Starting phenix.real_space_refine on Fri Sep 11 18:41:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5x0m_6698/09_2026/5x0m_6698.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x0m_6698/09_2026/5x0m_6698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5x0m_6698/09_2026/5x0m_6698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x0m_6698/09_2026/5x0m_6698.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5x0m_6698/09_2026/5x0m_6698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x0m_6698/09_2026/5x0m_6698.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5x0m_6698/09_2026/5x0m_6698.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5x0m_6698/09_2026/5x0m_6698.cif" } resolution = 3.8 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 7031 2.51 5 N 1683 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10654 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10395 Classifications: {'peptide': 1323} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 45, 'TRANS': 1274} Chain breaks: 2 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 566 Unresolved non-hydrogen dihedrals: 376 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASP:plan': 11, 'ARG:plan': 12, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLN:plan1': 7, 'GLU:plan': 6, 'PHE:plan': 8, 'TYR:plan': 1, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 247 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" 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 chiralities: 3 Chain: "D" 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 chiralities: 3 Chain: "E" 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 chiralities: 3 Chain: "F" 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 chiralities: 3 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 chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.77, per 1000 atoms: 0.26 Number of scatterers: 10654 At special positions: 0 Unit cell: (131.58, 130.29, 125.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1878 8.00 N 1683 7.00 C 7031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 337 " distance=2.24 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=1.72 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.02 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.02 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=1.83 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 BETA1-3 " BMA B 3 " - " BMA B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " BETA1-6 " BMA B 3 " - " BMA B 5 " NAG-ASN " NAG A1606 " - " ASN A1028 " " NAG B 1 " - " ASN A 330 " " NAG C 1 " - " ASN A1034 " " NAG D 1 " - " ASN A1015 " " NAG E 1 " - " ASN A 312 " " NAG F 1 " - " ASN A 308 " " NAG G 1 " - " ASN A 300 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 573.3 milliseconds 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 69.2% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 139 through 159 removed outlier: 4.053A pdb=" N SER A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 187 removed outlier: 3.764A pdb=" N PHE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.647A pdb=" N THR A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.565A pdb=" N ARG A 230 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 238 " --> pdb=" O TRP A 235 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 240 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 241 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 256 removed outlier: 3.670A pdb=" N THR A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 281 removed outlier: 4.123A pdb=" N LEU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 360 through 374 removed outlier: 3.703A pdb=" N ALA A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 388 removed outlier: 4.065A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 403 removed outlier: 3.543A pdb=" N ILE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 435 removed outlier: 3.581A pdb=" N LEU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 520 through 537 removed outlier: 3.861A pdb=" N THR A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 573 removed outlier: 3.803A pdb=" N ASN A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 560 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 561 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 581 through 604 removed outlier: 3.989A pdb=" N VAL A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 618 removed outlier: 3.617A pdb=" N PHE A 609 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 612 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 4.112A pdb=" N PHE A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 635 removed outlier: 3.515A pdb=" N VAL A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 663 removed outlier: 3.613A pdb=" N ILE A 658 " --> pdb=" O ILE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.742A pdb=" N MET A 671 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 700 removed outlier: 4.047A pdb=" N VAL A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 714 removed outlier: 3.550A pdb=" N MET A 706 " --> pdb=" O TRP A 702 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 714 " --> pdb=" O MET A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 724 Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.582A pdb=" N LEU A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 855 removed outlier: 4.307A pdb=" N GLN A 839 " --> pdb=" O ASP A 835 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 875 removed outlier: 3.940A pdb=" N PHE A 861 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 875 " --> pdb=" O VAL A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 912 removed outlier: 3.973A pdb=" N LEU A 891 " --> pdb=" O VAL A 887 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 912 " --> pdb=" O MET A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.511A pdb=" N PHE A 918 " --> pdb=" O PHE A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 938 removed outlier: 3.821A pdb=" N ASP A 926 " --> pdb=" O TRP A 922 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 937 " --> pdb=" O TYR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 953 Processing helix chain 'A' and resid 954 through 957 removed outlier: 3.556A pdb=" N ARG A 957 " --> pdb=" O ARG A 954 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 954 through 957' Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.791A pdb=" N LEU A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1002 removed outlier: 3.503A pdb=" N GLU A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) Proline residue: A 980 - end of helix removed outlier: 3.710A pdb=" N LEU A 987 " --> pdb=" O PHE A 983 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP A 993 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1032 removed outlier: 3.817A pdb=" N CYS A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1059 removed outlier: 4.148A pdb=" N VAL A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1073 removed outlier: 4.044A pdb=" N ASP A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1089 Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 3.518A pdb=" N PHE A1094 " --> pdb=" O LEU A1090 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A1098 " --> pdb=" O PHE A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1124 removed outlier: 4.416A pdb=" N ASP A1113 " --> pdb=" O CYS A1109 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN A1117 " --> pdb=" O ASP A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1146 removed outlier: 4.066A pdb=" N ALA A1146 " --> pdb=" O ARG A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1168 removed outlier: 3.851A pdb=" N MET A1163 " --> pdb=" O PRO A1159 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A1164 " --> pdb=" O GLN A1160 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A1168 " --> pdb=" O TYR A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1188 removed outlier: 3.784A pdb=" N MET A1187 " --> pdb=" O ASN A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1225 removed outlier: 4.275A pdb=" N PHE A1198 " --> pdb=" O GLN A1194 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A1199 " --> pdb=" O SER A1195 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1201 " --> pdb=" O GLU A1197 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A1218 " --> pdb=" O PHE A1214 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A1223 " --> pdb=" O ILE A1219 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1224 " --> pdb=" O LYS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1249 removed outlier: 3.821A pdb=" N VAL A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1271 removed outlier: 4.057A pdb=" N LEU A1264 " --> pdb=" O SER A1260 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A1265 " --> pdb=" O PRO A1261 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1278 removed outlier: 3.662A pdb=" N LEU A1275 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A1276 " --> pdb=" O GLY A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1319 removed outlier: 3.580A pdb=" N ARG A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG A1297 " --> pdb=" O ARG A1293 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR A1298 " --> pdb=" O LYS A1294 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1305 " --> pdb=" O ASN A1301 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A1315 " --> pdb=" O PHE A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1351 removed outlier: 3.818A pdb=" N LEU A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 3.605A pdb=" N VAL A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1396 removed outlier: 3.593A pdb=" N ALA A1389 " --> pdb=" O ALA A1385 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A1393 " --> pdb=" O ALA A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1424 removed outlier: 3.916A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A1410 " --> pdb=" O TYR A1406 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A1418 " --> pdb=" O VAL A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1441 removed outlier: 4.052A pdb=" N TYR A1430 " --> pdb=" O THR A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1459 Processing helix chain 'A' and resid 1470 through 1475 Processing helix chain 'A' and resid 1489 through 1505 Processing helix chain 'A' and resid 1508 through 1521 removed outlier: 3.582A pdb=" N ASP A1512 " --> pdb=" O VAL A1508 " (cutoff:3.500A) Proline residue: A1516 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 290 removed outlier: 3.569A pdb=" N LYS A 287 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 344 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1012 through 1013 removed outlier: 3.510A pdb=" N ASP A1013 " --> pdb=" O THR A1017 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1447 through 1449 549 hydrogen bonds defined for protein. 1584 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: 1.81 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1794 1.32 - 1.45: 3059 1.45 - 1.57: 5966 1.57 - 1.69: 3 1.69 - 1.82: 105 Bond restraints: 10927 Sorted by residual: bond pdb=" C ASP A1072 " pdb=" N SER A1073 " ideal model delta sigma weight residual 1.330 1.574 -0.243 1.42e-02 4.96e+03 2.94e+02 bond pdb=" C LEU A 935 " pdb=" N ASN A 936 " ideal model delta sigma weight residual 1.334 1.485 -0.151 1.33e-02 5.65e+03 1.29e+02 bond pdb=" C VAL A1047 " pdb=" N GLY A1048 " ideal model delta sigma weight residual 1.335 1.231 0.104 1.26e-02 6.30e+03 6.77e+01 bond pdb=" C PHE A 674 " pdb=" N PRO A 675 " ideal model delta sigma weight residual 1.334 1.493 -0.160 2.34e-02 1.83e+03 4.65e+01 bond pdb=" C SER A 574 " pdb=" N PRO A 575 " ideal model delta sigma weight residual 1.335 1.421 -0.086 1.30e-02 5.92e+03 4.36e+01 ... (remaining 10922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 14546 3.53 - 7.05: 250 7.05 - 10.58: 54 10.58 - 14.11: 7 14.11 - 17.63: 17 Bond angle restraints: 14874 Sorted by residual: angle pdb=" CA VAL A 503 " pdb=" C VAL A 503 " pdb=" N PRO A 504 " ideal model delta sigma weight residual 120.83 114.03 6.80 6.10e-01 2.69e+00 1.24e+02 angle pdb=" CA ASP A1072 " pdb=" C ASP A1072 " pdb=" N SER A1073 " ideal model delta sigma weight residual 118.36 104.60 13.76 1.33e+00 5.65e-01 1.07e+02 angle pdb=" CA PRO A 519 " pdb=" N PRO A 519 " pdb=" CD PRO A 519 " ideal model delta sigma weight residual 112.00 99.57 12.43 1.40e+00 5.10e-01 7.88e+01 angle pdb=" CA VAL A1047 " pdb=" C VAL A1047 " pdb=" N GLY A1048 " ideal model delta sigma weight residual 117.27 130.68 -13.41 1.51e+00 4.39e-01 7.88e+01 angle pdb=" O ASP A1072 " pdb=" C ASP A1072 " pdb=" N SER A1073 " ideal model delta sigma weight residual 122.41 134.39 -11.98 1.42e+00 4.96e-01 7.12e+01 ... (remaining 14869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 5584 26.78 - 53.57: 471 53.57 - 80.35: 106 80.35 - 107.13: 18 107.13 - 133.91: 2 Dihedral angle restraints: 6181 sinusoidal: 2286 harmonic: 3895 Sorted by residual: dihedral pdb=" CA TRP A 121 " pdb=" C TRP A 121 " pdb=" N MET A 122 " pdb=" CA MET A 122 " ideal model delta harmonic sigma weight residual -180.00 -46.09 -133.91 0 5.00e+00 4.00e-02 7.17e+02 dihedral pdb=" CA GLY A 605 " pdb=" C GLY A 605 " pdb=" N LEU A 606 " pdb=" CA LEU A 606 " ideal model delta harmonic sigma weight residual 180.00 58.11 121.89 0 5.00e+00 4.00e-02 5.94e+02 dihedral pdb=" CA CYS A1157 " pdb=" C CYS A1157 " pdb=" N HIS A1158 " pdb=" CA HIS A1158 " ideal model delta harmonic sigma weight residual 180.00 75.27 104.73 0 5.00e+00 4.00e-02 4.39e+02 ... (remaining 6178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1707 0.131 - 0.261: 47 0.261 - 0.392: 8 0.392 - 0.522: 2 0.522 - 0.653: 1 Chirality restraints: 1765 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A1015 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA PRO A 719 " pdb=" N PRO A 719 " pdb=" C PRO A 719 " pdb=" CB PRO A 719 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA PRO A 575 " pdb=" N PRO A 575 " pdb=" C PRO A 575 " pdb=" CB PRO A 575 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.53e+00 ... (remaining 1762 not shown) Planarity restraints: 1825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 245 " -1.054 9.50e-02 1.11e+02 4.72e-01 1.35e+02 pdb=" NE ARG A 245 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 245 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 245 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 245 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 935 " 0.041 2.00e-02 2.50e+03 7.35e-02 5.41e+01 pdb=" C LEU A 935 " -0.127 2.00e-02 2.50e+03 pdb=" O LEU A 935 " 0.048 2.00e-02 2.50e+03 pdb=" N ASN A 936 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 330 " 0.049 2.00e-02 2.50e+03 5.50e-02 3.78e+01 pdb=" CG ASN A 330 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 330 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 330 " -0.089 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.066 2.00e-02 2.50e+03 ... (remaining 1822 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 144 2.55 - 3.14: 9304 3.14 - 3.73: 15820 3.73 - 4.31: 22555 4.31 - 4.90: 33847 Nonbonded interactions: 81670 Sorted by model distance: nonbonded pdb=" SD MET A1477 " pdb=" OD2 ASP A1499 " model vdw 1.965 3.400 nonbonded pdb=" O LEU A 531 " pdb=" OG1 THR A 534 " model vdw 1.973 3.040 nonbonded pdb=" CE1 PHE A 401 " pdb=" OH TYR A1406 " model vdw 2.009 3.340 nonbonded pdb=" O ILE A1330 " pdb=" N ASP A1332 " model vdw 2.025 3.120 nonbonded pdb=" O GLY A 221 " pdb=" ND1 HIS A 222 " model vdw 2.025 3.120 ... (remaining 81665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.660 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 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 : 0.010 0.307 10952 Z= 0.555 Angle : 1.475 29.579 14944 Z= 0.902 Chirality : 0.059 0.653 1765 Planarity : 0.013 0.472 1818 Dihedral : 21.102 133.913 3652 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 54.20 Ramachandran Plot: Outliers : 5.24 % Allowed : 12.91 % Favored : 81.85 % Rotamer: Outliers : 11.48 % Allowed : 12.14 % Favored : 76.38 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 48.94 % Twisted General : 7.70 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.95 (0.16), residues: 1317 helix: -3.44 (0.12), residues: 821 sheet: None (None), residues: 0 loop : -4.70 (0.20), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 305 TYR 0.081 0.002 TYR A1089 PHE 0.036 0.001 PHE A 684 TRP 0.048 0.002 TRP A 316 HIS 0.012 0.002 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00862 / 0.52 (10927) covalent geometry : angle 1.40698 / 0.89 (14874) SS BOND : bond 0.18901 / 10.81 ( 5) SS BOND : angle 11.37339 / 6.61 ( 10) hydrogen bonds : bond 0.30330 / 22.54 ( 549) hydrogen bonds : angle 11.03970 / 7.84 ( 1584) link_BETA1-3 : bond 0.00305 / 0.16 ( 1) link_BETA1-3 : angle 2.31723 / 1.04 ( 3) link_BETA1-4 : bond 0.00663 / 0.43 ( 11) link_BETA1-4 : angle 4.48506 / 3.91 ( 33) link_BETA1-6 : bond 0.00219 / 0.12 ( 1) link_BETA1-6 : angle 3.29527 / 1.43 ( 3) link_NAG-ASN : bond 0.01327 / 0.82 ( 7) link_NAG-ASN : angle 7.13685 / 5.20 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 380 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 PHE cc_start: 0.6576 (t80) cc_final: 0.5715 (m-80) REVERT: A 183 LYS cc_start: 0.8446 (mmtt) cc_final: 0.7788 (mtmt) REVERT: A 219 ASP cc_start: 0.0666 (OUTLIER) cc_final: 0.0054 (t0) REVERT: A 227 ARG cc_start: 0.6226 (mmt90) cc_final: 0.6004 (mmt180) REVERT: A 259 LYS cc_start: 0.2473 (OUTLIER) cc_final: 0.1820 (mtmt) REVERT: A 281 MET cc_start: 0.7065 (ttp) cc_final: 0.6278 (ttm) REVERT: A 331 SER cc_start: 0.6957 (m) cc_final: 0.6741 (t) REVERT: A 379 ASP cc_start: 0.5424 (OUTLIER) cc_final: 0.5114 (t0) REVERT: A 425 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.4195 (ttm-80) REVERT: A 556 TYR cc_start: 0.8356 (m-80) cc_final: 0.6459 (t80) REVERT: A 557 ILE cc_start: 0.8727 (mt) cc_final: 0.8349 (mt) REVERT: A 590 ILE cc_start: 0.7398 (mm) cc_final: 0.7171 (mt) REVERT: A 613 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7611 (ttm110) REVERT: A 631 MET cc_start: 0.6904 (tpt) cc_final: 0.6377 (tmm) REVERT: A 706 MET cc_start: 0.7510 (ttp) cc_final: 0.6787 (ttp) REVERT: A 711 LEU cc_start: 0.7357 (tm) cc_final: 0.6322 (tm) REVERT: A 735 LEU cc_start: 0.6008 (tp) cc_final: 0.5387 (tt) REVERT: A 854 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6219 (mmtm) REVERT: A 856 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7333 (ptpt) REVERT: A 905 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7695 (tpp) REVERT: A 966 ASN cc_start: 0.5686 (OUTLIER) cc_final: 0.5024 (t0) REVERT: A 1003 LEU cc_start: 0.4543 (OUTLIER) cc_final: 0.4294 (pp) REVERT: A 1010 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6811 (pttm) REVERT: A 1015 ASN cc_start: 0.6776 (m-40) cc_final: 0.6505 (m-40) REVERT: A 1017 THR cc_start: 0.6255 (p) cc_final: 0.5519 (m) REVERT: A 1032 HIS cc_start: 0.6870 (t70) cc_final: 0.6592 (t70) REVERT: A 1074 ARG cc_start: 0.7304 (pmt-80) cc_final: 0.6546 (pmt-80) REVERT: A 1125 LEU cc_start: 0.4952 (OUTLIER) cc_final: 0.3200 (mt) REVERT: A 1131 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6762 (tpt170) REVERT: A 1134 LEU cc_start: 0.8728 (mt) cc_final: 0.8497 (mt) REVERT: A 1135 ILE cc_start: 0.8360 (mt) cc_final: 0.7973 (mt) REVERT: A 1136 TYR cc_start: 0.7168 (m-80) cc_final: 0.6914 (m-80) REVERT: A 1147 LYS cc_start: 0.8683 (mttt) cc_final: 0.8433 (mmtt) REVERT: A 1149 VAL cc_start: 0.7673 (t) cc_final: 0.7169 (t) REVERT: A 1156 THR cc_start: 0.6575 (OUTLIER) cc_final: 0.6209 (m) REVERT: A 1170 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6442 (ttp80) REVERT: A 1187 MET cc_start: 0.6390 (mtm) cc_final: 0.5825 (mtm) REVERT: A 1197 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: A 1258 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.5517 (m-80) REVERT: A 1268 ARG cc_start: 0.7180 (ttp-170) cc_final: 0.6810 (ttp80) REVERT: A 1276 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7090 (mt) REVERT: A 1277 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.6157 (mtt180) REVERT: A 1310 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.6109 (mtp) REVERT: A 1316 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.5988 (m-80) REVERT: A 1319 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6715 (mm-30) REVERT: A 1338 THR cc_start: 0.7453 (p) cc_final: 0.7034 (t) REVERT: A 1346 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4800 (pp) REVERT: A 1378 PRO cc_start: 0.5105 (Cg_exo) cc_final: 0.4047 (Cg_endo) REVERT: A 1406 TYR cc_start: 0.5478 (OUTLIER) cc_final: 0.4995 (t80) REVERT: A 1416 GLU cc_start: 0.6875 (tt0) cc_final: 0.6467 (tt0) REVERT: A 1429 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6388 (t70) REVERT: A 1432 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7805 (ppp) REVERT: A 1438 GLN cc_start: 0.8691 (tt0) cc_final: 0.8180 (tp-100) REVERT: A 1455 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8693 (mm-30) REVERT: A 1473 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8401 (mmtm) REVERT: A 1479 ILE cc_start: 0.8730 (mt) cc_final: 0.8469 (mt) REVERT: A 1494 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8079 (tp30) outliers start: 121 outliers final: 11 residues processed: 455 average time/residue: 0.1171 time to fit residues: 73.0279 Evaluate side-chains 293 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1131 ARG Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1170 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1227 HIS Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1310 MET Chi-restraints excluded: chain A residue 1316 PHE Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1406 TYR Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1473 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS A 286 GLN A 291 HIS A 382 GLN A 392 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN A 670 ASN A1002 GLN A1021 HIS ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 ASN A1079 GLN A1194 GLN ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1446 GLN A1465 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.184772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.151293 restraints weight = 16155.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.153063 restraints weight = 10158.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.154469 restraints weight = 7297.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.154555 restraints weight = 5861.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.155617 restraints weight = 5449.867| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10952 Z= 0.233 Angle : 1.053 14.068 14944 Z= 0.524 Chirality : 0.051 0.434 1765 Planarity : 0.007 0.067 1818 Dihedral : 13.753 87.087 1530 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 1.90 % Allowed : 11.16 % Favored : 86.94 % Rotamer: Outliers : 6.36 % Allowed : 18.79 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 19.15 % Twisted General : 2.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.22), residues: 1317 helix: -1.40 (0.17), residues: 852 sheet: -4.73 (1.00), residues: 20 loop : -3.88 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 681 TYR 0.043 0.003 TYR A1089 PHE 0.024 0.002 PHE A 653 TRP 0.033 0.003 TRP A 316 HIS 0.009 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (10927) covalent geometry : angle 1.02840 / 0.52 (14874) SS BOND : bond 0.01820 / 0.95 ( 5) SS BOND : angle 2.75731 / 1.61 ( 10) hydrogen bonds : bond 0.06125 / 4.60 ( 549) hydrogen bonds : angle 6.15993 / 4.28 ( 1584) link_BETA1-3 : bond 0.00308 / 0.16 ( 1) link_BETA1-3 : angle 2.70261 / 1.35 ( 3) link_BETA1-4 : bond 0.00636 / 0.42 ( 11) link_BETA1-4 : angle 2.80792 / 2.39 ( 33) link_BETA1-6 : bond 0.00513 / 0.27 ( 1) link_BETA1-6 : angle 3.60530 / 1.69 ( 3) link_NAG-ASN : bond 0.00545 / 0.37 ( 7) link_NAG-ASN : angle 4.57807 / 3.53 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 313 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 TYR cc_start: 0.7622 (m-10) cc_final: 0.7038 (t80) REVERT: A 580 LYS cc_start: 0.5757 (tptt) cc_final: 0.5364 (tttp) REVERT: A 735 LEU cc_start: 0.7656 (tp) cc_final: 0.7165 (tt) REVERT: A 966 ASN cc_start: 0.6515 (t0) cc_final: 0.6310 (t0) REVERT: A 1052 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7224 (mp) REVERT: A 1074 ARG cc_start: 0.6961 (pmt-80) cc_final: 0.6219 (tpt170) REVERT: A 1151 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8072 (tpp80) REVERT: A 1170 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6600 (ttt90) REVERT: A 1197 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6675 (mt-10) REVERT: A 1231 ASP cc_start: 0.6450 (t70) cc_final: 0.6157 (t0) REVERT: A 1373 HIS cc_start: 0.7390 (t-90) cc_final: 0.6679 (t-90) REVERT: A 1438 GLN cc_start: 0.8113 (tt0) cc_final: 0.7622 (tt0) REVERT: A 1439 GLN cc_start: 0.8572 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 1455 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: A 1473 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8551 (mmtm) outliers start: 67 outliers final: 23 residues processed: 351 average time/residue: 0.0928 time to fit residues: 46.3414 Evaluate side-chains 272 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain A residue 1170 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1253 VAL Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1318 MET Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1473 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 0.2980 chunk 4 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS A 222 HIS A 286 GLN A 540 HIS A 555 ASN ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 ASN A1348 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.172926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139481 restraints weight = 16112.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139729 restraints weight = 9891.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140788 restraints weight = 7461.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141019 restraints weight = 6889.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141438 restraints weight = 6093.743| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.7456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 10952 Z= 0.293 Angle : 1.075 23.203 14944 Z= 0.529 Chirality : 0.056 0.651 1765 Planarity : 0.009 0.192 1818 Dihedral : 9.959 73.710 1460 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.99 % Allowed : 12.60 % Favored : 86.41 % Rotamer: Outliers : 7.21 % Allowed : 20.21 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 10.64 % Twisted General : 1.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.22), residues: 1317 helix: -1.00 (0.16), residues: 873 sheet: None (None), residues: 0 loop : -3.80 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1268 TYR 0.032 0.003 TYR A1089 PHE 0.028 0.003 PHE A 653 TRP 0.031 0.003 TRP A 203 HIS 0.010 0.003 HIS A1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.29 (10927) covalent geometry : angle 1.05138 / 0.52 (14874) SS BOND : bond 0.00746 / 0.38 ( 5) SS BOND : angle 1.93412 / 1.11 ( 10) hydrogen bonds : bond 0.05595 / 4.16 ( 549) hydrogen bonds : angle 5.71157 / 3.98 ( 1584) link_BETA1-3 : bond 0.00416 / 0.22 ( 1) link_BETA1-3 : angle 2.60005 / 1.33 ( 3) link_BETA1-4 : bond 0.00807 / 0.59 ( 11) link_BETA1-4 : angle 2.71383 / 2.33 ( 33) link_BETA1-6 : bond 0.00764 / 0.40 ( 1) link_BETA1-6 : angle 2.85506 / 1.29 ( 3) link_NAG-ASN : bond 0.01071 / 0.77 ( 7) link_NAG-ASN : angle 4.83984 / 3.64 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 306 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASN cc_start: 0.8277 (m-40) cc_final: 0.8039 (t0) REVERT: A 393 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7522 (pt) REVERT: A 394 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8606 (mt) REVERT: A 427 ASP cc_start: 0.6142 (t0) cc_final: 0.5640 (t70) REVERT: A 556 TYR cc_start: 0.7639 (m-10) cc_final: 0.6538 (t80) REVERT: A 580 LYS cc_start: 0.6054 (tptt) cc_final: 0.5358 (ttmm) REVERT: A 660 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7704 (mtm) REVERT: A 710 MET cc_start: 0.8141 (mtm) cc_final: 0.7927 (mtm) REVERT: A 733 LEU cc_start: 0.9124 (mt) cc_final: 0.8866 (mt) REVERT: A 873 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8459 (tt) REVERT: A 905 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7578 (ttp) REVERT: A 908 MET cc_start: 0.8103 (tpp) cc_final: 0.7433 (tpp) REVERT: A 916 LYS cc_start: 0.8097 (ptpp) cc_final: 0.7816 (ptpt) REVERT: A 951 ARG cc_start: 0.8296 (ttt-90) cc_final: 0.7974 (ttt180) REVERT: A 966 ASN cc_start: 0.7877 (t0) cc_final: 0.7617 (t0) REVERT: A 1042 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8583 (mmm) REVERT: A 1151 ARG cc_start: 0.8428 (tpp80) cc_final: 0.8136 (tpp80) REVERT: A 1170 ARG cc_start: 0.7549 (mmt90) cc_final: 0.6707 (ttt90) REVERT: A 1197 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: A 1288 LEU cc_start: 0.8983 (tt) cc_final: 0.8750 (tt) REVERT: A 1335 ASN cc_start: 0.8098 (p0) cc_final: 0.7892 (p0) REVERT: A 1373 HIS cc_start: 0.6907 (t-90) cc_final: 0.6649 (t-90) REVERT: A 1415 LEU cc_start: 0.8705 (tp) cc_final: 0.8387 (tt) REVERT: A 1438 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: A 1439 GLN cc_start: 0.8647 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 1450 TYR cc_start: 0.6629 (t80) cc_final: 0.6308 (t80) REVERT: A 1455 GLU cc_start: 0.8070 (tp30) cc_final: 0.7860 (mm-30) REVERT: A 1473 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8479 (mmtm) outliers start: 76 outliers final: 35 residues processed: 346 average time/residue: 0.0908 time to fit residues: 45.5785 Evaluate side-chains 299 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1079 GLN Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1438 GLN Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1458 GLU Chi-restraints excluded: chain A residue 1473 LYS Chi-restraints excluded: chain A residue 1492 VAL Chi-restraints excluded: chain A residue 1497 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 GLN A1160 GLN A1227 HIS ** A1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142251 restraints weight = 16052.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142642 restraints weight = 9911.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143747 restraints weight = 7790.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144640 restraints weight = 6318.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144653 restraints weight = 5803.064| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10952 Z= 0.157 Angle : 0.870 22.449 14944 Z= 0.419 Chirality : 0.046 0.432 1765 Planarity : 0.005 0.090 1818 Dihedral : 8.616 67.604 1449 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.33 % Favored : 88.84 % Rotamer: Outliers : 4.55 % Allowed : 25.43 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 6.38 % Twisted General : 1.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.23), residues: 1317 helix: -0.47 (0.17), residues: 867 sheet: -3.78 (0.85), residues: 20 loop : -3.46 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 386 TYR 0.024 0.002 TYR A1089 PHE 0.018 0.001 PHE A 623 TRP 0.037 0.002 TRP A 715 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (10927) covalent geometry : angle 0.84349 / 0.41 (14874) SS BOND : bond 0.00409 / 0.27 ( 5) SS BOND : angle 1.70567 / 1.14 ( 10) hydrogen bonds : bond 0.04374 / 3.27 ( 549) hydrogen bonds : angle 5.04183 / 3.49 ( 1584) link_BETA1-3 : bond 0.00411 / 0.22 ( 1) link_BETA1-3 : angle 2.15888 / 1.10 ( 3) link_BETA1-4 : bond 0.00597 / 0.44 ( 11) link_BETA1-4 : angle 2.55081 / 2.21 ( 33) link_BETA1-6 : bond 0.00334 / 0.18 ( 1) link_BETA1-6 : angle 2.66013 / 1.25 ( 3) link_NAG-ASN : bond 0.00454 / 0.30 ( 7) link_NAG-ASN : angle 4.56493 / 3.47 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TRP cc_start: 0.7838 (t60) cc_final: 0.7471 (m100) REVERT: A 252 SER cc_start: 0.8357 (t) cc_final: 0.7976 (m) REVERT: A 427 ASP cc_start: 0.6053 (t70) cc_final: 0.5731 (t70) REVERT: A 556 TYR cc_start: 0.7701 (m-10) cc_final: 0.6541 (t80) REVERT: A 580 LYS cc_start: 0.6033 (tptt) cc_final: 0.5295 (ttmm) REVERT: A 660 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7832 (mtm) REVERT: A 890 THR cc_start: 0.8785 (t) cc_final: 0.8581 (t) REVERT: A 908 MET cc_start: 0.8100 (tpp) cc_final: 0.7781 (tpp) REVERT: A 1094 PHE cc_start: 0.8005 (t80) cc_final: 0.7766 (t80) REVERT: A 1151 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8230 (tpp80) REVERT: A 1170 ARG cc_start: 0.7603 (mmt90) cc_final: 0.6856 (ttt90) REVERT: A 1177 MET cc_start: 0.7875 (tpp) cc_final: 0.7641 (tpp) REVERT: A 1197 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: A 1288 LEU cc_start: 0.9006 (tt) cc_final: 0.8643 (tt) REVERT: A 1415 LEU cc_start: 0.8666 (tp) cc_final: 0.8241 (tt) REVERT: A 1438 GLN cc_start: 0.8337 (tt0) cc_final: 0.7240 (tt0) REVERT: A 1439 GLN cc_start: 0.8645 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 1455 GLU cc_start: 0.8192 (tp30) cc_final: 0.7815 (mm-30) REVERT: A 1473 LYS cc_start: 0.9034 (mmtp) cc_final: 0.8646 (mmtm) outliers start: 48 outliers final: 26 residues processed: 303 average time/residue: 0.0873 time to fit residues: 38.4749 Evaluate side-chains 265 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1079 GLN Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1500 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 GLN A1234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.171623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137710 restraints weight = 16045.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141059 restraints weight = 10061.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141846 restraints weight = 6243.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141900 restraints weight = 5289.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141875 restraints weight = 5239.462| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.8813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10952 Z= 0.190 Angle : 0.880 22.025 14944 Z= 0.427 Chirality : 0.048 0.554 1765 Planarity : 0.005 0.087 1818 Dihedral : 8.003 65.757 1438 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.54 % Favored : 87.70 % Rotamer: Outliers : 5.69 % Allowed : 26.66 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 8.51 % Twisted General : 0.86 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.23), residues: 1317 helix: -0.29 (0.17), residues: 871 sheet: -2.94 (1.34), residues: 10 loop : -3.48 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1297 TYR 0.021 0.002 TYR A1089 PHE 0.021 0.002 PHE A1044 TRP 0.026 0.002 TRP A 316 HIS 0.005 0.001 HIS A1158 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (10927) covalent geometry : angle 0.85158 / 0.42 (14874) SS BOND : bond 0.01602 / 0.81 ( 5) SS BOND : angle 2.14323 / 1.54 ( 10) hydrogen bonds : bond 0.04331 / 3.21 ( 549) hydrogen bonds : angle 4.94293 / 3.42 ( 1584) link_BETA1-3 : bond 0.00348 / 0.18 ( 1) link_BETA1-3 : angle 2.18982 / 1.08 ( 3) link_BETA1-4 : bond 0.00603 / 0.45 ( 11) link_BETA1-4 : angle 2.44285 / 2.11 ( 33) link_BETA1-6 : bond 0.00490 / 0.26 ( 1) link_BETA1-6 : angle 2.50298 / 1.15 ( 3) link_NAG-ASN : bond 0.01071 / 0.82 ( 7) link_NAG-ASN : angle 4.87964 / 3.75 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7266 (m-10) REVERT: A 542 ASP cc_start: 0.6849 (m-30) cc_final: 0.6155 (p0) REVERT: A 556 TYR cc_start: 0.7764 (m-10) cc_final: 0.7029 (t80) REVERT: A 580 LYS cc_start: 0.6196 (tptt) cc_final: 0.5491 (ttmm) REVERT: A 587 ASP cc_start: 0.8205 (m-30) cc_final: 0.7931 (m-30) REVERT: A 710 MET cc_start: 0.8155 (mtm) cc_final: 0.7890 (mtm) REVERT: A 956 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8393 (t80) REVERT: A 1024 THR cc_start: 0.6432 (p) cc_final: 0.5932 (p) REVERT: A 1079 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: A 1094 PHE cc_start: 0.8102 (t80) cc_final: 0.7794 (t80) REVERT: A 1151 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8079 (tpp80) REVERT: A 1170 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6956 (ttt90) REVERT: A 1177 MET cc_start: 0.7993 (tpp) cc_final: 0.7722 (tpp) REVERT: A 1197 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: A 1346 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8220 (mp) REVERT: A 1415 LEU cc_start: 0.8927 (tp) cc_final: 0.8328 (tt) REVERT: A 1419 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7163 (mt-10) REVERT: A 1438 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: A 1439 GLN cc_start: 0.8616 (tm-30) cc_final: 0.7848 (tm-30) REVERT: A 1455 GLU cc_start: 0.7885 (tp30) cc_final: 0.6559 (mm-30) REVERT: A 1458 GLU cc_start: 0.6479 (mt-10) cc_final: 0.6098 (mt-10) REVERT: A 1473 LYS cc_start: 0.8931 (mmtp) cc_final: 0.8587 (mmtm) outliers start: 60 outliers final: 32 residues processed: 290 average time/residue: 0.0880 time to fit residues: 37.6722 Evaluate side-chains 276 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1079 GLN Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain A residue 1151 ARG Chi-restraints excluded: chain A residue 1170 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1419 GLU Chi-restraints excluded: chain A residue 1438 GLN Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1492 VAL Chi-restraints excluded: chain A residue 1500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 7 optimal weight: 50.0000 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS A 643 ASN ** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 ASN A1079 GLN ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.169209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136991 restraints weight = 16318.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138536 restraints weight = 10532.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139435 restraints weight = 8665.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139616 restraints weight = 6723.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139664 restraints weight = 6514.405| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.9497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10952 Z= 0.214 Angle : 0.892 22.675 14944 Z= 0.433 Chirality : 0.050 0.710 1765 Planarity : 0.005 0.080 1818 Dihedral : 7.768 67.014 1438 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.31 % Favored : 88.00 % Rotamer: Outliers : 5.69 % Allowed : 27.32 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 6.38 % Twisted General : 0.86 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.23), residues: 1317 helix: -0.22 (0.17), residues: 876 sheet: -2.82 (1.53), residues: 10 loop : -3.50 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 198 TYR 0.023 0.002 TYR A1089 PHE 0.022 0.002 PHE A 145 TRP 0.038 0.003 TRP A 203 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (10927) covalent geometry : angle 0.86066 / 0.43 (14874) SS BOND : bond 0.00991 / 0.52 ( 5) SS BOND : angle 1.90431 / 1.32 ( 10) hydrogen bonds : bond 0.04300 / 3.20 ( 549) hydrogen bonds : angle 4.80437 / 3.31 ( 1584) link_BETA1-3 : bond 0.00131 / 0.07 ( 1) link_BETA1-3 : angle 1.97854 / 0.98 ( 3) link_BETA1-4 : bond 0.00544 / 0.39 ( 11) link_BETA1-4 : angle 2.43551 / 2.09 ( 33) link_BETA1-6 : bond 0.00550 / 0.29 ( 1) link_BETA1-6 : angle 2.51408 / 1.17 ( 3) link_NAG-ASN : bond 0.00617 / 0.43 ( 7) link_NAG-ASN : angle 5.44359 / 4.13 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 268 time to evaluate : 0.405 Fit side-chains REVERT: A 292 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7446 (m-10) REVERT: A 531 LEU cc_start: 0.7423 (tp) cc_final: 0.7083 (tp) REVERT: A 556 TYR cc_start: 0.7928 (m-10) cc_final: 0.7148 (t80) REVERT: A 580 LYS cc_start: 0.6285 (tptt) cc_final: 0.5510 (ttmm) REVERT: A 587 ASP cc_start: 0.8373 (m-30) cc_final: 0.8074 (m-30) REVERT: A 956 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8394 (t80) REVERT: A 1170 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7183 (ttt90) REVERT: A 1197 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: A 1415 LEU cc_start: 0.8923 (tp) cc_final: 0.8539 (tp) REVERT: A 1419 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7353 (mm-30) REVERT: A 1438 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: A 1439 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 1473 LYS cc_start: 0.8883 (mmtp) cc_final: 0.8565 (mmtm) outliers start: 60 outliers final: 39 residues processed: 302 average time/residue: 0.0866 time to fit residues: 39.0516 Evaluate side-chains 286 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain A residue 1158 HIS Chi-restraints excluded: chain A residue 1170 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1419 GLU Chi-restraints excluded: chain A residue 1438 GLN Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1492 VAL Chi-restraints excluded: chain A residue 1500 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 126 optimal weight: 0.0270 chunk 73 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 ASN ** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.172073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138529 restraints weight = 16206.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139910 restraints weight = 9566.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141291 restraints weight = 6960.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141631 restraints weight = 5675.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141726 restraints weight = 5369.570| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.9814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10952 Z= 0.149 Angle : 0.852 21.307 14944 Z= 0.412 Chirality : 0.047 0.573 1765 Planarity : 0.005 0.122 1818 Dihedral : 7.428 65.223 1438 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.01 % Favored : 88.23 % Rotamer: Outliers : 3.80 % Allowed : 29.98 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.79 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.23), residues: 1317 helix: -0.05 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -3.36 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1151 TYR 0.021 0.002 TYR A1334 PHE 0.022 0.001 PHE A 577 TRP 0.048 0.002 TRP A 203 HIS 0.014 0.001 HIS A1373 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (10927) covalent geometry : angle 0.82319 / 0.41 (14874) SS BOND : bond 0.00547 / 0.27 ( 5) SS BOND : angle 1.77524 / 1.06 ( 10) hydrogen bonds : bond 0.04043 / 3.00 ( 549) hydrogen bonds : angle 4.59507 / 3.16 ( 1584) link_BETA1-3 : bond 0.00423 / 0.22 ( 1) link_BETA1-3 : angle 1.82517 / 0.91 ( 3) link_BETA1-4 : bond 0.00550 / 0.39 ( 11) link_BETA1-4 : angle 2.28857 / 1.99 ( 33) link_BETA1-6 : bond 0.00363 / 0.19 ( 1) link_BETA1-6 : angle 1.99841 / 0.94 ( 3) link_NAG-ASN : bond 0.01150 / 0.89 ( 7) link_NAG-ASN : angle 5.07300 / 3.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.373 Fit side-chains REVERT: A 292 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7677 (m-10) REVERT: A 531 LEU cc_start: 0.7637 (tp) cc_final: 0.7193 (tp) REVERT: A 556 TYR cc_start: 0.7844 (m-10) cc_final: 0.7068 (t80) REVERT: A 580 LYS cc_start: 0.6296 (tptt) cc_final: 0.5508 (ttmm) REVERT: A 615 LEU cc_start: 0.9023 (tp) cc_final: 0.8638 (tp) REVERT: A 1023 ILE cc_start: 0.5993 (OUTLIER) cc_final: 0.5251 (tp) REVERT: A 1170 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7135 (ttt90) REVERT: A 1177 MET cc_start: 0.8114 (tpp) cc_final: 0.7449 (mmm) REVERT: A 1197 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: A 1231 ASP cc_start: 0.8311 (m-30) cc_final: 0.8026 (t0) REVERT: A 1346 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 1406 TYR cc_start: 0.7960 (m-80) cc_final: 0.7531 (m-80) REVERT: A 1415 LEU cc_start: 0.8765 (tp) cc_final: 0.8185 (tt) REVERT: A 1473 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8655 (mmtm) REVERT: A 1479 ILE cc_start: 0.7952 (mt) cc_final: 0.7460 (mp) outliers start: 40 outliers final: 26 residues processed: 271 average time/residue: 0.0809 time to fit residues: 33.4375 Evaluate side-chains 263 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain A residue 1158 HIS Chi-restraints excluded: chain A residue 1170 ARG Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1500 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS A 532 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1234 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 = 0.3999 r_free = 0.3999 target = 0.171619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137874 restraints weight = 16254.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138610 restraints weight = 9834.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139639 restraints weight = 7460.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139777 restraints weight = 6763.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140012 restraints weight = 6127.920| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 1.0053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10952 Z= 0.154 Angle : 0.854 21.078 14944 Z= 0.410 Chirality : 0.047 0.550 1765 Planarity : 0.005 0.120 1818 Dihedral : 7.271 65.940 1438 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.31 % Favored : 87.93 % Rotamer: Outliers : 3.89 % Allowed : 30.17 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.79 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.23), residues: 1317 helix: 0.09 (0.17), residues: 869 sheet: None (None), residues: 0 loop : -3.35 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1268 TYR 0.019 0.002 TYR A1089 PHE 0.017 0.001 PHE A 653 TRP 0.026 0.002 TRP A 316 HIS 0.008 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (10927) covalent geometry : angle 0.82529 / 0.40 (14874) SS BOND : bond 0.00855 / 0.43 ( 5) SS BOND : angle 2.02180 / 1.16 ( 10) hydrogen bonds : bond 0.03914 / 2.92 ( 549) hydrogen bonds : angle 4.55437 / 3.13 ( 1584) link_BETA1-3 : bond 0.00392 / 0.21 ( 1) link_BETA1-3 : angle 1.77565 / 0.87 ( 3) link_BETA1-4 : bond 0.00530 / 0.38 ( 11) link_BETA1-4 : angle 2.14938 / 1.87 ( 33) link_BETA1-6 : bond 0.00408 / 0.21 ( 1) link_BETA1-6 : angle 1.89772 / 0.88 ( 3) link_NAG-ASN : bond 0.01076 / 0.83 ( 7) link_NAG-ASN : angle 5.08287 / 3.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 0.336 Fit side-chains REVERT: A 203 TRP cc_start: 0.8170 (m100) cc_final: 0.7831 (m100) REVERT: A 292 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7774 (m-10) REVERT: A 542 ASP cc_start: 0.6881 (m-30) cc_final: 0.6217 (p0) REVERT: A 556 TYR cc_start: 0.8066 (m-10) cc_final: 0.7098 (t80) REVERT: A 580 LYS cc_start: 0.6435 (tptt) cc_final: 0.5628 (ttmm) REVERT: A 615 LEU cc_start: 0.9044 (tp) cc_final: 0.8625 (tp) REVERT: A 956 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8674 (t80) REVERT: A 1170 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7107 (ttt90) REVERT: A 1231 ASP cc_start: 0.8456 (m-30) cc_final: 0.8126 (t0) REVERT: A 1346 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8295 (mp) REVERT: A 1406 TYR cc_start: 0.7990 (m-80) cc_final: 0.7538 (m-80) REVERT: A 1473 LYS cc_start: 0.9104 (mmtp) cc_final: 0.8770 (mptt) outliers start: 41 outliers final: 31 residues processed: 272 average time/residue: 0.0837 time to fit residues: 34.6212 Evaluate side-chains 269 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain A residue 1170 ARG Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1500 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 34 optimal weight: 0.0170 chunk 97 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS A 532 ASN ** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1234 ASN A1438 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.172740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139210 restraints weight = 16289.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139602 restraints weight = 10312.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140471 restraints weight = 7811.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141904 restraints weight = 6702.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141685 restraints weight = 5775.854| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 1.0331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10952 Z= 0.146 Angle : 0.850 20.242 14944 Z= 0.408 Chirality : 0.046 0.539 1765 Planarity : 0.005 0.113 1818 Dihedral : 6.847 45.649 1435 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.62 % Favored : 87.62 % Rotamer: Outliers : 3.70 % Allowed : 30.74 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.79 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.23), residues: 1317 helix: 0.22 (0.17), residues: 872 sheet: -1.90 (1.64), residues: 10 loop : -3.40 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1268 TYR 0.020 0.001 TYR A1334 PHE 0.017 0.001 PHE A1095 TRP 0.036 0.002 TRP A 922 HIS 0.005 0.001 HIS A1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (10927) covalent geometry : angle 0.82259 / 0.40 (14874) SS BOND : bond 0.00439 / 0.23 ( 5) SS BOND : angle 1.91627 / 1.05 ( 10) hydrogen bonds : bond 0.03872 / 2.87 ( 549) hydrogen bonds : angle 4.50053 / 3.09 ( 1584) link_BETA1-3 : bond 0.00415 / 0.22 ( 1) link_BETA1-3 : angle 1.65782 / 0.82 ( 3) link_BETA1-4 : bond 0.00521 / 0.38 ( 11) link_BETA1-4 : angle 2.04833 / 1.79 ( 33) link_BETA1-6 : bond 0.00384 / 0.20 ( 1) link_BETA1-6 : angle 1.74509 / 0.81 ( 3) link_NAG-ASN : bond 0.01086 / 0.84 ( 7) link_NAG-ASN : angle 5.05287 / 3.88 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 255 time to evaluate : 0.311 Fit side-chains REVERT: A 292 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: A 306 TRP cc_start: 0.7788 (t60) cc_final: 0.7569 (t60) REVERT: A 556 TYR cc_start: 0.7991 (m-10) cc_final: 0.7098 (t80) REVERT: A 580 LYS cc_start: 0.6404 (tptt) cc_final: 0.5608 (ttmm) REVERT: A 615 LEU cc_start: 0.9068 (tp) cc_final: 0.8719 (tp) REVERT: A 692 MET cc_start: 0.8054 (mmm) cc_final: 0.7482 (mmt) REVERT: A 707 TRP cc_start: 0.8754 (m100) cc_final: 0.8499 (m-10) REVERT: A 957 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8412 (tpp80) REVERT: A 1010 LYS cc_start: 0.7883 (pttm) cc_final: 0.7640 (pttm) REVERT: A 1170 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7111 (ttt90) REVERT: A 1177 MET cc_start: 0.8143 (tpp) cc_final: 0.7915 (mpp) REVERT: A 1231 ASP cc_start: 0.8438 (m-30) cc_final: 0.8094 (t0) REVERT: A 1346 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 1406 TYR cc_start: 0.7992 (m-80) cc_final: 0.7491 (m-80) REVERT: A 1473 LYS cc_start: 0.9028 (mmtp) cc_final: 0.8685 (mptt) outliers start: 39 outliers final: 26 residues processed: 276 average time/residue: 0.0814 time to fit residues: 33.9786 Evaluate side-chains 268 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain A residue 1170 ARG Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1456 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 0.6980 chunk 107 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS ** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.173303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140077 restraints weight = 16285.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140328 restraints weight = 10274.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141424 restraints weight = 7639.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142227 restraints weight = 6840.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142449 restraints weight = 5848.075| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 1.0539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10952 Z= 0.149 Angle : 0.878 20.028 14944 Z= 0.420 Chirality : 0.047 0.541 1765 Planarity : 0.005 0.113 1818 Dihedral : 6.730 44.228 1435 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.47 % Favored : 87.78 % Rotamer: Outliers : 2.94 % Allowed : 32.07 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.23), residues: 1317 helix: 0.23 (0.17), residues: 870 sheet: -1.73 (1.66), residues: 10 loop : -3.33 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1268 TYR 0.023 0.001 TYR A1089 PHE 0.021 0.001 PHE A 535 TRP 0.018 0.002 TRP A1063 HIS 0.005 0.001 HIS A1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (10927) covalent geometry : angle 0.85229 / 0.41 (14874) SS BOND : bond 0.00417 / 0.23 ( 5) SS BOND : angle 1.95918 / 1.08 ( 10) hydrogen bonds : bond 0.03847 / 2.86 ( 549) hydrogen bonds : angle 4.52866 / 3.11 ( 1584) link_BETA1-3 : bond 0.00404 / 0.21 ( 1) link_BETA1-3 : angle 1.61710 / 0.80 ( 3) link_BETA1-4 : bond 0.00524 / 0.38 ( 11) link_BETA1-4 : angle 2.00720 / 1.75 ( 33) link_BETA1-6 : bond 0.00392 / 0.21 ( 1) link_BETA1-6 : angle 1.69121 / 0.79 ( 3) link_NAG-ASN : bond 0.01071 / 0.83 ( 7) link_NAG-ASN : angle 5.03976 / 3.88 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.387 Fit side-chains REVERT: A 292 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7651 (m-80) REVERT: A 306 TRP cc_start: 0.7713 (t60) cc_final: 0.7490 (t60) REVERT: A 556 TYR cc_start: 0.7940 (m-10) cc_final: 0.7075 (t80) REVERT: A 580 LYS cc_start: 0.6363 (tptt) cc_final: 0.5578 (ttmm) REVERT: A 615 LEU cc_start: 0.9077 (tp) cc_final: 0.8701 (tp) REVERT: A 905 MET cc_start: 0.8107 (tpp) cc_final: 0.7729 (tpt) REVERT: A 999 MET cc_start: 0.8068 (tpp) cc_final: 0.7731 (tpt) REVERT: A 1010 LYS cc_start: 0.7849 (pttm) cc_final: 0.7638 (pttm) REVERT: A 1170 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7050 (ttt90) REVERT: A 1346 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8405 (mp) REVERT: A 1406 TYR cc_start: 0.7921 (m-80) cc_final: 0.7481 (m-80) REVERT: A 1473 LYS cc_start: 0.9041 (mmtp) cc_final: 0.8634 (mmtm) outliers start: 31 outliers final: 24 residues processed: 265 average time/residue: 0.0805 time to fit residues: 32.5092 Evaluate side-chains 269 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain A residue 1170 ARG Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1456 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 115 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS A 345 GLN A 532 ASN ** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 HIS ** A1438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133427 restraints weight = 16385.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133563 restraints weight = 10765.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.134437 restraints weight = 9097.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135166 restraints weight = 7285.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135448 restraints weight = 6316.915| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 1.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10952 Z= 0.240 Angle : 0.948 20.678 14944 Z= 0.459 Chirality : 0.051 0.567 1765 Planarity : 0.006 0.115 1818 Dihedral : 6.965 45.513 1435 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.84 % Allowed : 12.07 % Favored : 87.09 % Rotamer: Outliers : 3.32 % Allowed : 32.54 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.23), residues: 1317 helix: 0.09 (0.17), residues: 879 sheet: -1.89 (1.55), residues: 10 loop : -3.41 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1268 TYR 0.021 0.002 TYR A 381 PHE 0.037 0.002 PHE A 593 TRP 0.041 0.003 TRP A 707 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (10927) covalent geometry : angle 0.92142 / 0.45 (14874) SS BOND : bond 0.00687 / 0.37 ( 5) SS BOND : angle 2.25318 / 1.27 ( 10) hydrogen bonds : bond 0.04394 / 3.24 ( 549) hydrogen bonds : angle 4.77054 / 3.27 ( 1584) link_BETA1-3 : bond 0.00141 / 0.07 ( 1) link_BETA1-3 : angle 2.08304 / 1.02 ( 3) link_BETA1-4 : bond 0.00563 / 0.41 ( 11) link_BETA1-4 : angle 2.09374 / 1.77 ( 33) link_BETA1-6 : bond 0.00521 / 0.27 ( 1) link_BETA1-6 : angle 2.14133 / 0.96 ( 3) link_NAG-ASN : bond 0.01131 / 0.84 ( 7) link_NAG-ASN : angle 5.29278 / 4.03 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1819.96 seconds wall clock time: 32 minutes 10.02 seconds (1930.02 seconds total)