Starting phenix.real_space_refine on Sat Jul 4 13:02:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8q9t_18288/07_2026/8q9t_18288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9t_18288/07_2026/8q9t_18288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q9t_18288/07_2026/8q9t_18288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9t_18288/07_2026/8q9t_18288.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9t_18288/07_2026/8q9t_18288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9t_18288/07_2026/8q9t_18288.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8q9t_18288/07_2026/8q9t_18288.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8q9t_18288/07_2026/8q9t_18288.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.173 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 93 5.16 5 C 13436 2.51 5 N 3521 2.21 5 O 3873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20927 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 7950 Classifications: {'peptide': 1075} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1026} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 755 Unresolved non-hydrogen angles: 900 Unresolved non-hydrogen dihedrals: 621 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLU:plan': 30, 'ASP:plan': 21, 'ARG:plan': 16, 'ASN:plan1': 12, 'HIS:plan': 4, 'GLN:plan1': 10} Unresolved non-hydrogen planarities: 359 Chain: "C" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2711 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 8, 'TRANS': 349} Chain breaks: 7 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 5, 'ARG:plan': 2, 'GLU:plan': 7, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2347 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 307} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "E" Number of atoms: 7849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 7849 Classifications: {'peptide': 1060} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 206} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 1037} Chain breaks: 11 Unresolved non-hydrogen bonds: 680 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 554 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'ASN:plan1': 11, 'GLU:plan': 29, 'ASP:plan': 15, 'HIS:plan': 2, 'GLN:plan1': 12, 'PHE:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 313 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Classifications: {'RNA': 4} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.39, per 1000 atoms: 0.21 Number of scatterers: 20927 At special positions: 0 Unit cell: (119.168, 131.936, 196.627, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 P 4 15.00 O 3873 8.00 N 3521 7.00 C 13436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 851.0 milliseconds 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5360 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 21 sheets defined 53.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 removed outlier: 3.628A pdb=" N SER A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.601A pdb=" N LEU A 91 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 92 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 331 through 344 Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.781A pdb=" N ALA A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 432 through 436 removed outlier: 3.543A pdb=" N ILE A 435 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 480 through 493 removed outlier: 3.949A pdb=" N PHE A 484 " --> pdb=" O ASN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 539 Processing helix chain 'A' and resid 612 through 625 removed outlier: 3.549A pdb=" N GLU A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 645 removed outlier: 3.795A pdb=" N GLU A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 668 Processing helix chain 'A' and resid 669 through 671 No H-bonds generated for 'chain 'A' and resid 669 through 671' Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 678 through 689 Processing helix chain 'A' and resid 700 through 714 Processing helix chain 'A' and resid 723 through 726 Processing helix chain 'A' and resid 753 through 762 Processing helix chain 'A' and resid 785 through 794 removed outlier: 3.541A pdb=" N PHE A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 817 Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 842 through 855 Processing helix chain 'A' and resid 861 through 865 removed outlier: 3.973A pdb=" N ASP A 865 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 889 Processing helix chain 'A' and resid 890 through 891 No H-bonds generated for 'chain 'A' and resid 890 through 891' Processing helix chain 'A' and resid 892 through 893 No H-bonds generated for 'chain 'A' and resid 892 through 893' Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 954 through 962 Processing helix chain 'A' and resid 991 through 998 removed outlier: 4.098A pdb=" N VAL A 995 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1016 removed outlier: 3.798A pdb=" N GLY A1016 " --> pdb=" O ASN A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1028 removed outlier: 3.567A pdb=" N GLN A1028 " --> pdb=" O ILE A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1048 Processing helix chain 'A' and resid 1049 through 1053 removed outlier: 4.100A pdb=" N ILE A1052 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A1053 " --> pdb=" O LYS A1050 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1049 through 1053' Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1061 through 1078 Processing helix chain 'A' and resid 1088 through 1102 Processing helix chain 'A' and resid 1112 through 1119 Processing helix chain 'A' and resid 1125 through 1135 removed outlier: 3.605A pdb=" N LEU A1129 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP A1135 " --> pdb=" O GLU A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1141 removed outlier: 3.543A pdb=" N GLY A1139 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER A1140 " --> pdb=" O PHE A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1150 Processing helix chain 'A' and resid 1151 through 1154 Processing helix chain 'A' and resid 1168 through 1192 removed outlier: 3.712A pdb=" N HIS A1192 " --> pdb=" O VAL A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1202 Processing helix chain 'A' and resid 1211 through 1221 Processing helix chain 'A' and resid 1223 through 1231 Processing helix chain 'A' and resid 1234 through 1260 removed outlier: 3.830A pdb=" N GLU A1247 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1276 removed outlier: 3.510A pdb=" N LYS A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.840A pdb=" N VAL A1280 " --> pdb=" O ARG A1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.873A pdb=" N LYS C 121 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.002A pdb=" N ILE C 336 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 removed outlier: 3.669A pdb=" N ILE C 342 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 53 removed outlier: 3.600A pdb=" N ASP D 53 " --> pdb=" O ASN D 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 50 through 53' Processing helix chain 'D' and resid 118 through 122 Processing helix chain 'E' and resid 282 through 292 Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 315 through 327 Processing helix chain 'E' and resid 333 through 341 Processing helix chain 'E' and resid 407 through 421 Processing helix chain 'E' and resid 424 through 438 Processing helix chain 'E' and resid 444 through 461 Processing helix chain 'E' and resid 466 through 485 removed outlier: 4.546A pdb=" N LYS E 470 " --> pdb=" O LEU E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 504 Processing helix chain 'E' and resid 507 through 521 removed outlier: 3.803A pdb=" N LYS E 511 " --> pdb=" O ASN E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 538 removed outlier: 3.955A pdb=" N THR E 529 " --> pdb=" O LYS E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 555 removed outlier: 3.828A pdb=" N MET E 555 " --> pdb=" O SER E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 565 removed outlier: 4.089A pdb=" N LEU E 562 " --> pdb=" O MET E 558 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA E 563 " --> pdb=" O ASP E 559 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU E 565 " --> pdb=" O ALA E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 571 Processing helix chain 'E' and resid 576 through 600 removed outlier: 4.035A pdb=" N SER E 600 " --> pdb=" O MET E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 624 Processing helix chain 'E' and resid 626 through 640 removed outlier: 3.537A pdb=" N PHE E 630 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 658 Processing helix chain 'E' and resid 662 through 674 Processing helix chain 'E' and resid 677 through 692 removed outlier: 3.934A pdb=" N GLU E 692 " --> pdb=" O LEU E 688 " (cutoff:3.500A) Processing helix chain 'E' and resid 696 through 700 removed outlier: 3.510A pdb=" N ARG E 699 " --> pdb=" O ALA E 696 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER E 700 " --> pdb=" O GLU E 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 696 through 700' Processing helix chain 'E' and resid 702 through 715 Processing helix chain 'E' and resid 721 through 732 removed outlier: 3.606A pdb=" N VAL E 731 " --> pdb=" O SER E 727 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 750 Processing helix chain 'E' and resid 751 through 766 Processing helix chain 'E' and resid 769 through 782 removed outlier: 3.751A pdb=" N GLN E 773 " --> pdb=" O HIS E 769 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP E 782 " --> pdb=" O ILE E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 800 removed outlier: 3.608A pdb=" N SER E 789 " --> pdb=" O GLU E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 803 through 824 removed outlier: 3.746A pdb=" N GLN E 807 " --> pdb=" O GLU E 803 " (cutoff:3.500A) Processing helix chain 'E' and resid 826 through 848 removed outlier: 4.083A pdb=" N VAL E 831 " --> pdb=" O LEU E 827 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER E 832 " --> pdb=" O LEU E 828 " (cutoff:3.500A) Processing helix chain 'E' and resid 852 through 863 removed outlier: 3.850A pdb=" N TRP E 856 " --> pdb=" O ASN E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 869 Processing helix chain 'E' and resid 870 through 876 removed outlier: 3.616A pdb=" N VAL E 873 " --> pdb=" O GLU E 870 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP E 874 " --> pdb=" O SER E 871 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 876 " --> pdb=" O VAL E 873 " (cutoff:3.500A) Processing helix chain 'E' and resid 877 through 888 removed outlier: 3.569A pdb=" N SER E 888 " --> pdb=" O ILE E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 903 through 907 removed outlier: 3.528A pdb=" N LEU E 907 " --> pdb=" O ILE E 904 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 929 removed outlier: 3.664A pdb=" N ILE E 918 " --> pdb=" O ASP E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 941 through 963 removed outlier: 3.824A pdb=" N ALA E 945 " --> pdb=" O GLY E 941 " (cutoff:3.500A) Processing helix chain 'E' and resid 964 through 982 removed outlier: 4.071A pdb=" N ARG E 968 " --> pdb=" O GLU E 964 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP E 969 " --> pdb=" O PRO E 965 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 970 " --> pdb=" O GLN E 966 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 996 removed outlier: 4.141A pdb=" N TRP E 989 " --> pdb=" O THR E 985 " (cutoff:3.500A) Processing helix chain 'E' and resid 1000 through 1015 Processing helix chain 'E' and resid 1019 through 1032 Processing helix chain 'E' and resid 1034 through 1049 Processing helix chain 'E' and resid 1053 through 1067 Processing helix chain 'E' and resid 1069 through 1084 removed outlier: 3.708A pdb=" N ASN E1084 " --> pdb=" O PHE E1080 " (cutoff:3.500A) Processing helix chain 'E' and resid 1087 through 1102 removed outlier: 3.585A pdb=" N GLN E1091 " --> pdb=" O SER E1087 " (cutoff:3.500A) Processing helix chain 'E' and resid 1111 through 1132 removed outlier: 3.528A pdb=" N VAL E1115 " --> pdb=" O ASP E1111 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS E1131 " --> pdb=" O GLN E1127 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1150 removed outlier: 3.550A pdb=" N ARG E1148 " --> pdb=" O LEU E1144 " (cutoff:3.500A) Processing helix chain 'E' and resid 1151 through 1170 Processing helix chain 'E' and resid 1176 through 1197 Processing helix chain 'E' and resid 1198 through 1213 removed outlier: 3.620A pdb=" N ILE E1212 " --> pdb=" O LEU E1208 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E1213 " --> pdb=" O SER E1209 " (cutoff:3.500A) Processing helix chain 'E' and resid 1221 through 1238 Processing helix chain 'E' and resid 1242 through 1253 Processing helix chain 'E' and resid 1261 through 1274 removed outlier: 3.853A pdb=" N GLY E1274 " --> pdb=" O LEU E1270 " (cutoff:3.500A) Processing helix chain 'E' and resid 1275 through 1294 Processing helix chain 'E' and resid 1296 through 1311 removed outlier: 3.781A pdb=" N THR E1300 " --> pdb=" O ASP E1296 " (cutoff:3.500A) Processing helix chain 'E' and resid 1312 through 1325 removed outlier: 3.961A pdb=" N SER E1317 " --> pdb=" O ARG E1313 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE E1318 " --> pdb=" O GLU E1314 " (cutoff:3.500A) Processing helix chain 'E' and resid 1327 through 1334 Processing helix chain 'E' and resid 1337 through 1352 removed outlier: 3.924A pdb=" N TYR E1341 " --> pdb=" O LYS E1337 " (cutoff:3.500A) Processing helix chain 'E' and resid 1356 through 1367 removed outlier: 4.229A pdb=" N TRP E1360 " --> pdb=" O GLY E1356 " (cutoff:3.500A) Processing helix chain 'E' and resid 1373 through 1378 removed outlier: 3.825A pdb=" N LEU E1377 " --> pdb=" O VAL E1373 " (cutoff:3.500A) Processing helix chain 'E' and resid 1378 through 1386 Processing helix chain 'E' and resid 1394 through 1404 Processing helix chain 'E' and resid 1407 through 1418 Processing helix chain 'E' and resid 1421 through 1432 removed outlier: 3.683A pdb=" N PHE E1432 " --> pdb=" O LEU E1428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 107 Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 305 removed outlier: 6.995A pdb=" N HIS A 304 " --> pdb=" O VAL A 498 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N SER A 500 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 347 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU A 439 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE A 472 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 441 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU A 474 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 443 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS A 374 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ILE A 442 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 376 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR A 420 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 522 removed outlier: 6.794A pdb=" N ILE A 510 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 630 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 742 through 744 Processing sheet with id=AA5, first strand: chain 'A' and resid 835 through 838 removed outlier: 3.643A pdb=" N GLN A1084 " --> pdb=" O LYS A 835 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR A 837 " --> pdb=" O SER A1082 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N SER A1082 " --> pdb=" O THR A 837 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 967 through 976 removed outlier: 6.084A pdb=" N ASP A 969 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR A 935 " --> pdb=" O ASP A 969 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL A 928 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL A 922 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 930 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 934 " --> pdb=" O LEU A 916 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU A 916 " --> pdb=" O PHE A 934 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 903 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU A 904 " --> pdb=" O THR A 984 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG A 908 " --> pdb=" O ILE A 980 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE A 980 " --> pdb=" O ARG A 908 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 5 through 11 removed outlier: 6.934A pdb=" N TRP C 390 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN C 10 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 388 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER C 378 " --> pdb=" O PHE C 362 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N PHE C 362 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N CYS C 380 " --> pdb=" O VAL C 360 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL C 360 " --> pdb=" O CYS C 380 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 382 " --> pdb=" O PHE C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 24 removed outlier: 4.232A pdb=" N SER C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 65 through 73 removed outlier: 3.724A pdb=" N HIS C 67 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS C 82 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE C 95 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 124 through 130 removed outlier: 4.007A pdb=" N ALA C 126 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS C 139 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR C 150 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR C 178 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 152 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 189 through 194 removed outlier: 3.624A pdb=" N SER C 191 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 209 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN C 222 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 211 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 236 through 241 removed outlier: 6.670A pdb=" N ALA C 251 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C 239 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA C 249 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE C 241 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU C 247 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE C 260 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER C 273 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU C 262 " --> pdb=" O ILE C 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 294 through 299 removed outlier: 6.687A pdb=" N ALA C 309 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU C 297 " --> pdb=" O CYS C 307 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS C 307 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE C 299 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR C 305 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS C 314 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 315 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR C 328 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE C 317 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 324 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 11 removed outlier: 3.584A pdb=" N ALA D 9 " --> pdb=" O TRP D 390 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP D 359 " --> pdb=" O VAL D 382 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 19 through 24 removed outlier: 4.060A pdb=" N SER D 21 " --> pdb=" O CYS D 32 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 33 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR D 37 " --> pdb=" O SER D 33 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 72 removed outlier: 3.820A pdb=" N HIS D 67 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 124 through 130 removed outlier: 4.013A pdb=" N ALA D 126 " --> pdb=" O THR D 144 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS D 139 " --> pdb=" O PHE D 155 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 141 " --> pdb=" O TRP D 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 124 through 130 removed outlier: 4.013A pdb=" N ALA D 126 " --> pdb=" O THR D 144 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS D 139 " --> pdb=" O PHE D 155 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 141 " --> pdb=" O TRP D 153 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 177 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 189 through 194 removed outlier: 4.356A pdb=" N THR D 208 " --> pdb=" O PHE D 204 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL D 209 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASN D 222 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE D 211 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.841A pdb=" N SER D 238 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE D 260 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY D 272 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU D 264 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG D 270 " --> pdb=" O GLU D 264 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 294 through 299 removed outlier: 3.587A pdb=" N GLY D 310 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU D 315 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR D 328 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE D 317 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 324 " --> pdb=" O ASP D 319 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.79 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6802 1.34 - 1.46: 4079 1.46 - 1.57: 10317 1.57 - 1.69: 7 1.69 - 1.81: 144 Bond restraints: 21349 Sorted by residual: bond pdb=" CG LEU E 436 " pdb=" CD2 LEU E 436 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" CG MET A 875 " pdb=" SD MET A 875 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" N VAL A 456 " pdb=" CA VAL A 456 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.07e+00 bond pdb=" CB THR A 481 " pdb=" CG2 THR A 481 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.33e-01 bond pdb=" CA ASN C 255 " pdb=" CB ASN C 255 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.96e-01 ... (remaining 21344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 28843 2.11 - 4.21: 191 4.21 - 6.32: 22 6.32 - 8.42: 3 8.42 - 10.53: 1 Bond angle restraints: 29060 Sorted by residual: angle pdb=" N PRO A 281 " pdb=" CA PRO A 281 " pdb=" CB PRO A 281 " ideal model delta sigma weight residual 103.00 110.69 -7.69 1.10e+00 8.26e-01 4.88e+01 angle pdb=" C LEU A 874 " pdb=" N MET A 875 " pdb=" CA MET A 875 " ideal model delta sigma weight residual 121.14 114.35 6.79 1.75e+00 3.27e-01 1.50e+01 angle pdb=" CA LEU E 436 " pdb=" CB LEU E 436 " pdb=" CG LEU E 436 " ideal model delta sigma weight residual 116.30 126.83 -10.53 3.50e+00 8.16e-02 9.05e+00 angle pdb=" N ILE A 229 " pdb=" CA ILE A 229 " pdb=" C ILE A 229 " ideal model delta sigma weight residual 107.15 111.64 -4.49 1.53e+00 4.27e-01 8.62e+00 angle pdb=" C TYR E 435 " pdb=" N LEU E 436 " pdb=" CA LEU E 436 " ideal model delta sigma weight residual 120.72 116.29 4.43 1.67e+00 3.59e-01 7.04e+00 ... (remaining 29055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 11450 17.43 - 34.86: 958 34.86 - 52.29: 119 52.29 - 69.73: 20 69.73 - 87.16: 16 Dihedral angle restraints: 12563 sinusoidal: 4358 harmonic: 8205 Sorted by residual: dihedral pdb=" CA GLY D 356 " pdb=" C GLY D 356 " pdb=" N VAL D 357 " pdb=" CA VAL D 357 " ideal model delta harmonic sigma weight residual -180.00 -160.60 -19.40 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ASP E1311 " pdb=" CB ASP E1311 " pdb=" CG ASP E1311 " pdb=" OD1 ASP E1311 " ideal model delta sinusoidal sigma weight residual -30.00 -87.60 57.60 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CG ARG A 676 " pdb=" CD ARG A 676 " pdb=" NE ARG A 676 " pdb=" CZ ARG A 676 " ideal model delta sinusoidal sigma weight residual 90.00 133.91 -43.91 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 12560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2505 0.041 - 0.083: 699 0.083 - 0.124: 196 0.124 - 0.165: 13 0.165 - 0.206: 2 Chirality restraints: 3415 Sorted by residual: chirality pdb=" CA PRO A 281 " pdb=" N PRO A 281 " pdb=" C PRO A 281 " pdb=" CB PRO A 281 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ASN C 255 " pdb=" N ASN C 255 " pdb=" C ASN C 255 " pdb=" CB ASN C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" C1' U B 1 " pdb=" O4' U B 1 " pdb=" C2' U B 1 " pdb=" N1 U B 1 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 3412 not shown) Planarity restraints: 3691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E1189 " 0.026 2.00e-02 2.50e+03 2.39e-02 1.00e+01 pdb=" CG PHE E1189 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE E1189 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE E1189 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E1189 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E1189 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE E1189 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 354 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO D 355 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 355 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 355 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 746 " -0.021 2.00e-02 2.50e+03 1.39e-02 3.88e+00 pdb=" CG TYR E 746 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR E 746 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 746 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 746 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 746 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 746 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 746 " -0.003 2.00e-02 2.50e+03 ... (remaining 3688 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1484 2.74 - 3.28: 19557 3.28 - 3.82: 33364 3.82 - 4.36: 38630 4.36 - 4.90: 69630 Nonbonded interactions: 162665 Sorted by model distance: nonbonded pdb=" OD1 ASP E 635 " pdb=" OH TYR E 651 " model vdw 2.200 3.040 nonbonded pdb=" O LEU E 297 " pdb=" OH TYR E 332 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A1223 " pdb=" OE1 GLU A1226 " model vdw 2.258 3.040 nonbonded pdb=" O TYR E 288 " pdb=" OG1 THR E 292 " model vdw 2.263 3.040 nonbonded pdb=" OG SER D 33 " pdb=" OD1 ASP D 35 " model vdw 2.266 3.040 ... (remaining 162660 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 3 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 25 or (resid 26 through 27 a \ nd (name N or name CA or name C or name O or name CB )) or resid 28 through 43 o \ r (resid 44 and (name N or name CA or name C or name O or name CB )) or resid 50 \ through 73 or (resid 80 and (name N or name CA or name C or name O or name CB ) \ ) or resid 81 through 98 or resid 109 through 119 or (resid 120 through 121 and \ (name N or name CA or name C or name O or name CB )) or resid 122 through 131 or \ (resid 132 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 144 or (resid 145 and (name N or name CA or name C or name O or name C \ B )) or resid 146 through 157 or resid 170 through 195 or (resid 196 through 197 \ and (name N or name CA or name C or name O or name CB )) or resid 198 through 2 \ 11 or (resid 212 and (name N or name CA or name C or name O or name CB )) or res \ id 213 or (resid 214 through 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 219 or (resid 220 and (name N or name CA or name \ C or name O or name CB )) or resid 221 through 225 or (resid 231 through 234 and \ (name N or name CA or name C or name O or name CB )) or resid 235 through 253 o \ r (resid 254 through 255 and (name N or name CA or name C or name O or name CB ) \ ) or resid 256 through 264 or (resid 265 through 267 and (name N or name CA or n \ ame C or name O or name CB )) or resid 268 or (resid 269 and (name N or name CA \ or name C or name O or name CB )) or resid 270 through 276 or resid 287 through \ 291 or (resid 292 and (name N or name CA or name C or name O or name CB )) or re \ sid 293 through 301 or (resid 302 and (name N or name CA or name C or name O or \ name CB )) or resid 303 through 320 or (resid 321 and (name N or name CA or name \ C or name O or name CB )) or resid 322 or (resid 323 through 324 and (name N or \ name CA or name C or name O or name CB )) or resid 325 through 329 or (resid 33 \ 0 through 331 and (name N or name CA or name C or name O or name CB )) or resid \ 332 or resid 343 through 350 or (resid 351 and (name N or name CA or name C or n \ ame O or name CB )) or resid 352 through 367 or resid 377 or (resid 378 and (nam \ e N or name CA or name C or name O or name CB )) or resid 379 through 384 or (re \ sid 385 through 387 and (name N or name CA or name C or name O or name CB )) or \ resid 388 through 391)) selection = (chain 'D' and (resid 3 through 20 or (resid 21 and (name N or name CA or name C \ or name O or name CB )) or resid 22 through 61 or (resid 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 146 or (resid 147 and \ (name N or name CA or name C or name O or name CB )) or resid 148 through 183 or \ (resid 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 217 or (resid 218 and (name N or name CA or name C or name O or name C \ B )) or resid 219 through 266 or (resid 267 and (name N or name CA or name C or \ name O or name CB )) or resid 268 through 326 or (resid 327 and (name N or name \ CA or name C or name O or name CB )) or resid 328 through 346 or (resid 347 and \ (name N or name CA or name C or name O or name CB )) or resid 348 through 363 or \ (resid 364 through 365 and (name N or name CA or name C or name O or name CB )) \ or resid 366 through 386 or (resid 387 and (name N or name CA or name C or name \ O or name CB )) or resid 388 through 391)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.080 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.003 0.035 21349 Z= 0.123 Angle : 0.474 10.528 29060 Z= 0.257 Chirality : 0.040 0.206 3415 Planarity : 0.003 0.052 3691 Dihedral : 13.231 87.157 7203 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.16), residues: 2719 helix: 1.98 (0.14), residues: 1353 sheet: 0.58 (0.25), residues: 433 loop : -1.12 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1116 TYR 0.033 0.001 TYR E 746 PHE 0.055 0.001 PHE E1189 TRP 0.013 0.001 TRP E 550 HIS 0.006 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (21349) covalent geometry : angle 0.47384 / 0.26 (29060) hydrogen bonds : bond 0.15926 / 10.92 ( 1169) hydrogen bonds : angle 5.45224 / 3.92 ( 3438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 794 MET cc_start: 0.7039 (mtp) cc_final: 0.6809 (mtp) REVERT: A 1266 MET cc_start: 0.7478 (mtm) cc_final: 0.7251 (mtt) REVERT: D 50 ASN cc_start: 0.6486 (p0) cc_final: 0.6115 (p0) REVERT: D 325 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7463 (ttp80) REVERT: E 640 TYR cc_start: 0.6826 (m-80) cc_final: 0.6363 (m-80) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.6416 time to fit residues: 118.9759 Evaluate side-chains 120 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 ASN A 387 GLN C 72 GLN D 10 ASN D 50 ASN D 252 HIS E 417 ASN E 428 HIS E 535 HIS E1336 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.148650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111381 restraints weight = 28895.725| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.25 r_work: 0.3039 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 21349 Z= 0.263 Angle : 0.622 7.361 29060 Z= 0.327 Chirality : 0.046 0.199 3415 Planarity : 0.005 0.053 3691 Dihedral : 4.342 30.286 2977 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.20 % Allowed : 6.72 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 2719 helix: 1.61 (0.14), residues: 1364 sheet: 0.52 (0.25), residues: 429 loop : -1.35 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1116 TYR 0.017 0.002 TYR E 947 PHE 0.020 0.002 PHE E 973 TRP 0.017 0.002 TRP E 550 HIS 0.010 0.002 HIS C 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.26 (21349) covalent geometry : angle 0.62207 / 0.33 (29060) hydrogen bonds : bond 0.06448 / 4.35 ( 1169) hydrogen bonds : angle 4.41702 / 3.17 ( 3438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 372 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7198 (mtt) REVERT: A 536 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7279 (t-90) REVERT: C 81 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8542 (pt) REVERT: C 229 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8938 (mtt) REVERT: D 325 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8281 (ttp80) REVERT: E 562 LEU cc_start: 0.5903 (mt) cc_final: 0.5620 (tm) REVERT: E 575 MET cc_start: 0.5384 (tpp) cc_final: 0.4012 (pp-130) outliers start: 24 outliers final: 7 residues processed: 134 average time/residue: 0.6050 time to fit residues: 92.6501 Evaluate side-chains 130 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1244 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 67 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 142 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 ASN D 10 ASN D 252 HIS E 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113790 restraints weight = 28926.065| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.99 r_work: 0.3103 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21349 Z= 0.111 Angle : 0.458 6.224 29060 Z= 0.243 Chirality : 0.040 0.182 3415 Planarity : 0.003 0.048 3691 Dihedral : 3.777 30.396 2977 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.90 % Allowed : 8.93 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.16), residues: 2719 helix: 2.03 (0.14), residues: 1363 sheet: 0.60 (0.24), residues: 439 loop : -1.14 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 140 TYR 0.014 0.001 TYR E 947 PHE 0.011 0.001 PHE C 109 TRP 0.016 0.001 TRP E 550 HIS 0.006 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (21349) covalent geometry : angle 0.45789 / 0.24 (29060) hydrogen bonds : bond 0.04009 / 2.70 ( 1169) hydrogen bonds : angle 3.91758 / 2.80 ( 3438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.815 Fit side-chains REVERT: A 372 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.6994 (mtt) REVERT: A 536 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7397 (t-90) REVERT: A 825 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7541 (ttt) REVERT: A 875 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5754 (pmm) REVERT: C 229 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8884 (mtt) REVERT: D 325 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8222 (ttp80) REVERT: E 319 MET cc_start: 0.4462 (OUTLIER) cc_final: 0.4143 (pmm) REVERT: E 562 LEU cc_start: 0.5839 (mt) cc_final: 0.5538 (tm) REVERT: E 575 MET cc_start: 0.5334 (tpp) cc_final: 0.4157 (pp-130) REVERT: E 640 TYR cc_start: 0.7907 (m-80) cc_final: 0.7650 (m-80) outliers start: 18 outliers final: 6 residues processed: 137 average time/residue: 0.6082 time to fit residues: 95.5368 Evaluate side-chains 132 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1244 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 31 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 192 optimal weight: 30.0000 chunk 110 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 145 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.113189 restraints weight = 28967.495| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.19 r_work: 0.3052 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21349 Z= 0.205 Angle : 0.552 11.157 29060 Z= 0.289 Chirality : 0.043 0.186 3415 Planarity : 0.004 0.051 3691 Dihedral : 4.069 30.194 2977 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.30 % Allowed : 10.34 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2719 helix: 1.88 (0.14), residues: 1359 sheet: 0.51 (0.24), residues: 434 loop : -1.24 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1116 TYR 0.016 0.001 TYR E 947 PHE 0.017 0.002 PHE E 973 TRP 0.014 0.002 TRP E 550 HIS 0.009 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.20 (21349) covalent geometry : angle 0.55210 / 0.29 (29060) hydrogen bonds : bond 0.05400 / 3.64 ( 1169) hydrogen bonds : angle 4.06934 / 2.91 ( 3438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.916 Fit side-chains REVERT: A 372 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7076 (mtt) REVERT: A 536 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7411 (t-90) REVERT: A 875 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5608 (pmm) REVERT: C 81 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8508 (pt) REVERT: C 229 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8920 (mtt) REVERT: D 325 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8226 (ttp80) REVERT: E 319 MET cc_start: 0.4312 (OUTLIER) cc_final: 0.3824 (tpp) REVERT: E 562 LEU cc_start: 0.5832 (mt) cc_final: 0.5493 (tm) REVERT: E 1189 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8143 (t80) outliers start: 26 outliers final: 13 residues processed: 137 average time/residue: 0.6529 time to fit residues: 102.6888 Evaluate side-chains 137 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1189 PHE Chi-restraints excluded: chain E residue 1244 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 114 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 212 optimal weight: 0.8980 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 ASN D 252 HIS E 984 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112170 restraints weight = 28799.662| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.18 r_work: 0.3065 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21349 Z= 0.160 Angle : 0.509 7.446 29060 Z= 0.268 Chirality : 0.041 0.183 3415 Planarity : 0.004 0.051 3691 Dihedral : 3.965 29.959 2977 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.51 % Allowed : 11.04 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.16), residues: 2719 helix: 2.00 (0.14), residues: 1352 sheet: 0.52 (0.24), residues: 436 loop : -1.19 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 140 TYR 0.016 0.001 TYR E 947 PHE 0.015 0.001 PHE E 973 TRP 0.012 0.001 TRP C 129 HIS 0.011 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (21349) covalent geometry : angle 0.50917 / 0.27 (29060) hydrogen bonds : bond 0.04810 / 3.24 ( 1169) hydrogen bonds : angle 3.94125 / 2.82 ( 3438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.903 Fit side-chains REVERT: A 372 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7026 (mtt) REVERT: A 536 HIS cc_start: 0.8240 (OUTLIER) cc_final: 0.7415 (t-90) REVERT: A 875 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.5728 (pmm) REVERT: C 81 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8496 (pt) REVERT: C 229 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8899 (mtt) REVERT: D 325 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8222 (ttp80) REVERT: E 319 MET cc_start: 0.4305 (OUTLIER) cc_final: 0.4003 (pmm) REVERT: E 562 LEU cc_start: 0.5808 (mt) cc_final: 0.5463 (tm) REVERT: E 575 MET cc_start: 0.5451 (tpp) cc_final: 0.4040 (pp-130) outliers start: 30 outliers final: 16 residues processed: 138 average time/residue: 0.6282 time to fit residues: 99.5571 Evaluate side-chains 137 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1244 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 121 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111312 restraints weight = 28548.271| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.95 r_work: 0.3067 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21349 Z= 0.179 Angle : 0.531 9.619 29060 Z= 0.278 Chirality : 0.042 0.184 3415 Planarity : 0.004 0.051 3691 Dihedral : 4.049 29.700 2977 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.91 % Allowed : 11.29 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 2719 helix: 1.90 (0.14), residues: 1365 sheet: 0.57 (0.25), residues: 427 loop : -1.19 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 140 TYR 0.016 0.001 TYR E 947 PHE 0.016 0.002 PHE E 973 TRP 0.015 0.001 TRP E 550 HIS 0.013 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (21349) covalent geometry : angle 0.53123 / 0.28 (29060) hydrogen bonds : bond 0.05109 / 3.44 ( 1169) hydrogen bonds : angle 3.96884 / 2.83 ( 3438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.849 Fit side-chains REVERT: A 372 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7058 (mtt) REVERT: A 536 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7425 (t-90) REVERT: A 875 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.5698 (pmm) REVERT: C 81 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8494 (pt) REVERT: C 229 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8893 (mtt) REVERT: D 325 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8230 (ttp80) REVERT: E 319 MET cc_start: 0.4207 (OUTLIER) cc_final: 0.3932 (pmm) REVERT: E 562 LEU cc_start: 0.5848 (mt) cc_final: 0.5494 (tm) REVERT: E 575 MET cc_start: 0.5411 (tpp) cc_final: 0.4123 (pp-130) REVERT: E 1189 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.8129 (t80) outliers start: 38 outliers final: 18 residues processed: 144 average time/residue: 0.5984 time to fit residues: 99.7528 Evaluate side-chains 139 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 831 VAL Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1189 PHE Chi-restraints excluded: chain E residue 1244 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 183 optimal weight: 40.0000 chunk 259 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.149678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112315 restraints weight = 28847.102| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.49 r_work: 0.3047 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21349 Z= 0.189 Angle : 0.539 9.684 29060 Z= 0.283 Chirality : 0.042 0.184 3415 Planarity : 0.004 0.051 3691 Dihedral : 4.095 29.313 2977 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.96 % Allowed : 12.09 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 2719 helix: 1.85 (0.14), residues: 1366 sheet: 0.54 (0.24), residues: 427 loop : -1.21 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 140 TYR 0.016 0.001 TYR E 947 PHE 0.017 0.002 PHE E 973 TRP 0.013 0.001 TRP E 550 HIS 0.015 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (21349) covalent geometry : angle 0.53949 / 0.28 (29060) hydrogen bonds : bond 0.05218 / 3.52 ( 1169) hydrogen bonds : angle 3.98102 / 2.84 ( 3438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.846 Fit side-chains REVERT: A 372 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7046 (mtt) REVERT: A 536 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7355 (t-90) REVERT: A 875 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.5670 (pmm) REVERT: C 81 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8511 (pt) REVERT: C 229 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8906 (mtt) REVERT: D 325 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8243 (ttp80) REVERT: E 319 MET cc_start: 0.4235 (OUTLIER) cc_final: 0.3773 (tpp) REVERT: E 562 LEU cc_start: 0.5958 (mt) cc_final: 0.5558 (tm) REVERT: E 1189 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8202 (t80) outliers start: 39 outliers final: 20 residues processed: 145 average time/residue: 0.5695 time to fit residues: 95.7065 Evaluate side-chains 142 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 831 VAL Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1189 PHE Chi-restraints excluded: chain E residue 1244 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 ASN D 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113213 restraints weight = 28612.979| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.26 r_work: 0.3065 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21349 Z= 0.153 Angle : 0.508 12.995 29060 Z= 0.266 Chirality : 0.041 0.180 3415 Planarity : 0.004 0.051 3691 Dihedral : 3.951 29.110 2977 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.91 % Allowed : 12.44 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.16), residues: 2719 helix: 1.99 (0.14), residues: 1365 sheet: 0.58 (0.24), residues: 427 loop : -1.15 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 140 TYR 0.016 0.001 TYR E 947 PHE 0.014 0.001 PHE E 973 TRP 0.014 0.001 TRP E 550 HIS 0.014 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (21349) covalent geometry : angle 0.50765 / 0.27 (29060) hydrogen bonds : bond 0.04628 / 3.11 ( 1169) hydrogen bonds : angle 3.88134 / 2.77 ( 3438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.767 Fit side-chains REVERT: A 372 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7044 (mtt) REVERT: A 536 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7420 (t-90) REVERT: A 875 MET cc_start: 0.5960 (OUTLIER) cc_final: 0.5646 (pmm) REVERT: A 876 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6057 (mm) REVERT: C 81 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8487 (pt) REVERT: C 229 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8908 (mtt) REVERT: D 325 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8242 (ttp80) REVERT: E 319 MET cc_start: 0.4317 (OUTLIER) cc_final: 0.3995 (pmm) REVERT: E 562 LEU cc_start: 0.5960 (mt) cc_final: 0.5556 (tm) REVERT: E 575 MET cc_start: 0.5560 (tpp) cc_final: 0.4220 (pp-130) REVERT: E 1189 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8155 (t80) outliers start: 38 outliers final: 21 residues processed: 145 average time/residue: 0.5561 time to fit residues: 93.1720 Evaluate side-chains 145 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 831 VAL Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1189 PHE Chi-restraints excluded: chain E residue 1244 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 53 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.113480 restraints weight = 28585.864| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.29 r_work: 0.3065 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21349 Z= 0.150 Angle : 0.507 13.650 29060 Z= 0.264 Chirality : 0.041 0.177 3415 Planarity : 0.004 0.051 3691 Dihedral : 3.936 29.115 2977 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.76 % Allowed : 12.84 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.16), residues: 2719 helix: 2.05 (0.14), residues: 1358 sheet: 0.59 (0.25), residues: 427 loop : -1.15 (0.18), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 140 TYR 0.016 0.001 TYR E 947 PHE 0.014 0.001 PHE E 973 TRP 0.014 0.001 TRP E 550 HIS 0.014 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (21349) covalent geometry : angle 0.50711 / 0.26 (29060) hydrogen bonds : bond 0.04614 / 3.11 ( 1169) hydrogen bonds : angle 3.85294 / 2.74 ( 3438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.897 Fit side-chains REVERT: A 372 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7049 (mtt) REVERT: A 536 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7499 (t-90) REVERT: A 875 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5627 (pmm) REVERT: A 876 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.6009 (mm) REVERT: C 81 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8486 (pt) REVERT: C 229 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8906 (mtt) REVERT: D 174 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8535 (pp20) REVERT: D 325 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8238 (ttp80) REVERT: E 319 MET cc_start: 0.4319 (OUTLIER) cc_final: 0.4001 (pmm) REVERT: E 575 MET cc_start: 0.5399 (tpp) cc_final: 0.4167 (pp-130) REVERT: E 1189 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8159 (t80) outliers start: 35 outliers final: 22 residues processed: 136 average time/residue: 0.6036 time to fit residues: 94.7046 Evaluate side-chains 142 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 435 TYR Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 831 VAL Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1189 PHE Chi-restraints excluded: chain E residue 1244 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 147 optimal weight: 10.0000 chunk 179 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 192 optimal weight: 0.0980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.151132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114073 restraints weight = 28874.625| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.34 r_work: 0.3076 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21349 Z= 0.136 Angle : 0.495 14.047 29060 Z= 0.258 Chirality : 0.041 0.173 3415 Planarity : 0.004 0.051 3691 Dihedral : 3.862 29.036 2977 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.61 % Allowed : 13.10 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.16), residues: 2719 helix: 2.11 (0.14), residues: 1360 sheet: 0.62 (0.25), residues: 427 loop : -1.13 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 140 TYR 0.015 0.001 TYR E 947 PHE 0.012 0.001 PHE E 973 TRP 0.013 0.001 TRP E 550 HIS 0.015 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (21349) covalent geometry : angle 0.49494 / 0.26 (29060) hydrogen bonds : bond 0.04331 / 2.91 ( 1169) hydrogen bonds : angle 3.80078 / 2.71 ( 3438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.845 Fit side-chains REVERT: A 372 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7030 (mtt) REVERT: A 536 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7440 (t-90) REVERT: A 875 MET cc_start: 0.5987 (OUTLIER) cc_final: 0.5676 (pmm) REVERT: A 876 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6049 (mm) REVERT: C 229 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8904 (mtt) REVERT: D 174 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8499 (pp20) REVERT: D 325 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8237 (ttp80) REVERT: E 319 MET cc_start: 0.4276 (OUTLIER) cc_final: 0.3958 (pmm) REVERT: E 575 MET cc_start: 0.5500 (tpp) cc_final: 0.4225 (pp-130) REVERT: E 1189 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8136 (t80) outliers start: 32 outliers final: 18 residues processed: 135 average time/residue: 0.6073 time to fit residues: 94.4838 Evaluate side-chains 139 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 435 TYR Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1189 PHE Chi-restraints excluded: chain E residue 1244 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 163 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 68 optimal weight: 0.0270 chunk 20 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 10 ASN D 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.152881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115133 restraints weight = 28740.511| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.29 r_work: 0.3110 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21349 Z= 0.097 Angle : 0.454 13.903 29060 Z= 0.235 Chirality : 0.039 0.165 3415 Planarity : 0.003 0.050 3691 Dihedral : 3.620 28.954 2977 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.35 % Allowed : 13.35 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.16), residues: 2719 helix: 2.30 (0.14), residues: 1366 sheet: 0.80 (0.25), residues: 424 loop : -1.05 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 140 TYR 0.014 0.001 TYR E 947 PHE 0.011 0.001 PHE A 333 TRP 0.014 0.001 TRP E 550 HIS 0.015 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (21349) covalent geometry : angle 0.45393 / 0.24 (29060) hydrogen bonds : bond 0.03461 / 2.32 ( 1169) hydrogen bonds : angle 3.61111 / 2.57 ( 3438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7183.15 seconds wall clock time: 122 minutes 50.82 seconds (7370.82 seconds total)