Starting phenix.real_space_refine on Wed Jun 18 09:14:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9t_18288/06_2025/8q9t_18288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9t_18288/06_2025/8q9t_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_18288/06_2025/8q9t_18288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9t_18288/06_2025/8q9t_18288.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9t_18288/06_2025/8q9t_18288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9t_18288/06_2025/8q9t_18288.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 10, 'ASP:plan': 21, 'ASN:plan1': 12, 'HIS:plan': 4, 'GLU:plan': 30, 'ARG:plan': 16} 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: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLN:plan1': 12, 'ARG:plan': 6, 'ASN:plan1': 11, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 29, 'ASP:plan': 15} 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 dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 8 Time building chain proxies: 11.93, per 1000 atoms: 0.57 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: 4.67 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.89 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: 8.89 Time building geometry restraints manager: 5.57 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: 11457 17.43 - 34.86: 961 34.86 - 52.29: 119 52.29 - 69.73: 24 69.73 - 87.16: 16 Dihedral angle restraints: 12577 sinusoidal: 4372 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 12574 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: 1.860 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: 1.020 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 48.730 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 13.304 87.157 7217 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (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 TRP 0.013 0.001 TRP E 550 HIS 0.006 0.001 HIS A 536 PHE 0.055 0.001 PHE E1189 TYR 0.033 0.001 TYR E 746 ARG 0.007 0.000 ARG A1116 Details of bonding type rmsd hydrogen bonds : bond 0.15926 ( 1169) hydrogen bonds : angle 5.45224 ( 3438) covalent geometry : bond 0.00279 (21349) covalent geometry : angle 0.47384 (29060) *********************** 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 : 2.459 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: 1.4847 time to fit residues: 275.6660 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 : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 84 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3800 r_free = 0.3800 target = 0.148563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111247 restraints weight = 28825.294| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.28 r_work: 0.3038 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 21349 Z= 0.267 Angle : 0.626 7.330 29060 Z= 0.330 Chirality : 0.046 0.201 3415 Planarity : 0.005 0.054 3691 Dihedral : 4.943 58.305 2991 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.20 % Allowed : 6.92 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.16), residues: 2719 helix: 1.60 (0.14), residues: 1364 sheet: 0.52 (0.25), residues: 429 loop : -1.32 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 550 HIS 0.010 0.002 HIS C 227 PHE 0.021 0.002 PHE E 973 TYR 0.017 0.002 TYR E 947 ARG 0.012 0.001 ARG A1116 Details of bonding type rmsd hydrogen bonds : bond 0.06474 ( 1169) hydrogen bonds : angle 4.41602 ( 3438) covalent geometry : bond 0.00662 (21349) covalent geometry : angle 0.62646 (29060) *********************** 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 : 2.610 Fit side-chains REVERT: A 372 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7286 (mmt) REVERT: A 536 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7298 (t-90) REVERT: C 81 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8542 (pt) REVERT: C 229 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8952 (mtt) REVERT: D 325 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8276 (ttp80) REVERT: E 562 LEU cc_start: 0.5916 (mt) cc_final: 0.5625 (tm) REVERT: E 575 MET cc_start: 0.5381 (tpp) cc_final: 0.4012 (pp-130) outliers start: 24 outliers final: 7 residues processed: 134 average time/residue: 1.3923 time to fit residues: 213.9111 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 : 2.584 ------------------------------------------------------------------------------- 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 56 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 265 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3840 r_free = 0.3840 target = 0.151965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116307 restraints weight = 28609.488| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.62 r_work: 0.3083 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0917 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= 0.112 Angle : 0.465 6.779 29060 Z= 0.246 Chirality : 0.040 0.183 3415 Planarity : 0.003 0.049 3691 Dihedral : 4.471 58.259 2991 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.95 % Allowed : 9.03 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.16), residues: 2719 helix: 2.01 (0.14), residues: 1362 sheet: 0.58 (0.24), residues: 439 loop : -1.15 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 550 HIS 0.007 0.001 HIS D 252 PHE 0.012 0.001 PHE E 973 TYR 0.014 0.001 TYR E 947 ARG 0.007 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 1169) hydrogen bonds : angle 3.96684 ( 3438) covalent geometry : bond 0.00252 (21349) covalent geometry : angle 0.46465 (29060) *********************** 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 142 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 2.436 Fit side-chains REVERT: A 372 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7010 (mtt) REVERT: A 536 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7297 (t-90) REVERT: A 825 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7551 (ttt) REVERT: A 875 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.5694 (pmm) REVERT: C 229 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8917 (mtt) REVERT: D 325 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8206 (ttp80) REVERT: E 319 MET cc_start: 0.4400 (OUTLIER) cc_final: 0.4091 (pmm) REVERT: E 562 LEU cc_start: 0.5826 (mt) cc_final: 0.5523 (tm) REVERT: E 575 MET cc_start: 0.5306 (tpp) cc_final: 0.4068 (pp-130) REVERT: E 640 TYR cc_start: 0.7903 (m-80) cc_final: 0.7632 (m-80) outliers start: 19 outliers final: 7 residues processed: 134 average time/residue: 1.3919 time to fit residues: 213.9025 Evaluate side-chains 133 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 2.608 ------------------------------------------------------------------------------- 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 480 ASN 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 21 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 159 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 189 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 116 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.151719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115133 restraints weight = 28979.254| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.25 r_work: 0.3079 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0993 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= 0.125 Angle : 0.470 9.628 29060 Z= 0.247 Chirality : 0.040 0.170 3415 Planarity : 0.003 0.048 3691 Dihedral : 4.413 58.201 2991 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.10 % Allowed : 9.98 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.16), residues: 2719 helix: 2.16 (0.14), residues: 1356 sheet: 0.61 (0.24), residues: 439 loop : -1.11 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 129 HIS 0.008 0.001 HIS D 252 PHE 0.012 0.001 PHE A 333 TYR 0.015 0.001 TYR E 947 ARG 0.008 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 1169) hydrogen bonds : angle 3.84552 ( 3438) covalent geometry : bond 0.00293 (21349) covalent geometry : angle 0.46996 (29060) *********************** 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 145 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 2.476 Fit side-chains REVERT: A 372 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7036 (mtt) REVERT: A 536 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7389 (t-90) REVERT: A 825 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7696 (ttt) REVERT: A 875 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5694 (pmm) REVERT: C 81 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8477 (pt) REVERT: D 110 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: D 325 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8235 (ttp80) REVERT: E 319 MET cc_start: 0.4343 (OUTLIER) cc_final: 0.4050 (pmm) REVERT: E 562 LEU cc_start: 0.5789 (mt) cc_final: 0.5473 (tm) REVERT: E 640 TYR cc_start: 0.7896 (m-80) cc_final: 0.7634 (m-80) outliers start: 22 outliers final: 8 residues processed: 135 average time/residue: 1.3915 time to fit residues: 215.8336 Evaluate side-chains 132 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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 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 D residue 110 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 1244 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 185 optimal weight: 40.0000 chunk 218 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 246 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.150006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.111929 restraints weight = 28879.948| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.30 r_work: 0.3053 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1072 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 : 0.524 7.494 29060 Z= 0.275 Chirality : 0.042 0.179 3415 Planarity : 0.004 0.050 3691 Dihedral : 4.617 58.271 2991 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.66 % Allowed : 10.49 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2719 helix: 2.04 (0.14), residues: 1352 sheet: 0.52 (0.24), residues: 436 loop : -1.18 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 153 HIS 0.011 0.001 HIS D 252 PHE 0.016 0.002 PHE E 973 TYR 0.016 0.001 TYR E 947 ARG 0.009 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.05094 ( 1169) hydrogen bonds : angle 3.96105 ( 3438) covalent geometry : bond 0.00438 (21349) covalent geometry : angle 0.52444 (29060) *********************** 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 153 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 2.272 Fit side-chains REVERT: A 372 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7203 (mtt) REVERT: A 536 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7316 (t-90) REVERT: A 875 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5600 (pmm) REVERT: C 81 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8473 (pt) REVERT: C 229 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8938 (mtt) REVERT: D 325 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8168 (ttp80) REVERT: E 319 MET cc_start: 0.4333 (OUTLIER) cc_final: 0.3854 (tpp) REVERT: E 575 MET cc_start: 0.5482 (tpp) cc_final: 0.4063 (pp-130) REVERT: E 1189 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8076 (t80) outliers start: 33 outliers final: 14 residues processed: 142 average time/residue: 1.2285 time to fit residues: 201.6014 Evaluate side-chains 138 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 2.245 ------------------------------------------------------------------------------- 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 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 99 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 359 ASP 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 1189 PHE 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 34 optimal weight: 1.9990 chunk 245 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 chunk 227 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3837 r_free = 0.3837 target = 0.151752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114320 restraints weight = 28693.846| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.36 r_work: 0.3078 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21349 Z= 0.122 Angle : 0.467 9.851 29060 Z= 0.246 Chirality : 0.040 0.170 3415 Planarity : 0.003 0.049 3691 Dihedral : 4.413 58.223 2991 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.25 % Allowed : 11.74 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.16), residues: 2719 helix: 2.17 (0.14), residues: 1363 sheet: 0.68 (0.25), residues: 427 loop : -1.09 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 129 HIS 0.012 0.001 HIS D 252 PHE 0.012 0.001 PHE E 973 TYR 0.015 0.001 TYR E 947 ARG 0.008 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 1169) hydrogen bonds : angle 3.77409 ( 3438) covalent geometry : bond 0.00288 (21349) covalent geometry : angle 0.46730 (29060) *********************** 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 143 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 2.245 Fit side-chains REVERT: A 372 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7048 (mtt) REVERT: A 536 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7410 (t-90) REVERT: A 825 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7801 (ttt) REVERT: A 875 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.5692 (pmm) REVERT: C 229 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8906 (mtt) REVERT: D 325 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8226 (ttp80) REVERT: E 319 MET cc_start: 0.4247 (OUTLIER) cc_final: 0.3969 (pmm) REVERT: E 575 MET cc_start: 0.5453 (tpp) cc_final: 0.4210 (pp-130) REVERT: E 1189 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8114 (t80) outliers start: 25 outliers final: 10 residues processed: 135 average time/residue: 1.3189 time to fit residues: 205.2670 Evaluate side-chains 132 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 2.308 ------------------------------------------------------------------------------- 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 480 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 621 LEU 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 229 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 227 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 263 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114425 restraints weight = 28548.318| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.24 r_work: 0.3072 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21349 Z= 0.161 Angle : 0.504 8.919 29060 Z= 0.265 Chirality : 0.041 0.172 3415 Planarity : 0.004 0.051 3691 Dihedral : 4.541 58.251 2991 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.56 % Allowed : 11.79 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.16), residues: 2719 helix: 2.09 (0.14), residues: 1359 sheet: 0.68 (0.25), residues: 425 loop : -1.13 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 153 HIS 0.014 0.001 HIS D 252 PHE 0.015 0.001 PHE E 973 TYR 0.016 0.001 TYR E 947 ARG 0.007 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 1169) hydrogen bonds : angle 3.86118 ( 3438) covalent geometry : bond 0.00391 (21349) covalent geometry : angle 0.50427 (29060) *********************** 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 148 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 2.495 Fit side-chains REVERT: A 372 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7069 (mtt) REVERT: A 536 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7471 (t-90) REVERT: A 875 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5724 (pmm) REVERT: A 972 MET cc_start: 0.3447 (OUTLIER) cc_final: 0.2619 (mmp) REVERT: C 81 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8481 (pt) REVERT: C 229 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8907 (mtt) REVERT: D 325 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8215 (ttp80) REVERT: E 319 MET cc_start: 0.4319 (OUTLIER) cc_final: 0.4003 (pmm) REVERT: E 575 MET cc_start: 0.5382 (tpp) cc_final: 0.4221 (pp-130) REVERT: E 1189 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8110 (t80) outliers start: 31 outliers final: 15 residues processed: 136 average time/residue: 1.3006 time to fit residues: 204.9946 Evaluate side-chains 138 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 2.456 ------------------------------------------------------------------------------- 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 621 LEU 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 972 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 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 154 optimal weight: 3.9990 chunk 273 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 179 optimal weight: 30.0000 chunk 97 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 256 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.149992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111395 restraints weight = 28752.362| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.10 r_work: 0.3058 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1195 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 : 0.530 14.206 29060 Z= 0.277 Chirality : 0.042 0.179 3415 Planarity : 0.004 0.051 3691 Dihedral : 4.635 58.296 2991 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.66 % Allowed : 11.99 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2719 helix: 2.00 (0.14), residues: 1359 sheet: 0.62 (0.25), residues: 427 loop : -1.16 (0.18), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 129 HIS 0.014 0.001 HIS D 252 PHE 0.016 0.001 PHE E 973 TYR 0.016 0.001 TYR E 947 ARG 0.009 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 1169) hydrogen bonds : angle 3.92331 ( 3438) covalent geometry : bond 0.00438 (21349) covalent geometry : angle 0.53014 (29060) *********************** 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 148 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 2.235 Fit side-chains REVERT: A 372 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7031 (mtt) REVERT: A 536 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7472 (t-90) REVERT: A 875 MET cc_start: 0.5939 (OUTLIER) cc_final: 0.5698 (pmm) REVERT: A 972 MET cc_start: 0.3496 (OUTLIER) cc_final: 0.2584 (mmp) REVERT: C 81 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8523 (pt) REVERT: C 229 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8920 (mtt) REVERT: D 325 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8240 (ttp80) REVERT: E 319 MET cc_start: 0.4244 (OUTLIER) cc_final: 0.3947 (pmm) REVERT: E 1189 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8120 (t80) REVERT: E 1296 ASP cc_start: 0.7999 (t0) cc_final: 0.7792 (p0) outliers start: 33 outliers final: 15 residues processed: 137 average time/residue: 1.2736 time to fit residues: 201.7367 Evaluate side-chains 136 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 2.545 ------------------------------------------------------------------------------- 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 972 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 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 120 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 30.0000 chunk 70 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 277 optimal weight: 0.6980 chunk 224 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113696 restraints weight = 28793.170| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.24 r_work: 0.3085 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1221 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= 0.110 Angle : 0.465 11.619 29060 Z= 0.242 Chirality : 0.040 0.171 3415 Planarity : 0.003 0.050 3691 Dihedral : 4.372 58.216 2991 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.40 % Allowed : 12.34 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.16), residues: 2719 helix: 2.24 (0.14), residues: 1365 sheet: 0.81 (0.25), residues: 424 loop : -1.06 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 129 HIS 0.015 0.001 HIS D 252 PHE 0.011 0.001 PHE E 973 TYR 0.015 0.001 TYR E 947 ARG 0.010 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 1169) hydrogen bonds : angle 3.70028 ( 3438) covalent geometry : bond 0.00253 (21349) covalent geometry : angle 0.46467 (29060) *********************** 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 144 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 2.552 Fit side-chains REVERT: A 372 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7008 (mtt) REVERT: A 536 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7462 (t-90) REVERT: A 825 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7617 (ttt) REVERT: A 875 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5625 (pmm) REVERT: A 876 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6048 (mm) REVERT: C 81 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8448 (pt) REVERT: C 229 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8895 (mtt) REVERT: D 325 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8218 (ttp80) REVERT: E 319 MET cc_start: 0.4302 (OUTLIER) cc_final: 0.4022 (pmm) REVERT: E 575 MET cc_start: 0.5291 (tpp) cc_final: 0.4012 (pp-130) REVERT: E 1189 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8122 (t80) outliers start: 28 outliers final: 12 residues processed: 135 average time/residue: 1.3079 time to fit residues: 203.4199 Evaluate side-chains 133 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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 536 HIS Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 849 LEU 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 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 998 ASP Chi-restraints excluded: chain E residue 1189 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 121 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 chunk 266 optimal weight: 6.9990 chunk 245 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.151398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113696 restraints weight = 28752.553| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.30 r_work: 0.3070 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21349 Z= 0.137 Angle : 0.495 14.729 29060 Z= 0.256 Chirality : 0.041 0.164 3415 Planarity : 0.003 0.051 3691 Dihedral : 4.445 58.211 2991 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.25 % Allowed : 12.59 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.16), residues: 2719 helix: 2.20 (0.14), residues: 1362 sheet: 0.77 (0.25), residues: 419 loop : -1.08 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 129 HIS 0.014 0.001 HIS D 252 PHE 0.012 0.001 PHE E 973 TYR 0.016 0.001 TYR E 947 ARG 0.010 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 1169) hydrogen bonds : angle 3.76356 ( 3438) covalent geometry : bond 0.00329 (21349) covalent geometry : angle 0.49496 (29060) ********************** 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 138 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 2.575 Fit side-chains REVERT: A 372 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7050 (mtt) REVERT: A 536 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7504 (t-90) REVERT: A 875 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5643 (pmm) REVERT: A 876 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.6031 (mm) REVERT: C 81 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8466 (pt) REVERT: C 229 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8903 (mtt) REVERT: D 325 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8203 (ttp80) REVERT: E 319 MET cc_start: 0.4302 (OUTLIER) cc_final: 0.4008 (pmm) REVERT: E 575 MET cc_start: 0.5230 (tpp) cc_final: 0.4032 (pp-130) REVERT: E 1189 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8132 (t80) outliers start: 25 outliers final: 16 residues processed: 131 average time/residue: 1.2923 time to fit residues: 196.0490 Evaluate side-chains 136 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 2.241 ------------------------------------------------------------------------------- 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 621 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 849 LEU 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 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 862 VAL Chi-restraints excluded: chain E residue 998 ASP Chi-restraints excluded: chain E residue 1189 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 171 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110704 restraints weight = 28806.953| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.23 r_work: 0.3048 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21349 Z= 0.217 Angle : 0.570 12.419 29060 Z= 0.296 Chirality : 0.044 0.187 3415 Planarity : 0.004 0.052 3691 Dihedral : 4.755 58.316 2991 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.35 % Allowed : 12.59 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2719 helix: 1.90 (0.14), residues: 1366 sheet: 0.59 (0.25), residues: 427 loop : -1.19 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 129 HIS 0.013 0.001 HIS D 252 PHE 0.018 0.002 PHE E 973 TYR 0.016 0.001 TYR E 947 ARG 0.009 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.05560 ( 1169) hydrogen bonds : angle 3.98872 ( 3438) covalent geometry : bond 0.00536 (21349) covalent geometry : angle 0.56978 (29060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14942.52 seconds wall clock time: 255 minutes 7.71 seconds (15307.71 seconds total)