Starting phenix.real_space_refine on Sun Aug 24 10:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e56_27904/08_2025/8e56_27904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e56_27904/08_2025/8e56_27904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e56_27904/08_2025/8e56_27904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e56_27904/08_2025/8e56_27904.map" model { file = "/net/cci-nas-00/data/ceres_data/8e56_27904/08_2025/8e56_27904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e56_27904/08_2025/8e56_27904.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians I 2 10.91 5 Ca 2 9.91 5 P 1 5.49 5 S 109 5.16 5 C 11982 2.51 5 N 2981 2.21 5 O 3384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18461 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8919 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 1068} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {' CA': 1, '3PE': 1, 'BBI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {' CA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.99, per 1000 atoms: 0.27 Number of scatterers: 18461 At special positions: 0 Unit cell: (144.82, 138.136, 158.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) I 2 52.95 Ca 2 19.99 S 109 16.00 P 1 15.00 O 3384 8.00 N 2981 7.00 C 11982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.04 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.03 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.04 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.03 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 1 " - " ASN F 350 " " NAG C 1 " - " ASN F 615 " " NAG D 1 " - " ASN F 898 " " NAG F1202 " - " ASN F 326 " " NAG F1203 " - " ASN F 891 " " NAG F1204 " - " ASN F 92 " " NAG F1205 " - " ASN F 606 " " NAG F1206 " - " ASN F 784 " " NAG F1207 " - " ASN F1001 " " NAG F1208 " - " ASN F 988 " " NAG H 1 " - " ASN F 827 " " NAG I 1 " - " ASN F 186 " " NAG J 1 " - " ASN F 470 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 767.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 16 sheets defined 57.4% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 46 through 51 removed outlier: 4.156A pdb=" N TRP A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 51' Processing helix chain 'A' and resid 52 through 71 removed outlier: 3.990A pdb=" N ILE A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 108 removed outlier: 3.587A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 141 removed outlier: 3.908A pdb=" N ASP A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 172 removed outlier: 4.040A pdb=" N LEU A 164 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 165 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.561A pdb=" N SER A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 196 through 219 removed outlier: 3.704A pdb=" N LYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 293 through 306 Processing helix chain 'A' and resid 309 through 322 removed outlier: 4.319A pdb=" N TYR A 313 " --> pdb=" O TRP A 309 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 346 Processing helix chain 'A' and resid 434 through 451 removed outlier: 3.703A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 487 removed outlier: 3.840A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 494 removed outlier: 3.633A pdb=" N TYR A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 492 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER A 494 " --> pdb=" O TYR A 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 494' Processing helix chain 'A' and resid 497 through 515 removed outlier: 4.124A pdb=" N CYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.804A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 4.088A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 4.044A pdb=" N LEU A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 582 removed outlier: 3.957A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.632A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 636 removed outlier: 4.283A pdb=" N LEU A 636 " --> pdb=" O TYR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 670 removed outlier: 3.844A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 818 Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.900A pdb=" N VAL A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 848 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 850 " --> pdb=" O GLU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.517A pdb=" N ASP A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 882 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 904 removed outlier: 4.018A pdb=" N ARG A 900 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 902 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 903 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Proline residue: A 904 - end of helix Processing helix chain 'A' and resid 905 through 911 removed outlier: 4.140A pdb=" N ASN A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 910 " --> pdb=" O ARG A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 928 Processing helix chain 'A' and resid 931 through 951 Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1015 through 1025 removed outlier: 3.613A pdb=" N ASP A1025 " --> pdb=" O TYR A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1040 No H-bonds generated for 'chain 'A' and resid 1038 through 1040' Processing helix chain 'A' and resid 1041 through 1052 removed outlier: 3.636A pdb=" N PHE A1045 " --> pdb=" O MET A1041 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A1048 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A1049 " --> pdb=" O PHE A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1072 removed outlier: 3.662A pdb=" N PHE A1060 " --> pdb=" O MET A1056 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A1071 " --> pdb=" O THR A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1094 Processing helix chain 'A' and resid 1105 through 1117 removed outlier: 4.194A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1137 removed outlier: 3.539A pdb=" N GLU A1121 " --> pdb=" O SER A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1173 Processing helix chain 'A' and resid 1180 through 1206 Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1239 through 1249 removed outlier: 3.747A pdb=" N LEU A1243 " --> pdb=" O VAL A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1266 removed outlier: 3.662A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1289 removed outlier: 3.792A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1322 Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1355 through 1383 removed outlier: 4.251A pdb=" N TYR A1359 " --> pdb=" O ASN A1355 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A1363 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A1372 " --> pdb=" O CYS A1368 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A1373 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1395 through 1410 removed outlier: 4.161A pdb=" N LEU A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1429 removed outlier: 3.630A pdb=" N VAL A1422 " --> pdb=" O LYS A1418 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.672A pdb=" N ALA E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2 through 6' Processing helix chain 'E' and resid 6 through 29 removed outlier: 3.550A pdb=" N ARG E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 129 removed outlier: 3.774A pdb=" N PHE E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 136 through 163 removed outlier: 3.587A pdb=" N ALA E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 204 removed outlier: 3.520A pdb=" N CYS E 184 " --> pdb=" O TRP E 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 53 Processing helix chain 'F' and resid 53 through 65 removed outlier: 3.907A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN F 65 " --> pdb=" O TYR F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 109 removed outlier: 3.588A pdb=" N ARG F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 189 removed outlier: 3.741A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 202 removed outlier: 4.405A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 242 Processing helix chain 'F' and resid 243 through 251 removed outlier: 3.573A pdb=" N ALA F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 283 removed outlier: 3.616A pdb=" N LYS F 272 " --> pdb=" O GLY F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 334 through 347 removed outlier: 3.521A pdb=" N GLY F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 Processing helix chain 'F' and resid 398 through 406 Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'F' and resid 420 through 425 Processing helix chain 'F' and resid 427 through 433 removed outlier: 3.933A pdb=" N VAL F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 440 removed outlier: 3.804A pdb=" N GLY F 440 " --> pdb=" O MET F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 444 Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 542 through 546 removed outlier: 3.740A pdb=" N ARG F 546 " --> pdb=" O LEU F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 566 Processing helix chain 'F' and resid 570 through 582 removed outlier: 3.636A pdb=" N VAL F 574 " --> pdb=" O ASN F 570 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP F 582 " --> pdb=" O ASN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 630 Processing helix chain 'F' and resid 640 through 650 removed outlier: 3.853A pdb=" N GLN F 644 " --> pdb=" O GLU F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 654 No H-bonds generated for 'chain 'F' and resid 652 through 654' Processing helix chain 'F' and resid 655 through 660 Processing helix chain 'F' and resid 678 through 693 Processing helix chain 'F' and resid 701 through 722 Processing helix chain 'F' and resid 748 through 753 removed outlier: 3.779A pdb=" N GLU F 753 " --> pdb=" O LYS F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 763 Processing helix chain 'F' and resid 764 through 773 Processing helix chain 'F' and resid 820 through 830 Processing helix chain 'F' and resid 869 through 873 Processing helix chain 'F' and resid 877 through 881 Processing helix chain 'F' and resid 882 through 892 Processing helix chain 'F' and resid 1045 through 1050 removed outlier: 3.574A pdb=" N MET F1049 " --> pdb=" O ASP F1045 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 955 through 956 Processing sheet with id=AA3, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA4, first strand: chain 'E' and resid 79 through 81 removed outlier: 4.312A pdb=" N ALA E 49 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU E 35 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA E 33 " --> pdb=" O PHE E 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=AA6, first strand: chain 'F' and resid 124 through 125 removed outlier: 6.059A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.913A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.913A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 152 through 154 removed outlier: 3.961A pdb=" N ASP F 154 " --> pdb=" O ARG F 159 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG F 159 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 300 through 302 removed outlier: 6.862A pdb=" N MET F 256 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASP F 255 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET F 361 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU F 257 " --> pdb=" O MET F 361 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE F 363 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU F 259 " --> pdb=" O PHE F 363 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS F 358 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE F 387 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR F 364 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N TYR F 413 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR F 388 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE F 415 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER F 390 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 523 through 525 removed outlier: 6.045A pdb=" N ALA F 516 " --> pdb=" O LEU F 524 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 540 through 541 Processing sheet with id=AB4, first strand: chain 'F' and resid 661 through 664 removed outlier: 4.045A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS F 818 " --> pdb=" O LYS F 733 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG F 735 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY F 816 " --> pdb=" O ARG F 735 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL F 737 " --> pdb=" O VAL F 814 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL F 814 " --> pdb=" O VAL F 737 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 803 through 804 Processing sheet with id=AB6, first strand: chain 'F' and resid 862 through 864 removed outlier: 6.692A pdb=" N LEU F 862 " --> pdb=" O ASP F 857 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASP F 857 " --> pdb=" O LEU F 862 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 896 through 907 removed outlier: 4.178A pdb=" N GLN F 904 " --> pdb=" O CYS F 977 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS F 977 " --> pdb=" O GLN F 904 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL F 906 " --> pdb=" O GLN F 975 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLN F 975 " --> pdb=" O VAL F 906 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) 977 hydrogen bonds defined for protein. 2765 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: 3.54 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 5782 1.36 - 1.52: 6900 1.52 - 1.67: 6028 1.67 - 1.83: 168 1.83 - 1.99: 2 Bond restraints: 18880 Sorted by residual: bond pdb=" CAR BBI A1902 " pdb=" IAS BBI A1902 " ideal model delta sigma weight residual 2.098 1.988 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" CBC BBI A1902 " pdb=" IBD BBI A1902 " ideal model delta sigma weight residual 2.097 1.988 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CAV BBI A1902 " pdb=" CAW BBI A1902 " ideal model delta sigma weight residual 1.510 1.616 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CAW BBI A1902 " pdb=" NAX BBI A1902 " ideal model delta sigma weight residual 1.449 1.534 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CAD BBI A1902 " pdb=" CAE BBI A1902 " ideal model delta sigma weight residual 1.481 1.545 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 18875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 25370 2.66 - 5.32: 196 5.32 - 7.99: 26 7.99 - 10.65: 7 10.65 - 13.31: 2 Bond angle restraints: 25601 Sorted by residual: angle pdb=" CAM BBI A1902 " pdb=" CAN BBI A1902 " pdb=" CAP BBI A1902 " ideal model delta sigma weight residual 118.51 131.82 -13.31 3.00e+00 1.11e-01 1.97e+01 angle pdb=" CAC BBI A1902 " pdb=" CAD BBI A1902 " pdb=" CAE BBI A1902 " ideal model delta sigma weight residual 112.57 124.92 -12.35 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N LEU A 527 " pdb=" CA LEU A 527 " pdb=" C LEU A 527 " ideal model delta sigma weight residual 111.36 107.11 4.25 1.09e+00 8.42e-01 1.52e+01 angle pdb=" N GLN F 806 " pdb=" CA GLN F 806 " pdb=" CB GLN F 806 " ideal model delta sigma weight residual 110.49 116.97 -6.48 1.69e+00 3.50e-01 1.47e+01 angle pdb=" CA TYR F1071 " pdb=" CB TYR F1071 " pdb=" CG TYR F1071 " ideal model delta sigma weight residual 113.90 120.33 -6.43 1.80e+00 3.09e-01 1.27e+01 ... (remaining 25596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 10676 24.88 - 49.75: 720 49.75 - 74.63: 86 74.63 - 99.51: 32 99.51 - 124.38: 25 Dihedral angle restraints: 11539 sinusoidal: 4952 harmonic: 6587 Sorted by residual: dihedral pdb=" CB CYS F 999 " pdb=" SG CYS F 999 " pdb=" SG CYS F1029 " pdb=" CB CYS F1029 " ideal model delta sinusoidal sigma weight residual 93.00 7.99 85.01 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS A 226 " pdb=" SG CYS A 226 " pdb=" SG CYS A 254 " pdb=" CB CYS A 254 " ideal model delta sinusoidal sigma weight residual 93.00 159.30 -66.30 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual -86.00 -143.24 57.24 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 11536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 2922 0.133 - 0.266: 19 0.266 - 0.399: 4 0.399 - 0.532: 1 0.532 - 0.665: 2 Chirality restraints: 2948 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN F 898 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN F 827 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN F 350 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 2945 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 51 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO A 52 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 653 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C LEU A 653 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A 653 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN A 654 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 868 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" CG ASP F 868 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP F 868 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 868 " -0.014 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.75: 2325 2.75 - 3.30: 19005 3.30 - 3.86: 31731 3.86 - 4.41: 39015 4.41 - 4.96: 65275 Nonbonded interactions: 157351 Sorted by model distance: nonbonded pdb=" OD2 ASP F 154 " pdb=" OH TYR F 163 " model vdw 2.201 3.040 nonbonded pdb=" N GLN A 830 " pdb=" OE1 GLN A 830 " model vdw 2.211 3.120 nonbonded pdb=" O GLN F 720 " pdb=" OG SER F 724 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR F 513 " pdb=" OE2 GLU F 567 " model vdw 2.232 3.040 nonbonded pdb=" O TYR A1359 " pdb=" OG SER A1363 " model vdw 2.248 3.040 ... (remaining 157346 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) } 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=0.00 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.060 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.004 0.110 18916 Z= 0.183 Angle : 0.673 17.688 25696 Z= 0.320 Chirality : 0.047 0.665 2948 Planarity : 0.004 0.063 3191 Dihedral : 17.184 124.385 7246 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.06 % Allowed : 11.84 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.18), residues: 2212 helix: 0.81 (0.16), residues: 1110 sheet: -0.22 (0.33), residues: 219 loop : -1.18 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.016 0.001 TYR F 609 PHE 0.021 0.001 PHE F 689 TRP 0.015 0.001 TRP F 187 HIS 0.003 0.001 HIS F 169 Details of bonding type rmsd covalent geometry : bond 0.00379 (18880) covalent geometry : angle 0.62372 (25601) SS BOND : bond 0.00278 ( 13) SS BOND : angle 1.08631 ( 26) hydrogen bonds : bond 0.16877 ( 958) hydrogen bonds : angle 6.23688 ( 2765) link_BETA1-4 : bond 0.00463 ( 10) link_BETA1-4 : angle 2.07148 ( 30) link_NAG-ASN : bond 0.01241 ( 13) link_NAG-ASN : angle 6.27391 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 932 VAL cc_start: 0.7420 (t) cc_final: 0.7158 (p) REVERT: F 1045 ASP cc_start: 0.8530 (t0) cc_final: 0.8189 (t0) outliers start: 21 outliers final: 14 residues processed: 248 average time/residue: 0.4742 time to fit residues: 134.4277 Evaluate side-chains 243 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1382 ASP Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 855 ILE Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 996 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 GLN A1398 HIS F 108 GLN F 697 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124939 restraints weight = 32994.436| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.58 r_work: 0.3128 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18916 Z= 0.149 Angle : 0.648 16.418 25696 Z= 0.314 Chirality : 0.046 0.546 2948 Planarity : 0.005 0.074 3191 Dihedral : 11.806 95.781 3022 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.32 % Allowed : 12.85 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.18), residues: 2212 helix: 1.06 (0.16), residues: 1148 sheet: -0.39 (0.32), residues: 239 loop : -1.21 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 199 TYR 0.021 0.001 TYR F 609 PHE 0.021 0.001 PHE A1060 TRP 0.015 0.001 TRP F 187 HIS 0.003 0.001 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00342 (18880) covalent geometry : angle 0.60376 (25601) SS BOND : bond 0.00329 ( 13) SS BOND : angle 1.10382 ( 26) hydrogen bonds : bond 0.04353 ( 958) hydrogen bonds : angle 4.40752 ( 2765) link_BETA1-4 : bond 0.00524 ( 10) link_BETA1-4 : angle 2.24188 ( 30) link_NAG-ASN : bond 0.01206 ( 13) link_NAG-ASN : angle 5.68998 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 479 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.5186 (tpp) REVERT: A 536 PHE cc_start: 0.7510 (m-10) cc_final: 0.7171 (m-80) REVERT: A 625 MET cc_start: 0.9254 (mmm) cc_final: 0.9029 (mmp) REVERT: A 666 GLU cc_start: 0.5771 (mm-30) cc_final: 0.5188 (mm-30) REVERT: A 932 VAL cc_start: 0.7326 (t) cc_final: 0.7040 (p) REVERT: A 1056 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7666 (mtt) REVERT: A 1098 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6984 (pp) REVERT: A 1124 MET cc_start: 0.7743 (mmp) cc_final: 0.7495 (mmm) REVERT: A 1163 LEU cc_start: 0.8466 (mm) cc_final: 0.8171 (tp) REVERT: A 1198 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7633 (mp) REVERT: F 501 ARG cc_start: 0.8772 (mtm-85) cc_final: 0.8370 (mtm110) REVERT: F 846 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7712 (mmm-85) REVERT: F 1013 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7376 (m110) outliers start: 46 outliers final: 18 residues processed: 256 average time/residue: 0.4667 time to fit residues: 136.7061 Evaluate side-chains 247 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 33 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118491 restraints weight = 37300.922| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.87 r_work: 0.3101 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18916 Z= 0.147 Angle : 0.633 15.909 25696 Z= 0.306 Chirality : 0.046 0.518 2948 Planarity : 0.004 0.071 3191 Dihedral : 9.554 84.131 3001 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.37 % Allowed : 14.16 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.18), residues: 2212 helix: 1.15 (0.16), residues: 1153 sheet: -0.40 (0.31), residues: 239 loop : -1.29 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 199 TYR 0.017 0.001 TYR F 609 PHE 0.041 0.001 PHE A1384 TRP 0.016 0.001 TRP F 187 HIS 0.003 0.001 HIS F 169 Details of bonding type rmsd covalent geometry : bond 0.00342 (18880) covalent geometry : angle 0.58800 (25601) SS BOND : bond 0.00333 ( 13) SS BOND : angle 1.12206 ( 26) hydrogen bonds : bond 0.04105 ( 958) hydrogen bonds : angle 4.27323 ( 2765) link_BETA1-4 : bond 0.00598 ( 10) link_BETA1-4 : angle 2.49734 ( 30) link_NAG-ASN : bond 0.01191 ( 13) link_NAG-ASN : angle 5.61417 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 479 MET cc_start: 0.5676 (OUTLIER) cc_final: 0.5255 (tpp) REVERT: A 536 PHE cc_start: 0.7511 (m-10) cc_final: 0.7094 (m-80) REVERT: A 625 MET cc_start: 0.9240 (mmm) cc_final: 0.8971 (mmp) REVERT: A 649 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8757 (m-40) REVERT: A 666 GLU cc_start: 0.5676 (mm-30) cc_final: 0.5116 (mm-30) REVERT: A 932 VAL cc_start: 0.7501 (t) cc_final: 0.7215 (p) REVERT: A 1098 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7021 (pp) REVERT: A 1124 MET cc_start: 0.7775 (mmp) cc_final: 0.7467 (mmm) REVERT: F 311 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.7428 (tp40) REVERT: F 501 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8437 (mtm110) REVERT: F 674 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7334 (mtpp) REVERT: F 846 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7696 (mmm-85) REVERT: F 1013 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7327 (m110) outliers start: 47 outliers final: 22 residues processed: 251 average time/residue: 0.4406 time to fit residues: 126.9722 Evaluate side-chains 247 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 868 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 464 GLN A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 GLN F 556 GLN F 697 ASN F 872 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.170073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117802 restraints weight = 36356.856| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.60 r_work: 0.3062 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 18916 Z= 0.231 Angle : 0.710 15.277 25696 Z= 0.349 Chirality : 0.050 0.500 2948 Planarity : 0.005 0.070 3191 Dihedral : 8.915 72.623 2999 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.87 % Allowed : 14.72 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.18), residues: 2212 helix: 0.96 (0.15), residues: 1148 sheet: -0.37 (0.32), residues: 240 loop : -1.49 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 199 TYR 0.020 0.002 TYR F1071 PHE 0.022 0.002 PHE A1060 TRP 0.014 0.002 TRP F 187 HIS 0.006 0.001 HIS A1397 Details of bonding type rmsd covalent geometry : bond 0.00563 (18880) covalent geometry : angle 0.66988 (25601) SS BOND : bond 0.00424 ( 13) SS BOND : angle 1.54919 ( 26) hydrogen bonds : bond 0.04632 ( 958) hydrogen bonds : angle 4.44412 ( 2765) link_BETA1-4 : bond 0.00480 ( 10) link_BETA1-4 : angle 2.60474 ( 30) link_NAG-ASN : bond 0.01098 ( 13) link_NAG-ASN : angle 5.55919 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 345 LYS cc_start: 0.5044 (tmmt) cc_final: 0.4559 (pttt) REVERT: A 464 GLN cc_start: 0.8106 (mt0) cc_final: 0.7893 (mt0) REVERT: A 479 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5323 (tpp) REVERT: A 536 PHE cc_start: 0.7679 (m-10) cc_final: 0.7298 (m-80) REVERT: A 625 MET cc_start: 0.9364 (mmm) cc_final: 0.9111 (mmp) REVERT: A 649 ASN cc_start: 0.9026 (OUTLIER) cc_final: 0.8713 (m110) REVERT: A 662 ASP cc_start: 0.6422 (m-30) cc_final: 0.6180 (m-30) REVERT: A 666 GLU cc_start: 0.5821 (mm-30) cc_final: 0.5082 (mt-10) REVERT: A 828 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6809 (ptp-170) REVERT: A 894 LYS cc_start: 0.6570 (OUTLIER) cc_final: 0.5826 (pptt) REVERT: A 932 VAL cc_start: 0.7508 (t) cc_final: 0.7191 (p) REVERT: A 1098 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7061 (pp) REVERT: A 1099 ARG cc_start: 0.6981 (mtp180) cc_final: 0.5535 (ttt-90) REVERT: A 1124 MET cc_start: 0.7998 (mmp) cc_final: 0.7602 (mmm) REVERT: A 1198 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7632 (mp) REVERT: E 110 ILE cc_start: 0.6334 (OUTLIER) cc_final: 0.6116 (mp) REVERT: E 142 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7739 (mpp) REVERT: F 42 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: F 77 GLN cc_start: 0.8044 (tt0) cc_final: 0.7842 (tt0) REVERT: F 311 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.7631 (tp40) REVERT: F 501 ARG cc_start: 0.8799 (mtm-85) cc_final: 0.8503 (mtm110) REVERT: F 646 ARG cc_start: 0.7077 (ptt-90) cc_final: 0.6840 (ptt-90) REVERT: F 674 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7440 (mtpp) REVERT: F 846 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7719 (mmm-85) REVERT: F 1013 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7739 (m110) outliers start: 57 outliers final: 32 residues processed: 264 average time/residue: 0.4657 time to fit residues: 141.7423 Evaluate side-chains 266 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1382 ASP Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 545 LYS Chi-restraints excluded: chain F residue 597 GLN Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 855 ILE Chi-restraints excluded: chain F residue 868 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 165 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 213 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 GLN F 872 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.173463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120793 restraints weight = 29286.752| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.81 r_work: 0.3157 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18916 Z= 0.123 Angle : 0.608 15.190 25696 Z= 0.296 Chirality : 0.045 0.495 2948 Planarity : 0.004 0.070 3191 Dihedral : 8.241 71.003 2999 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.37 % Allowed : 15.78 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.18), residues: 2212 helix: 1.18 (0.15), residues: 1150 sheet: -0.44 (0.31), residues: 241 loop : -1.43 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 199 TYR 0.014 0.001 TYR F1071 PHE 0.018 0.001 PHE E 152 TRP 0.025 0.001 TRP F 187 HIS 0.002 0.001 HIS F 888 Details of bonding type rmsd covalent geometry : bond 0.00275 (18880) covalent geometry : angle 0.56546 (25601) SS BOND : bond 0.00347 ( 13) SS BOND : angle 0.99582 ( 26) hydrogen bonds : bond 0.03623 ( 958) hydrogen bonds : angle 4.19064 ( 2765) link_BETA1-4 : bond 0.00496 ( 10) link_BETA1-4 : angle 2.59361 ( 30) link_NAG-ASN : bond 0.01163 ( 13) link_NAG-ASN : angle 5.30152 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 341 ARG cc_start: 0.7324 (ttp-170) cc_final: 0.7061 (ttp-170) REVERT: A 345 LYS cc_start: 0.4929 (ttmt) cc_final: 0.4466 (pttt) REVERT: A 464 GLN cc_start: 0.8073 (mt0) cc_final: 0.7854 (mt0) REVERT: A 536 PHE cc_start: 0.7522 (m-10) cc_final: 0.7112 (m-80) REVERT: A 625 MET cc_start: 0.9264 (mmm) cc_final: 0.8990 (mmp) REVERT: A 649 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8665 (m110) REVERT: A 659 ILE cc_start: 0.7734 (mt) cc_final: 0.7417 (mp) REVERT: A 662 ASP cc_start: 0.6228 (m-30) cc_final: 0.5959 (m-30) REVERT: A 666 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5540 (mt-10) REVERT: A 828 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.6658 (ptp-170) REVERT: A 894 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.5830 (pptt) REVERT: A 932 VAL cc_start: 0.7547 (t) cc_final: 0.7275 (p) REVERT: A 1098 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6991 (pp) REVERT: A 1099 ARG cc_start: 0.6990 (mtp180) cc_final: 0.5488 (ttt-90) REVERT: A 1124 MET cc_start: 0.7904 (mmp) cc_final: 0.7594 (mmm) REVERT: A 1198 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7587 (mp) REVERT: A 1201 GLU cc_start: 0.7314 (tp30) cc_final: 0.6701 (tt0) REVERT: A 1419 HIS cc_start: 0.2239 (OUTLIER) cc_final: 0.1671 (t-90) REVERT: A 1426 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5456 (tm) REVERT: E 110 ILE cc_start: 0.6224 (OUTLIER) cc_final: 0.6017 (mp) REVERT: F 42 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: F 442 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8073 (tttt) REVERT: F 501 ARG cc_start: 0.8777 (mtm-85) cc_final: 0.8502 (mtm110) outliers start: 47 outliers final: 17 residues processed: 263 average time/residue: 0.4640 time to fit residues: 140.6612 Evaluate side-chains 253 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1419 HIS Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 868 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 GLN F 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.172889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120357 restraints weight = 29980.959| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.79 r_work: 0.3117 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18916 Z= 0.136 Angle : 0.613 14.993 25696 Z= 0.299 Chirality : 0.045 0.484 2948 Planarity : 0.004 0.071 3191 Dihedral : 7.838 71.324 2999 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.42 % Allowed : 16.13 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.18), residues: 2212 helix: 1.25 (0.15), residues: 1148 sheet: -0.40 (0.31), residues: 241 loop : -1.40 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 199 TYR 0.014 0.001 TYR F1071 PHE 0.020 0.001 PHE A1060 TRP 0.016 0.001 TRP F 187 HIS 0.002 0.001 HIS F 169 Details of bonding type rmsd covalent geometry : bond 0.00316 (18880) covalent geometry : angle 0.57211 (25601) SS BOND : bond 0.00327 ( 13) SS BOND : angle 1.36261 ( 26) hydrogen bonds : bond 0.03686 ( 958) hydrogen bonds : angle 4.15814 ( 2765) link_BETA1-4 : bond 0.00467 ( 10) link_BETA1-4 : angle 2.56679 ( 30) link_NAG-ASN : bond 0.01072 ( 13) link_NAG-ASN : angle 5.13517 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7539 (mtt-85) REVERT: A 341 ARG cc_start: 0.7330 (ttp-170) cc_final: 0.7092 (ttp-170) REVERT: A 345 LYS cc_start: 0.5052 (ttmt) cc_final: 0.4605 (pttt) REVERT: A 464 GLN cc_start: 0.8084 (mt0) cc_final: 0.7860 (mt0) REVERT: A 536 PHE cc_start: 0.7526 (m-10) cc_final: 0.7095 (m-80) REVERT: A 625 MET cc_start: 0.9301 (mmm) cc_final: 0.9005 (mmp) REVERT: A 649 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8746 (m110) REVERT: A 659 ILE cc_start: 0.7725 (mt) cc_final: 0.7406 (mp) REVERT: A 662 ASP cc_start: 0.6238 (m-30) cc_final: 0.5990 (m-30) REVERT: A 666 GLU cc_start: 0.6237 (mm-30) cc_final: 0.5477 (mt-10) REVERT: A 828 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.6820 (ptp-170) REVERT: A 894 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.5695 (pptt) REVERT: A 932 VAL cc_start: 0.7493 (t) cc_final: 0.7203 (p) REVERT: A 1098 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7017 (pp) REVERT: A 1124 MET cc_start: 0.7926 (mmp) cc_final: 0.7604 (mmm) REVERT: A 1198 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7579 (mp) REVERT: A 1201 GLU cc_start: 0.7217 (tp30) cc_final: 0.6644 (tt0) REVERT: A 1419 HIS cc_start: 0.2287 (OUTLIER) cc_final: 0.1759 (t-90) REVERT: A 1426 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5478 (tm) REVERT: F 42 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: F 311 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.7568 (tp40) REVERT: F 442 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8054 (tttt) REVERT: F 501 ARG cc_start: 0.8780 (mtm-85) cc_final: 0.8496 (mtm110) REVERT: F 1013 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7639 (m110) outliers start: 48 outliers final: 25 residues processed: 264 average time/residue: 0.4808 time to fit residues: 145.3526 Evaluate side-chains 265 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1382 ASP Chi-restraints excluded: chain A residue 1419 HIS Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 868 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 171 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 135 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 40 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 145 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 GLN F 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122180 restraints weight = 31192.442| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.52 r_work: 0.3179 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 18916 Z= 0.108 Angle : 0.587 14.965 25696 Z= 0.286 Chirality : 0.043 0.485 2948 Planarity : 0.004 0.071 3191 Dihedral : 7.424 69.458 2999 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.27 % Allowed : 16.48 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.18), residues: 2212 helix: 1.32 (0.15), residues: 1150 sheet: -0.37 (0.32), residues: 231 loop : -1.33 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 199 TYR 0.012 0.001 TYR F1071 PHE 0.021 0.001 PHE E 152 TRP 0.023 0.001 TRP F 187 HIS 0.002 0.000 HIS F 308 Details of bonding type rmsd covalent geometry : bond 0.00238 (18880) covalent geometry : angle 0.54919 (25601) SS BOND : bond 0.00290 ( 13) SS BOND : angle 1.05820 ( 26) hydrogen bonds : bond 0.03293 ( 958) hydrogen bonds : angle 4.07120 ( 2765) link_BETA1-4 : bond 0.00463 ( 10) link_BETA1-4 : angle 2.41670 ( 30) link_NAG-ASN : bond 0.01084 ( 13) link_NAG-ASN : angle 4.89204 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7538 (mtt-85) REVERT: A 341 ARG cc_start: 0.7390 (ttp-170) cc_final: 0.7137 (ttp-170) REVERT: A 345 LYS cc_start: 0.4992 (ttmt) cc_final: 0.4560 (pttt) REVERT: A 536 PHE cc_start: 0.7468 (m-10) cc_final: 0.7038 (m-80) REVERT: A 625 MET cc_start: 0.9244 (mmm) cc_final: 0.8927 (mmp) REVERT: A 659 ILE cc_start: 0.7663 (mt) cc_final: 0.7377 (mp) REVERT: A 666 GLU cc_start: 0.6254 (mm-30) cc_final: 0.5436 (mt-10) REVERT: A 828 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7262 (ptp-170) REVERT: A 932 VAL cc_start: 0.7514 (t) cc_final: 0.7234 (p) REVERT: A 1031 MET cc_start: 0.9106 (mtp) cc_final: 0.8813 (mtp) REVERT: A 1098 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6975 (pp) REVERT: A 1124 MET cc_start: 0.7932 (mmp) cc_final: 0.7676 (mmm) REVERT: A 1198 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7554 (mp) REVERT: A 1201 GLU cc_start: 0.7273 (tp30) cc_final: 0.6717 (tt0) REVERT: A 1426 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5466 (tm) REVERT: E 1 MET cc_start: 0.3732 (mmt) cc_final: 0.3447 (mmt) REVERT: F 42 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: F 442 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8026 (tttt) REVERT: F 501 ARG cc_start: 0.8767 (mtm-85) cc_final: 0.8481 (mtm110) outliers start: 45 outliers final: 16 residues processed: 267 average time/residue: 0.4876 time to fit residues: 148.8232 Evaluate side-chains 252 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 868 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 19 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 140 optimal weight: 0.0040 chunk 72 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.173911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121209 restraints weight = 35630.507| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.57 r_work: 0.3143 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18916 Z= 0.127 Angle : 0.610 14.913 25696 Z= 0.298 Chirality : 0.045 0.530 2948 Planarity : 0.004 0.071 3191 Dihedral : 7.184 70.218 2999 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.17 % Allowed : 17.19 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.18), residues: 2212 helix: 1.32 (0.15), residues: 1152 sheet: -0.34 (0.32), residues: 231 loop : -1.34 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 199 TYR 0.013 0.001 TYR F1071 PHE 0.020 0.001 PHE A1060 TRP 0.019 0.001 TRP F 187 HIS 0.002 0.001 HIS F 308 Details of bonding type rmsd covalent geometry : bond 0.00292 (18880) covalent geometry : angle 0.57057 (25601) SS BOND : bond 0.00271 ( 13) SS BOND : angle 1.10619 ( 26) hydrogen bonds : bond 0.03433 ( 958) hydrogen bonds : angle 4.07645 ( 2765) link_BETA1-4 : bond 0.00641 ( 10) link_BETA1-4 : angle 2.60648 ( 30) link_NAG-ASN : bond 0.01556 ( 13) link_NAG-ASN : angle 5.00728 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7553 (mtt-85) REVERT: A 341 ARG cc_start: 0.7365 (ttp-170) cc_final: 0.7117 (ttp-170) REVERT: A 345 LYS cc_start: 0.5064 (ttmt) cc_final: 0.4648 (pttt) REVERT: A 536 PHE cc_start: 0.7479 (m-10) cc_final: 0.7048 (m-80) REVERT: A 625 MET cc_start: 0.9284 (mmm) cc_final: 0.9035 (mmp) REVERT: A 659 ILE cc_start: 0.7669 (mt) cc_final: 0.7367 (mp) REVERT: A 666 GLU cc_start: 0.6265 (mm-30) cc_final: 0.5446 (mt-10) REVERT: A 828 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7356 (ptp-170) REVERT: A 932 VAL cc_start: 0.7468 (t) cc_final: 0.7166 (p) REVERT: A 1031 MET cc_start: 0.9126 (mtp) cc_final: 0.8829 (mtp) REVERT: A 1068 PHE cc_start: 0.7850 (m-10) cc_final: 0.7648 (m-10) REVERT: A 1098 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6990 (pp) REVERT: A 1124 MET cc_start: 0.7943 (mmp) cc_final: 0.7680 (mmm) REVERT: A 1198 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7550 (mp) REVERT: A 1201 GLU cc_start: 0.7250 (tp30) cc_final: 0.6682 (tt0) REVERT: A 1426 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5349 (tm) REVERT: E 1 MET cc_start: 0.3939 (mmt) cc_final: 0.3709 (mmt) REVERT: E 54 TRP cc_start: 0.4542 (OUTLIER) cc_final: 0.3760 (m100) REVERT: F 42 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: F 442 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8015 (tttt) REVERT: F 501 ARG cc_start: 0.8840 (mtm-85) cc_final: 0.8554 (mtm110) REVERT: F 1013 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7668 (m110) outliers start: 43 outliers final: 26 residues processed: 256 average time/residue: 0.4822 time to fit residues: 141.9803 Evaluate side-chains 262 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 248 GLN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 868 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 GLN F 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.170374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116918 restraints weight = 30682.371| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.85 r_work: 0.3086 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18916 Z= 0.230 Angle : 0.696 14.556 25696 Z= 0.345 Chirality : 0.050 0.577 2948 Planarity : 0.005 0.070 3191 Dihedral : 7.556 72.218 2999 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.12 % Allowed : 17.34 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.18), residues: 2212 helix: 1.07 (0.15), residues: 1162 sheet: -0.23 (0.32), residues: 240 loop : -1.57 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 199 TYR 0.021 0.002 TYR F1071 PHE 0.021 0.002 PHE A1060 TRP 0.013 0.002 TRP A1258 HIS 0.005 0.001 HIS A1397 Details of bonding type rmsd covalent geometry : bond 0.00559 (18880) covalent geometry : angle 0.65948 (25601) SS BOND : bond 0.00424 ( 13) SS BOND : angle 1.57211 ( 26) hydrogen bonds : bond 0.04320 ( 958) hydrogen bonds : angle 4.31832 ( 2765) link_BETA1-4 : bond 0.00665 ( 10) link_BETA1-4 : angle 2.60652 ( 30) link_NAG-ASN : bond 0.01600 ( 13) link_NAG-ASN : angle 5.18027 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7622 (mtt-85) REVERT: A 341 ARG cc_start: 0.7344 (ttp-170) cc_final: 0.7125 (ttp-170) REVERT: A 345 LYS cc_start: 0.5095 (ttmt) cc_final: 0.4718 (pttt) REVERT: A 497 ASN cc_start: 0.7274 (m-40) cc_final: 0.6666 (t0) REVERT: A 536 PHE cc_start: 0.7639 (m-10) cc_final: 0.7046 (m-80) REVERT: A 625 MET cc_start: 0.9356 (mmm) cc_final: 0.9065 (mmp) REVERT: A 659 ILE cc_start: 0.7699 (mt) cc_final: 0.7373 (mp) REVERT: A 662 ASP cc_start: 0.6291 (m-30) cc_final: 0.6065 (m-30) REVERT: A 666 GLU cc_start: 0.6195 (mm-30) cc_final: 0.5374 (mt-10) REVERT: A 828 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6788 (ptp-170) REVERT: A 932 VAL cc_start: 0.7641 (t) cc_final: 0.7311 (p) REVERT: A 1098 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7037 (pp) REVERT: A 1124 MET cc_start: 0.8071 (mmp) cc_final: 0.7794 (mmm) REVERT: A 1382 ASP cc_start: 0.8297 (t0) cc_final: 0.7951 (t0) REVERT: A 1426 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5486 (tm) REVERT: E 1 MET cc_start: 0.4068 (mmt) cc_final: 0.3829 (mmt) REVERT: E 54 TRP cc_start: 0.4631 (OUTLIER) cc_final: 0.3623 (m100) REVERT: F 42 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: F 311 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.7523 (tp40) REVERT: F 442 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8085 (tttt) REVERT: F 501 ARG cc_start: 0.8800 (mtm-85) cc_final: 0.8506 (mtm110) REVERT: F 1013 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7691 (m110) outliers start: 42 outliers final: 25 residues processed: 268 average time/residue: 0.4730 time to fit residues: 145.0490 Evaluate side-chains 267 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 248 GLN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 868 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 152 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 ASN A1183 ASN E 79 ASN F 556 GLN F 872 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.172629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122598 restraints weight = 27717.678| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.25 r_work: 0.3126 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18916 Z= 0.139 Angle : 0.630 14.648 25696 Z= 0.310 Chirality : 0.046 0.541 2948 Planarity : 0.004 0.071 3191 Dihedral : 7.334 71.065 2999 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.97 % Allowed : 17.74 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.18), residues: 2212 helix: 1.17 (0.15), residues: 1159 sheet: -0.22 (0.32), residues: 236 loop : -1.54 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 199 TYR 0.014 0.001 TYR F1071 PHE 0.017 0.001 PHE A1060 TRP 0.019 0.001 TRP F 187 HIS 0.002 0.001 HIS F 169 Details of bonding type rmsd covalent geometry : bond 0.00320 (18880) covalent geometry : angle 0.59354 (25601) SS BOND : bond 0.00320 ( 13) SS BOND : angle 1.18750 ( 26) hydrogen bonds : bond 0.03689 ( 958) hydrogen bonds : angle 4.21635 ( 2765) link_BETA1-4 : bond 0.00536 ( 10) link_BETA1-4 : angle 2.41251 ( 30) link_NAG-ASN : bond 0.01431 ( 13) link_NAG-ASN : angle 5.01551 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7546 (mtt-85) REVERT: A 341 ARG cc_start: 0.7266 (ttp-170) cc_final: 0.7057 (ttp-170) REVERT: A 345 LYS cc_start: 0.5081 (ttmt) cc_final: 0.4657 (pttt) REVERT: A 536 PHE cc_start: 0.7590 (m-10) cc_final: 0.7181 (m-80) REVERT: A 625 MET cc_start: 0.9284 (mmm) cc_final: 0.8969 (mmp) REVERT: A 659 ILE cc_start: 0.7626 (mt) cc_final: 0.7336 (mp) REVERT: A 666 GLU cc_start: 0.6081 (mm-30) cc_final: 0.5268 (mt-10) REVERT: A 828 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7119 (ptp-170) REVERT: A 932 VAL cc_start: 0.7551 (t) cc_final: 0.7240 (p) REVERT: A 1058 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7263 (m-40) REVERT: A 1068 PHE cc_start: 0.7866 (m-10) cc_final: 0.7662 (m-10) REVERT: A 1098 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7002 (pp) REVERT: A 1124 MET cc_start: 0.8043 (mmp) cc_final: 0.7824 (mmm) REVERT: A 1201 GLU cc_start: 0.7363 (tp30) cc_final: 0.6739 (tt0) REVERT: A 1382 ASP cc_start: 0.8172 (t0) cc_final: 0.7812 (t0) REVERT: A 1426 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5488 (tm) REVERT: E 1 MET cc_start: 0.3886 (mmt) cc_final: 0.3656 (mmt) REVERT: E 54 TRP cc_start: 0.4497 (OUTLIER) cc_final: 0.3471 (m100) REVERT: F 42 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: F 301 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: F 442 LYS cc_start: 0.8504 (mtmm) cc_final: 0.7998 (tttt) REVERT: F 501 ARG cc_start: 0.8785 (mtm-85) cc_final: 0.8488 (mtm110) REVERT: F 826 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: F 1013 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7635 (m110) outliers start: 39 outliers final: 26 residues processed: 257 average time/residue: 0.4704 time to fit residues: 138.0498 Evaluate side-chains 266 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 248 GLN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 868 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 19 optimal weight: 0.1980 chunk 96 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 216 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN F 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.172681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118286 restraints weight = 27521.683| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.47 r_work: 0.3149 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 18916 Z= 0.184 Angle : 0.800 59.199 25696 Z= 0.441 Chirality : 0.046 0.540 2948 Planarity : 0.004 0.071 3191 Dihedral : 7.330 70.995 2999 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.76 % Allowed : 17.99 % Favored : 80.24 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.18), residues: 2212 helix: 1.18 (0.15), residues: 1158 sheet: -0.28 (0.32), residues: 238 loop : -1.53 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 199 TYR 0.014 0.001 TYR F1071 PHE 0.017 0.001 PHE A1060 TRP 0.018 0.001 TRP F 187 HIS 0.002 0.001 HIS F 169 Details of bonding type rmsd covalent geometry : bond 0.00362 (18880) covalent geometry : angle 0.77206 (25601) SS BOND : bond 0.00302 ( 13) SS BOND : angle 1.17921 ( 26) hydrogen bonds : bond 0.03686 ( 958) hydrogen bonds : angle 4.21602 ( 2765) link_BETA1-4 : bond 0.00531 ( 10) link_BETA1-4 : angle 2.39201 ( 30) link_NAG-ASN : bond 0.01398 ( 13) link_NAG-ASN : angle 4.99170 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7362.17 seconds wall clock time: 125 minutes 39.09 seconds (7539.09 seconds total)