlier: 3.533A pdb=" N ASN F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS F 141 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 163 through 168 Processing helix chain 'F' and resid 175 through 186 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 10 removed outlier: 5.619A pdb=" N LEU C 5 " --> pdb=" O GLN C 349 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN C 349 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR C 344 " --> pdb=" O CYS C 340 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 326 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 20 removed outlier: 4.008A pdb=" N ASP C 17 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN C 47 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASP C 39 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU C 45 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 61 removed outlier: 3.550A pdb=" N CYS C 58 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 88 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 96 through 101 removed outlier: 4.309A pdb=" N CYS C 98 " --> pdb=" O CYS C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 135 through 140 removed outlier: 4.016A pdb=" N ILE C 155 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE C 156 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS C 168 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C 158 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.733A pdb=" N SER C 181 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 263 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS C 275 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE C 265 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 283 through 288 removed outlier: 4.433A pdb=" N ILE C 286 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU C 296 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR C 288 " --> pdb=" O TYR C 294 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR C 294 " --> pdb=" O TYR C 288 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C 304 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR C 316 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 306 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AA9, first strand: chain 'C' and resid 393 through 397 removed outlier: 6.156A pdb=" N GLU C 413 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL C 426 " --> pdb=" O GLU C 413 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 438 through 441 removed outlier: 3.516A pdb=" N LEU C 438 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 454 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU C 466 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS C 456 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 478 removed outlier: 4.189A pdb=" N GLN C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 497 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 519 through 522 removed outlier: 3.659A pdb=" N CYS C 519 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS C 538 " --> pdb=" O GLN C 551 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN C 551 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL C 540 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 557 through 560 removed outlier: 3.513A pdb=" N SER C 557 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 593 through 598 removed outlier: 5.885A pdb=" N VAL C 594 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU C 605 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 596 " --> pdb=" O PHE C 603 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 2 through 10 removed outlier: 6.714A pdb=" N PHE E 328 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS E 8 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE E 326 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 17 through 22 removed outlier: 3.926A pdb=" N LEU E 38 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET E 63 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 80 removed outlier: 4.235A pdb=" N LYS E 85 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N MET E 99 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLU E 107 " --> pdb=" O MET E 99 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR E 101 " --> pdb=" O TRP E 105 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TRP E 105 " --> pdb=" O TYR E 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 118 through 123 removed outlier: 6.852A pdb=" N VAL E 141 " --> pdb=" O ILE E 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 162 through 164 removed outlier: 6.424A pdb=" N ASP E 184 " --> pdb=" O PHE E 189 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE E 189 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 207 through 212 removed outlier: 4.023A pdb=" N ARG E 235 " --> pdb=" O PHE E 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 255 through 261 removed outlier: 5.204A pdb=" N VAL E 256 " --> pdb=" O PHE E 273 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE E 273 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN E 284 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY E 297 " --> pdb=" O PHE E 288 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 337 through 340 removed outlier: 4.218A pdb=" N ARG E 350 " --> pdb=" O GLU E 355 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU E 355 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 376 through 382 removed outlier: 6.783A pdb=" N ALA E 389 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE E 379 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE E 387 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR E 381 " --> pdb=" O PHE E 385 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE E 385 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE E 410 " --> pdb=" O TYR E 426 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR E 426 " --> pdb=" O PHE E 410 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU E 412 " --> pdb=" O PRO E 424 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU E 414 " --> pdb=" O LEU E 422 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 433 through 436 Processing sheet with id=AC7, first strand: chain 'E' and resid 507 through 512 removed outlier: 3.543A pdb=" N ALA E 509 " --> pdb=" O GLY E 520 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR E 525 " --> pdb=" O ARG E 521 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER E 530 " --> pdb=" O LEU E 536 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU E 536 " --> pdb=" O SER E 530 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 546 through 551 removed outlier: 4.250A pdb=" N VAL E 566 " --> pdb=" O ASP E 562 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N LEU E 572 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N LEU E 588 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA E 574 " --> pdb=" O GLY E 586 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 546 through 551 removed outlier: 4.250A pdb=" N VAL E 566 " --> pdb=" O ASP E 562 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG E 593 " --> pdb=" O LEU E 567 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 599 through 601 Processing sheet with id=AD2, first strand: chain 'E' and resid 616 through 617 Processing sheet with id=AD3, first strand: chain 'E' and resid 634 through 639 removed outlier: 5.750A pdb=" N ILE E 635 " --> pdb=" O VAL E 646 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL E 646 " --> pdb=" O ILE E 635 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 1153 through 1154 Processing sheet with id=AD5, first strand: chain 'F' and resid 147 through 148 1080 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.70 Time building geometry restraints manager: 6.39 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: 10.310 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: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 53.240 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (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 TRP 0.152 0.025 TRP C 259 HIS 0.012 0.003 HIS E1054 PHE 0.108 0.014 PHE E 751 TYR 0.318 0.024 TYR C 61 ARG 0.013 0.001 ARG C 453 Details of bonding type rmsd hydrogen bonds : bond 0.15566 ( 1071) hydrogen bonds : angle 7.05683 ( 3102) covalent geometry : bond 0.01261 (20583) covalent geometry : angle 1.79960 (27787) *********************** 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 : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 974 HIS cc_start: 0.5842 (m-70) cc_final: 0.5585 (m-70) REVERT: E 910 MET cc_start: 0.1506 (mmp) cc_final: 0.1248 (mmm) REVERT: E 937 TYR cc_start: 0.5249 (m-10) cc_final: 0.4921 (m-10) REVERT: E 1067 ILE cc_start: 0.7545 (mt) cc_final: 0.7280 (mm) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.3726 time to fit residues: 202.3904 Evaluate side-chains 194 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 0.4980 chunk 188 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN D 977 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.092085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.072550 restraints weight = 85382.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.074376 restraints weight = 45172.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.075597 restraints weight = 27327.605| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20583 Z= 0.169 Angle : 0.709 11.887 27787 Z= 0.377 Chirality : 0.047 0.204 3047 Planarity : 0.004 0.050 3552 Dihedral : 5.940 30.009 2746 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.19 % Allowed : 8.03 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2495 helix: 0.81 (0.15), residues: 1062 sheet: -0.26 (0.21), residues: 541 loop : -0.43 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D1258 HIS 0.013 0.001 HIS E 923 PHE 0.020 0.002 PHE C 608 TYR 0.042 0.002 TYR C 61 ARG 0.006 0.001 ARG E 938 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 1071) hydrogen bonds : angle 5.25326 ( 3102) covalent geometry : bond 0.00363 (20583) covalent geometry : angle 0.70931 (27787) *********************** 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 236 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7295 (mm) REVERT: C 247 LEU cc_start: 0.8684 (pt) cc_final: 0.8421 (mt) REVERT: D 957 MET cc_start: 0.7011 (mtp) cc_final: 0.6787 (mtp) REVERT: D 970 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8309 (tp-100) REVERT: D 974 HIS cc_start: 0.8437 (m-70) cc_final: 0.8084 (m170) REVERT: D 1163 MET cc_start: 0.8745 (mtm) cc_final: 0.8510 (ttm) REVERT: D 1168 MET cc_start: 0.7363 (mmm) cc_final: 0.7113 (mmm) REVERT: E 99 MET cc_start: 0.8347 (ptp) cc_final: 0.7932 (ptp) REVERT: E 910 MET cc_start: 0.1954 (mmp) cc_final: 0.1385 (mmm) REVERT: E 985 MET cc_start: 0.7926 (ptt) cc_final: 0.7585 (ptt) outliers start: 26 outliers final: 8 residues processed: 224 average time/residue: 0.3426 time to fit residues: 117.7355 Evaluate side-chains 170 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 2.439 ------------------------------------------------------------------------------- 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 D residue 970 GLN 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 105 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 701 HIS ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1169 HIS F 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.088260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.066892 restraints weight = 85018.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.068870 restraints weight = 43379.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.070154 restraints weight = 27654.495| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20583 Z= 0.283 Angle : 0.765 10.044 27787 Z= 0.407 Chirality : 0.049 0.236 3047 Planarity : 0.005 0.050 3552 Dihedral : 5.837 31.786 2746 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.65 % Allowed : 10.69 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2495 helix: 0.76 (0.15), residues: 1055 sheet: -0.57 (0.22), residues: 535 loop : -0.78 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP F 174 HIS 0.010 0.002 HIS E1054 PHE 0.027 0.003 PHE C 307 TYR 0.037 0.003 TYR C 61 ARG 0.012 0.001 ARG D 863 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 1071) hydrogen bonds : angle 5.44077 ( 3102) covalent geometry : bond 0.00638 (20583) covalent geometry : angle 0.76527 (27787) *********************** 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 199 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 2.299 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: C 84 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7431 (mm) REVERT: C 101 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.6989 (m-10) REVERT: C 247 LEU cc_start: 0.8753 (pt) cc_final: 0.8333 (mt) REVERT: D 706 MET cc_start: 0.6709 (mmm) cc_final: 0.6420 (mmm) REVERT: D 804 TRP cc_start: 0.8841 (m100) cc_final: 0.8359 (m100) REVERT: D 1092 GLU cc_start: 0.3692 (OUTLIER) cc_final: 0.3138 (pm20) REVERT: D 1168 MET cc_start: 0.8162 (mmm) cc_final: 0.7674 (mmm) REVERT: D 1256 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8820 (mmp) REVERT: E 99 MET cc_start: 0.8527 (ptp) cc_final: 0.7312 (ptp) REVERT: E 190 MET cc_start: 0.8441 (mtp) cc_final: 0.8181 (mtm) REVERT: E 254 MET cc_start: 0.7016 (ptt) cc_final: 0.6799 (ptm) REVERT: E 712 LEU cc_start: 0.7319 (mp) cc_final: 0.7095 (mm) REVERT: E 985 MET cc_start: 0.7655 (ptt) cc_final: 0.7397 (ptt) REVERT: E 1103 GLN cc_start: 0.9420 (tp40) cc_final: 0.9194 (tm-30) REVERT: E 1130 MET cc_start: 0.7327 (mtp) cc_final: 0.7065 (ptm) outliers start: 36 outliers final: 19 residues processed: 191 average time/residue: 0.3464 time to fit residues: 104.6504 Evaluate side-chains 158 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 2.482 ------------------------------------------------------------------------------- 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 101 TYR 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 426 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1173 THR 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 163 THR Chi-restraints excluded: chain E residue 500 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain E residue 1037 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 102 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 234 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 771 ASN E 26 GLN E 84 GLN ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.089309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.068185 restraints weight = 85269.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.070636 restraints weight = 47077.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.071607 restraints weight = 25746.897| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20583 Z= 0.168 Angle : 0.631 8.322 27787 Z= 0.335 Chirality : 0.045 0.234 3047 Planarity : 0.004 0.067 3552 Dihedral : 5.382 28.707 2746 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.47 % Allowed : 12.16 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2495 helix: 0.96 (0.15), residues: 1070 sheet: -0.53 (0.21), residues: 545 loop : -0.75 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 98 HIS 0.005 0.001 HIS E1054 PHE 0.020 0.002 PHE C 608 TYR 0.027 0.002 TYR E1041 ARG 0.010 0.000 ARG D 863 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 1071) hydrogen bonds : angle 5.10237 ( 3102) covalent geometry : bond 0.00372 (20583) covalent geometry : angle 0.63074 (27787) *********************** 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 189 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7293 (mm) REVERT: C 247 LEU cc_start: 0.8783 (pt) cc_final: 0.8351 (mt) REVERT: D 802 LEU cc_start: 0.9274 (mp) cc_final: 0.8966 (mp) REVERT: D 804 TRP cc_start: 0.8811 (m100) cc_final: 0.8310 (m100) REVERT: D 828 MET cc_start: 0.8483 (tmm) cc_final: 0.8224 (tmm) REVERT: D 1092 GLU cc_start: 0.4048 (OUTLIER) cc_final: 0.3610 (pm20) REVERT: D 1131 MET cc_start: 0.1393 (ptt) cc_final: 0.0525 (ptm) REVERT: D 1168 MET cc_start: 0.8223 (mmm) cc_final: 0.7761 (mmm) REVERT: D 1236 TYR cc_start: 0.6821 (m-80) cc_final: 0.6568 (m-80) REVERT: D 1256 MET cc_start: 0.9065 (mmt) cc_final: 0.8812 (mmp) REVERT: E 99 MET cc_start: 0.8619 (ptp) cc_final: 0.7387 (ptp) REVERT: E 190 MET cc_start: 0.8360 (mtp) cc_final: 0.8103 (mtm) REVERT: E 254 MET cc_start: 0.7047 (ptt) cc_final: 0.6776 (ptm) REVERT: E 712 LEU cc_start: 0.7342 (mp) cc_final: 0.7124 (mm) REVERT: E 985 MET cc_start: 0.7789 (ptt) cc_final: 0.7569 (ptt) REVERT: E 1103 GLN cc_start: 0.9328 (tp40) cc_final: 0.9102 (tm-30) outliers start: 32 outliers final: 16 residues processed: 183 average time/residue: 0.3191 time to fit residues: 93.1154 Evaluate side-chains 158 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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 169 ILE 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 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 TRP Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 681 VAL Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain E residue 1037 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 124 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 89 optimal weight: 0.0570 chunk 202 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 263 HIS ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.089251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.068294 restraints weight = 85014.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.070979 restraints weight = 46873.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.071829 restraints weight = 23939.846| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4610 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 : 0.603 8.463 27787 Z= 0.320 Chirality : 0.044 0.182 3047 Planarity : 0.004 0.042 3552 Dihedral : 5.122 31.647 2746 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.51 % Allowed : 12.02 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2495 helix: 1.01 (0.15), residues: 1084 sheet: -0.53 (0.21), residues: 557 loop : -0.73 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1258 HIS 0.003 0.001 HIS E1054 PHE 0.017 0.002 PHE C 68 TYR 0.025 0.001 TYR E1041 ARG 0.007 0.000 ARG D 863 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 1071) hydrogen bonds : angle 4.95858 ( 3102) covalent geometry : bond 0.00327 (20583) covalent geometry : angle 0.60342 (27787) *********************** 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 181 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7205 (mm) REVERT: C 247 LEU cc_start: 0.8783 (pt) cc_final: 0.8265 (mt) REVERT: D 694 MET cc_start: 0.6847 (mmt) cc_final: 0.6561 (mmt) REVERT: D 802 LEU cc_start: 0.9257 (mp) cc_final: 0.8800 (mp) REVERT: D 804 TRP cc_start: 0.8854 (m100) cc_final: 0.8255 (m100) REVERT: D 1092 GLU cc_start: 0.4182 (OUTLIER) cc_final: 0.3770 (pm20) REVERT: D 1131 MET cc_start: 0.1558 (ptt) cc_final: 0.0738 (ptm) REVERT: D 1168 MET cc_start: 0.8254 (mmm) cc_final: 0.7768 (mmm) REVERT: D 1192 ASP cc_start: 0.4893 (m-30) cc_final: 0.4040 (t0) REVERT: D 1236 TYR cc_start: 0.6856 (m-80) cc_final: 0.6612 (m-80) REVERT: D 1256 MET cc_start: 0.9121 (mmt) cc_final: 0.8832 (mmp) REVERT: E 99 MET cc_start: 0.8619 (ptp) cc_final: 0.7401 (ptp) REVERT: E 190 MET cc_start: 0.8325 (mtp) cc_final: 0.8051 (mtm) REVERT: E 254 MET cc_start: 0.7032 (ptt) cc_final: 0.6763 (ptm) REVERT: E 611 MET cc_start: 0.5931 (ttp) cc_final: 0.4372 (tmm) REVERT: E 796 ASP cc_start: 0.8213 (m-30) cc_final: 0.7584 (p0) REVERT: E 1103 GLN cc_start: 0.9310 (tp40) cc_final: 0.9089 (tm-30) REVERT: E 1130 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6598 (ptt) outliers start: 33 outliers final: 19 residues processed: 170 average time/residue: 0.2978 time to fit residues: 82.7241 Evaluate side-chains 164 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 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 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1092 GLU 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 681 VAL Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain E residue 1037 GLN 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 101 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 198 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1082 ASN D1296 HIS ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.087127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.067573 restraints weight = 86950.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.069685 restraints weight = 42087.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.070033 restraints weight = 25842.895| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20583 Z= 0.173 Angle : 0.622 14.796 27787 Z= 0.327 Chirality : 0.045 0.196 3047 Planarity : 0.004 0.042 3552 Dihedral : 5.091 35.062 2746 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.93 % Allowed : 12.39 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2495 helix: 1.01 (0.15), residues: 1090 sheet: -0.44 (0.21), residues: 536 loop : -0.93 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 98 HIS 0.006 0.001 HIS E 923 PHE 0.016 0.002 PHE C 68 TYR 0.022 0.002 TYR E1041 ARG 0.009 0.001 ARG D 926 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1071) hydrogen bonds : angle 4.97099 ( 3102) covalent geometry : bond 0.00390 (20583) covalent geometry : angle 0.62207 (27787) *********************** 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 189 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7321 (mm) REVERT: C 115 ASP cc_start: 0.6467 (OUTLIER) cc_final: 0.6117 (p0) REVERT: C 247 LEU cc_start: 0.8827 (pt) cc_final: 0.8292 (mt) REVERT: C 459 PHE cc_start: 0.5089 (m-80) cc_final: 0.4778 (m-10) REVERT: D 802 LEU cc_start: 0.9261 (mp) cc_final: 0.8751 (mp) REVERT: D 804 TRP cc_start: 0.8782 (m100) cc_final: 0.8179 (m100) REVERT: D 1092 GLU cc_start: 0.4071 (OUTLIER) cc_final: 0.3670 (pm20) REVERT: D 1131 MET cc_start: 0.1751 (ptt) cc_final: 0.0900 (ptm) REVERT: D 1168 MET cc_start: 0.8423 (mmm) cc_final: 0.8001 (mmm) REVERT: D 1192 ASP cc_start: 0.5197 (m-30) cc_final: 0.4148 (t0) REVERT: D 1236 TYR cc_start: 0.6916 (m-80) cc_final: 0.6679 (m-80) REVERT: D 1256 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8762 (mmp) REVERT: E 99 MET cc_start: 0.8613 (ptp) cc_final: 0.7409 (ptp) REVERT: E 190 MET cc_start: 0.8332 (mtp) cc_final: 0.8051 (mtm) REVERT: E 254 MET cc_start: 0.6918 (ptt) cc_final: 0.6708 (ptm) REVERT: E 742 MET cc_start: 0.9277 (mmm) cc_final: 0.9057 (mmp) REVERT: E 1103 GLN cc_start: 0.9268 (tp40) cc_final: 0.9037 (tm-30) REVERT: E 1130 MET cc_start: 0.6719 (ptm) cc_final: 0.6477 (ptt) REVERT: F 130 MET cc_start: 0.6738 (mpp) cc_final: 0.6472 (pmm) outliers start: 42 outliers final: 26 residues processed: 183 average time/residue: 0.3109 time to fit residues: 94.0614 Evaluate side-chains 167 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 2.318 ------------------------------------------------------------------------------- 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 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 13 ASN 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 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 681 VAL Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain F residue 145 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 64 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 217 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 220 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: E 928 ASN E 980 GLN ** E1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1177 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.088257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.067251 restraints weight = 85062.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.069251 restraints weight = 42887.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.070545 restraints weight = 27179.433| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20583 Z= 0.171 Angle : 0.617 10.830 27787 Z= 0.325 Chirality : 0.044 0.205 3047 Planarity : 0.004 0.044 3552 Dihedral : 5.056 36.789 2746 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.79 % Allowed : 12.75 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.17), residues: 2495 helix: 1.07 (0.15), residues: 1084 sheet: -0.49 (0.22), residues: 529 loop : -0.93 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 98 HIS 0.004 0.001 HIS E1160 PHE 0.019 0.002 PHE D 687 TYR 0.020 0.002 TYR E1041 ARG 0.005 0.000 ARG D 863 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 1071) hydrogen bonds : angle 4.95261 ( 3102) covalent geometry : bond 0.00385 (20583) covalent geometry : angle 0.61744 (27787) *********************** 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 185 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7304 (mm) REVERT: C 115 ASP cc_start: 0.6459 (OUTLIER) cc_final: 0.6094 (p0) REVERT: C 247 LEU cc_start: 0.8694 (pt) cc_final: 0.8150 (mt) REVERT: C 459 PHE cc_start: 0.5038 (m-80) cc_final: 0.4696 (m-10) REVERT: C 725 MET cc_start: 0.7755 (ppp) cc_final: 0.7435 (ppp) REVERT: D 802 LEU cc_start: 0.9260 (mp) cc_final: 0.8770 (mp) REVERT: D 804 TRP cc_start: 0.8880 (m100) cc_final: 0.8286 (m100) REVERT: D 957 MET cc_start: 0.8527 (mmp) cc_final: 0.7359 (mtp) REVERT: D 1092 GLU cc_start: 0.4319 (OUTLIER) cc_final: 0.3815 (pm20) REVERT: D 1131 MET cc_start: 0.1820 (ptt) cc_final: 0.0956 (ptm) REVERT: D 1168 MET cc_start: 0.8444 (mmm) cc_final: 0.8002 (mmm) REVERT: D 1192 ASP cc_start: 0.4902 (m-30) cc_final: 0.3969 (t70) REVERT: D 1236 TYR cc_start: 0.7022 (m-80) cc_final: 0.6754 (m-80) REVERT: D 1256 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8817 (mmp) REVERT: E 99 MET cc_start: 0.8515 (ptp) cc_final: 0.7405 (ptp) REVERT: E 190 MET cc_start: 0.8364 (mtp) cc_final: 0.8061 (mtm) REVERT: E 254 MET cc_start: 0.7011 (ptt) cc_final: 0.6800 (ptm) REVERT: E 611 MET cc_start: 0.6000 (ttp) cc_final: 0.4313 (tmm) REVERT: E 742 MET cc_start: 0.9146 (mmm) cc_final: 0.8903 (mmp) REVERT: E 1103 GLN cc_start: 0.9353 (tp40) cc_final: 0.9108 (tm-30) REVERT: E 1130 MET cc_start: 0.6686 (ptm) cc_final: 0.6442 (ptt) outliers start: 39 outliers final: 25 residues processed: 177 average time/residue: 0.2811 time to fit residues: 83.9951 Evaluate side-chains 166 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 2.430 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 1061 TYR Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1256 MET 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 681 VAL Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain E residue 1037 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 17 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 717 GLN 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 = 0.4191 r_free = 0.4191 target = 0.087076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.067795 restraints weight = 86880.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.070083 restraints weight = 41856.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.070457 restraints weight = 24867.539| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20583 Z= 0.153 Angle : 0.614 14.263 27787 Z= 0.322 Chirality : 0.044 0.214 3047 Planarity : 0.004 0.045 3552 Dihedral : 4.980 38.047 2746 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.74 % Allowed : 13.21 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2495 helix: 1.12 (0.15), residues: 1083 sheet: -0.60 (0.21), residues: 556 loop : -0.84 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 98 HIS 0.004 0.001 HIS D1226 PHE 0.026 0.002 PHE D 687 TYR 0.021 0.001 TYR E1041 ARG 0.005 0.000 ARG D 863 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 1071) hydrogen bonds : angle 4.92017 ( 3102) covalent geometry : bond 0.00341 (20583) covalent geometry : angle 0.61358 (27787) *********************** 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 182 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7315 (mm) REVERT: C 115 ASP cc_start: 0.6451 (OUTLIER) cc_final: 0.6118 (p0) REVERT: C 247 LEU cc_start: 0.8758 (pt) cc_final: 0.8213 (mt) REVERT: D 802 LEU cc_start: 0.9254 (mp) cc_final: 0.8733 (mp) REVERT: D 804 TRP cc_start: 0.8825 (m100) cc_final: 0.8240 (m100) REVERT: D 957 MET cc_start: 0.8635 (mmp) cc_final: 0.7435 (mtp) REVERT: D 1092 GLU cc_start: 0.4339 (OUTLIER) cc_final: 0.3876 (pm20) REVERT: D 1131 MET cc_start: 0.1863 (ptt) cc_final: 0.0990 (ptm) REVERT: D 1163 MET cc_start: 0.8645 (tpp) cc_final: 0.7622 (tpp) REVERT: D 1168 MET cc_start: 0.8473 (mmm) cc_final: 0.8022 (mmm) REVERT: D 1192 ASP cc_start: 0.4898 (m-30) cc_final: 0.3832 (t70) REVERT: D 1215 MET cc_start: 0.8377 (pmm) cc_final: 0.8110 (pmm) REVERT: D 1256 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8809 (mmp) REVERT: E 99 MET cc_start: 0.8547 (ptp) cc_final: 0.7411 (ptp) REVERT: E 239 MET cc_start: 0.8133 (mmm) cc_final: 0.7661 (mmm) REVERT: E 254 MET cc_start: 0.6973 (ptt) cc_final: 0.6767 (ptm) REVERT: E 742 MET cc_start: 0.9199 (mmm) cc_final: 0.8928 (mmp) REVERT: E 1103 GLN cc_start: 0.9260 (tp40) cc_final: 0.9006 (tm-30) REVERT: E 1130 MET cc_start: 0.6554 (ptm) cc_final: 0.6327 (ptt) outliers start: 38 outliers final: 28 residues processed: 175 average time/residue: 0.2770 time to fit residues: 81.6045 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 : 2.454 ------------------------------------------------------------------------------- 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 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 13 ASN 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 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 663 LEU Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 681 VAL Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain E residue 1037 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 107 optimal weight: 0.0670 chunk 83 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 928 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.087813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.068595 restraints weight = 86042.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.070193 restraints weight = 43920.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.070831 restraints weight = 26046.379| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20583 Z= 0.135 Angle : 0.593 12.695 27787 Z= 0.311 Chirality : 0.044 0.209 3047 Planarity : 0.003 0.044 3552 Dihedral : 4.879 38.155 2746 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.65 % Allowed : 13.53 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2495 helix: 1.21 (0.16), residues: 1083 sheet: -0.55 (0.21), residues: 543 loop : -0.87 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 98 HIS 0.004 0.001 HIS D1226 PHE 0.021 0.002 PHE C 608 TYR 0.021 0.001 TYR E1041 ARG 0.004 0.000 ARG D 718 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 1071) hydrogen bonds : angle 4.85323 ( 3102) covalent geometry : bond 0.00300 (20583) covalent geometry : angle 0.59264 (27787) *********************** 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 178 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7275 (mm) REVERT: C 115 ASP cc_start: 0.6378 (OUTLIER) cc_final: 0.6070 (p0) REVERT: C 247 LEU cc_start: 0.8880 (pt) cc_final: 0.8295 (mt) REVERT: D 719 MET cc_start: -0.0463 (pmm) cc_final: -0.1137 (ppp) REVERT: D 802 LEU cc_start: 0.9248 (mp) cc_final: 0.8704 (mp) REVERT: D 804 TRP cc_start: 0.8794 (m100) cc_final: 0.8192 (m100) REVERT: D 957 MET cc_start: 0.8701 (mmp) cc_final: 0.7788 (mtp) REVERT: D 1092 GLU cc_start: 0.4304 (OUTLIER) cc_final: 0.3849 (pm20) REVERT: D 1131 MET cc_start: 0.1985 (ptt) cc_final: 0.1076 (ptm) REVERT: D 1163 MET cc_start: 0.8670 (tpp) cc_final: 0.8257 (tpp) REVERT: D 1168 MET cc_start: 0.8486 (mmm) cc_final: 0.8002 (mmm) REVERT: D 1192 ASP cc_start: 0.4726 (m-30) cc_final: 0.3811 (t70) REVERT: D 1215 MET cc_start: 0.8364 (pmm) cc_final: 0.8084 (pmm) REVERT: D 1256 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8784 (mmp) REVERT: E 99 MET cc_start: 0.8651 (ptp) cc_final: 0.7462 (ptp) REVERT: E 239 MET cc_start: 0.8136 (mmm) cc_final: 0.7647 (mmm) REVERT: E 254 MET cc_start: 0.6911 (ptt) cc_final: 0.6677 (ptm) REVERT: E 490 MET cc_start: 0.8385 (ttm) cc_final: 0.7932 (mpp) REVERT: E 611 MET cc_start: 0.5740 (ttp) cc_final: 0.4031 (tmm) REVERT: E 742 MET cc_start: 0.9275 (mmm) cc_final: 0.8977 (mmp) REVERT: E 1103 GLN cc_start: 0.9236 (tp40) cc_final: 0.8994 (tm-30) outliers start: 36 outliers final: 29 residues processed: 170 average time/residue: 0.2743 time to fit residues: 78.1106 Evaluate side-chains 171 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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 567 MET 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 837 LEU Chi-restraints excluded: chain D residue 1061 TYR 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 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 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 663 LEU Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 681 VAL Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain E residue 928 ASN Chi-restraints excluded: chain E residue 1037 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 143 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 chunk 240 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 113 optimal weight: 0.0010 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1262 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 = 0.4220 r_free = 0.4220 target = 0.089071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.068561 restraints weight = 84026.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.071391 restraints weight = 43429.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.071703 restraints weight = 23653.115| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20583 Z= 0.132 Angle : 0.596 12.796 27787 Z= 0.312 Chirality : 0.044 0.206 3047 Planarity : 0.003 0.041 3552 Dihedral : 4.833 37.621 2746 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.56 % Allowed : 14.27 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2495 helix: 1.25 (0.16), residues: 1081 sheet: -0.52 (0.21), residues: 543 loop : -0.87 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 98 HIS 0.004 0.001 HIS D1226 PHE 0.018 0.001 PHE D 687 TYR 0.021 0.001 TYR E1041 ARG 0.004 0.000 ARG D 863 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 1071) hydrogen bonds : angle 4.82087 ( 3102) covalent geometry : bond 0.00293 (20583) covalent geometry : angle 0.59603 (27787) ********************** 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 171 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7232 (mm) REVERT: C 115 ASP cc_start: 0.6291 (OUTLIER) cc_final: 0.6020 (p0) REVERT: C 247 LEU cc_start: 0.8776 (pt) cc_final: 0.8197 (mt) REVERT: D 802 LEU cc_start: 0.9260 (mp) cc_final: 0.8717 (mp) REVERT: D 804 TRP cc_start: 0.8777 (m100) cc_final: 0.8173 (m100) REVERT: D 957 MET cc_start: 0.8744 (mmp) cc_final: 0.7673 (mtp) REVERT: D 958 MET cc_start: 0.8188 (ppp) cc_final: 0.6219 (ttt) REVERT: D 1092 GLU cc_start: 0.4274 (OUTLIER) cc_final: 0.3803 (pm20) REVERT: D 1131 MET cc_start: 0.2009 (ptt) cc_final: 0.1088 (ptm) REVERT: D 1163 MET cc_start: 0.8706 (tpp) cc_final: 0.8284 (tpp) REVERT: D 1168 MET cc_start: 0.8524 (mmm) cc_final: 0.8022 (mmm) REVERT: D 1192 ASP cc_start: 0.4714 (m-30) cc_final: 0.3772 (t70) REVERT: D 1215 MET cc_start: 0.8436 (pmm) cc_final: 0.8170 (pmm) REVERT: D 1256 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8791 (mmp) REVERT: D 1270 TYR cc_start: 0.7631 (t80) cc_final: 0.7284 (t80) REVERT: E 99 MET cc_start: 0.8588 (ptp) cc_final: 0.7422 (ptp) REVERT: E 190 MET cc_start: 0.8346 (mtp) cc_final: 0.8050 (mtm) REVERT: E 239 MET cc_start: 0.8145 (mmm) cc_final: 0.7647 (mmm) REVERT: E 254 MET cc_start: 0.6977 (ptt) cc_final: 0.6723 (ptm) REVERT: E 490 MET cc_start: 0.8383 (ttm) cc_final: 0.7964 (mpp) REVERT: E 611 MET cc_start: 0.5754 (ttp) cc_final: 0.3997 (tmm) REVERT: E 742 MET cc_start: 0.9228 (mmm) cc_final: 0.8950 (mmp) REVERT: E 788 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8151 (tptt) REVERT: E 1103 GLN cc_start: 0.9283 (tp40) cc_final: 0.9042 (tm-30) outliers start: 34 outliers final: 27 residues processed: 164 average time/residue: 0.2848 time to fit residues: 79.6325 Evaluate side-chains 166 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 2.454 ------------------------------------------------------------------------------- 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 567 MET 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 837 LEU Chi-restraints excluded: chain D residue 1061 TYR 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 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 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 663 LEU Chi-restraints excluded: chain E residue 681 VAL Chi-restraints excluded: chain E residue 893 VAL Chi-restraints excluded: chain E residue 1037 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 74 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 10 optimal weight: 0.0050 chunk 177 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 239 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.087356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.067030 restraints weight = 87267.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.069096 restraints weight = 41669.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.070392 restraints weight = 25776.272| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20583 Z= 0.156 Angle : 0.626 12.501 27787 Z= 0.328 Chirality : 0.044 0.204 3047 Planarity : 0.004 0.039 3552 Dihedral : 4.870 38.184 2746 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.38 % Allowed : 14.72 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2495 helix: 1.20 (0.16), residues: 1079 sheet: -0.60 (0.21), residues: 543 loop : -0.89 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 98 HIS 0.004 0.001 HIS D1226 PHE 0.015 0.002 PHE E 3 TYR 0.020 0.001 TYR E1041 ARG 0.004 0.000 ARG D1007 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 1071) hydrogen bonds : angle 4.87380 ( 3102) covalent geometry : bond 0.00350 (20583) covalent geometry : angle 0.62613 (27787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6862.29 seconds wall clock time: 120 minutes 13.23 seconds (7213.23 seconds total)