Starting phenix.real_space_refine on Tue Jul 29 04:07:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x0m_6698/07_2025/5x0m_6698.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x0m_6698/07_2025/5x0m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5x0m_6698/07_2025/5x0m_6698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x0m_6698/07_2025/5x0m_6698.map" model { file = "/net/cci-nas-00/data/ceres_data/5x0m_6698/07_2025/5x0m_6698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x0m_6698/07_2025/5x0m_6698.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 8, 'GLU:plan': 6, 'ARG:plan': 12} 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.98, per 1000 atoms: 0.66 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: 3.16 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.21 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: 3.88 Time building geometry restraints manager: 3.69 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: 5871 26.78 - 53.57: 509 53.57 - 80.35: 135 80.35 - 107.13: 58 107.13 - 133.91: 14 Dihedral angle restraints: 6587 sinusoidal: 2692 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 6584 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.690 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 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 : 24.001 133.913 4058 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.048 0.002 TRP A 316 HIS 0.012 0.002 HIS A 291 PHE 0.036 0.001 PHE A 684 TYR 0.081 0.002 TYR A1089 ARG 0.005 0.000 ARG A 305 Details of bonding type rmsd link_NAG-ASN : bond 0.01327 ( 7) link_NAG-ASN : angle 7.13685 ( 21) link_BETA1-4 : bond 0.00663 ( 11) link_BETA1-4 : angle 4.48506 ( 33) hydrogen bonds : bond 0.30330 ( 549) hydrogen bonds : angle 11.03970 ( 1584) link_BETA1-6 : bond 0.00219 ( 1) link_BETA1-6 : angle 3.29527 ( 3) SS BOND : bond 0.18901 ( 5) SS BOND : angle 11.37339 ( 10) link_BETA1-3 : bond 0.00305 ( 1) link_BETA1-3 : angle 2.31723 ( 3) covalent geometry : bond 0.00862 (10927) covalent geometry : angle 1.40698 (14874) *********************** 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 : 1.137 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: 0.6576 (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: 0.7450 (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: 0.7091 (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: 0.2596 time to fit residues: 159.6522 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 : 1.221 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 GLN A1194 GLN A1446 GLN A1465 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.185515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154564 restraints weight = 16137.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154984 restraints weight = 10360.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155989 restraints weight = 7650.836| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10952 Z= 0.225 Angle : 1.064 13.978 14944 Z= 0.522 Chirality : 0.052 0.519 1765 Planarity : 0.007 0.067 1818 Dihedral : 17.676 87.654 1936 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 1.90 % Allowed : 11.54 % Favored : 86.56 % Rotamer: Outliers : 6.17 % Allowed : 18.88 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 17.02 % Twisted General : 2.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.22), residues: 1317 helix: -1.41 (0.17), residues: 856 sheet: -4.75 (0.99), residues: 20 loop : -3.88 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 316 HIS 0.007 0.001 HIS A 192 PHE 0.024 0.002 PHE A 996 TYR 0.041 0.003 TYR A1089 ARG 0.012 0.001 ARG A 681 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 7) link_NAG-ASN : angle 4.70215 ( 21) link_BETA1-4 : bond 0.00625 ( 11) link_BETA1-4 : angle 3.25222 ( 33) hydrogen bonds : bond 0.06268 ( 549) hydrogen bonds : angle 6.16220 ( 1584) link_BETA1-6 : bond 0.01138 ( 1) link_BETA1-6 : angle 4.72646 ( 3) SS BOND : bond 0.01504 ( 5) SS BOND : angle 3.29327 ( 10) link_BETA1-3 : bond 0.00589 ( 1) link_BETA1-3 : angle 3.15769 ( 3) covalent geometry : bond 0.00481 (10927) covalent geometry : angle 1.03436 (14874) *********************** 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 381 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 316 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 TYR cc_start: 0.7460 (m-10) cc_final: 0.7035 (t80) REVERT: A 580 LYS cc_start: 0.5704 (tptt) cc_final: 0.5407 (tttp) REVERT: A 735 LEU cc_start: 0.7652 (tp) cc_final: 0.7134 (tt) REVERT: A 966 ASN cc_start: 0.6395 (t0) cc_final: 0.6121 (t0) REVERT: A 1042 MET cc_start: 0.7943 (mmp) cc_final: 0.7477 (mmm) REVERT: A 1052 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7307 (mp) REVERT: A 1074 ARG cc_start: 0.6853 (pmt-80) cc_final: 0.6211 (tpt170) REVERT: A 1079 GLN cc_start: 0.7794 (tp40) cc_final: 0.7542 (tp-100) REVERT: A 1170 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6654 (ttt90) REVERT: A 1231 ASP cc_start: 0.6427 (t70) cc_final: 0.6019 (t0) REVERT: A 1288 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8537 (tt) REVERT: A 1373 HIS cc_start: 0.7276 (t-90) cc_final: 0.6459 (t-90) REVERT: A 1438 GLN cc_start: 0.7931 (tt0) cc_final: 0.7448 (tt0) REVERT: A 1439 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7845 (tm-30) REVERT: A 1455 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: A 1473 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8448 (mmtm) REVERT: A 1490 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7569 (ptpp) outliers start: 65 outliers final: 21 residues processed: 356 average time/residue: 0.2799 time to fit residues: 140.9707 Evaluate side-chains 270 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 880 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 909 LEU 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 1170 ARG Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1288 LEU 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 Chi-restraints excluded: chain A residue 1490 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 130 optimal weight: 0.0170 chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 286 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 HIS A 555 ASN ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 GLN ** A1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.180874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147838 restraints weight = 15972.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148932 restraints weight = 10157.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150007 restraints weight = 7777.983| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10952 Z= 0.193 Angle : 0.965 18.887 14944 Z= 0.466 Chirality : 0.049 0.323 1765 Planarity : 0.007 0.146 1818 Dihedral : 12.354 70.812 1860 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.91 % Allowed : 12.00 % Favored : 87.09 % Rotamer: Outliers : 5.50 % Allowed : 21.73 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 10.64 % Twisted General : 1.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.22), residues: 1317 helix: -0.72 (0.17), residues: 869 sheet: None (None), residues: 0 loop : -3.76 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 316 HIS 0.009 0.002 HIS A1227 PHE 0.044 0.002 PHE A1501 TYR 0.026 0.002 TYR A1089 ARG 0.010 0.001 ARG A1268 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 7) link_NAG-ASN : angle 4.00880 ( 21) link_BETA1-4 : bond 0.00558 ( 11) link_BETA1-4 : angle 3.40861 ( 33) hydrogen bonds : bond 0.05017 ( 549) hydrogen bonds : angle 5.47392 ( 1584) link_BETA1-6 : bond 0.00733 ( 1) link_BETA1-6 : angle 4.79728 ( 3) SS BOND : bond 0.00306 ( 5) SS BOND : angle 1.82870 ( 10) link_BETA1-3 : bond 0.00555 ( 1) link_BETA1-3 : angle 2.69890 ( 3) covalent geometry : bond 0.00408 (10927) covalent geometry : angle 0.93743 (14874) *********************** 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 342 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 TYR cc_start: 0.7929 (m-80) cc_final: 0.7531 (m-80) REVERT: A 427 ASP cc_start: 0.5684 (t0) cc_final: 0.5355 (t70) REVERT: A 542 ASP cc_start: 0.6648 (m-30) cc_final: 0.5973 (p0) REVERT: A 556 TYR cc_start: 0.7409 (m-10) cc_final: 0.6403 (t80) REVERT: A 580 LYS cc_start: 0.5828 (tptt) cc_final: 0.5431 (tttp) REVERT: A 660 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7344 (mtm) REVERT: A 662 LEU cc_start: 0.7585 (tt) cc_final: 0.7380 (tp) REVERT: A 692 MET cc_start: 0.7353 (tpp) cc_final: 0.7047 (tpp) REVERT: A 908 MET cc_start: 0.7471 (tpp) cc_final: 0.7224 (tpp) REVERT: A 966 ASN cc_start: 0.7230 (t0) cc_final: 0.6840 (t0) REVERT: A 1052 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7451 (mt) REVERT: A 1170 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6636 (ttt90) REVERT: A 1177 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6975 (mmm) REVERT: A 1196 MET cc_start: 0.6791 (mmp) cc_final: 0.6551 (ppp) REVERT: A 1200 GLU cc_start: 0.7423 (tt0) cc_final: 0.7204 (tt0) REVERT: A 1227 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6865 (m90) REVERT: A 1288 LEU cc_start: 0.8779 (tt) cc_final: 0.8517 (tt) REVERT: A 1335 ASN cc_start: 0.7623 (p0) cc_final: 0.7357 (p0) REVERT: A 1432 MET cc_start: 0.6528 (ppp) cc_final: 0.5801 (ppp) REVERT: A 1438 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: A 1439 GLN cc_start: 0.8569 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 1455 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6237 (mm-30) REVERT: A 1473 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8484 (mptt) outliers start: 58 outliers final: 33 residues processed: 305 average time/residue: 0.2316 time to fit residues: 102.3519 Evaluate side-chains 292 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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 400 VAL Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 886 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 912 VAL Chi-restraints excluded: chain A residue 938 VAL 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 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 1170 ARG Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1227 HIS Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1438 GLN Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1456 LEU 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 38 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 40.0000 chunk 51 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN ** A1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.172209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140394 restraints weight = 16003.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141257 restraints weight = 10535.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142596 restraints weight = 8415.052| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.8033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10952 Z= 0.252 Angle : 0.974 22.406 14944 Z= 0.480 Chirality : 0.050 0.235 1765 Planarity : 0.006 0.082 1818 Dihedral : 9.705 59.542 1858 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.91 % Allowed : 11.01 % Favored : 88.08 % Rotamer: Outliers : 6.45 % Allowed : 24.95 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 4.26 % Twisted General : 1.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.22), residues: 1317 helix: -0.58 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -3.41 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 715 HIS 0.006 0.002 HIS A 315 PHE 0.032 0.002 PHE A 687 TYR 0.037 0.003 TYR A1089 ARG 0.007 0.001 ARG A1268 Details of bonding type rmsd link_NAG-ASN : bond 0.01077 ( 7) link_NAG-ASN : angle 3.44902 ( 21) link_BETA1-4 : bond 0.00666 ( 11) link_BETA1-4 : angle 3.02774 ( 33) hydrogen bonds : bond 0.04940 ( 549) hydrogen bonds : angle 5.15108 ( 1584) link_BETA1-6 : bond 0.00443 ( 1) link_BETA1-6 : angle 3.95587 ( 3) SS BOND : bond 0.01228 ( 5) SS BOND : angle 2.19825 ( 10) link_BETA1-3 : bond 0.00482 ( 1) link_BETA1-3 : angle 2.40187 ( 3) covalent geometry : bond 0.00560 (10927) covalent geometry : angle 0.95275 (14874) *********************** 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 345 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 277 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.8396 (t) cc_final: 0.7919 (m) REVERT: A 336 MET cc_start: 0.7795 (mpp) cc_final: 0.7457 (mpp) REVERT: A 393 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7695 (pt) REVERT: A 400 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8950 (t) REVERT: A 402 TYR cc_start: 0.8307 (m-80) cc_final: 0.7996 (m-80) REVERT: A 556 TYR cc_start: 0.7676 (m-10) cc_final: 0.7327 (t80) REVERT: A 580 LYS cc_start: 0.6072 (tptt) cc_final: 0.5385 (ttmm) REVERT: A 616 ARG cc_start: 0.8494 (mtt-85) cc_final: 0.8190 (mtm-85) REVERT: A 908 MET cc_start: 0.7823 (tpp) cc_final: 0.7600 (tpp) REVERT: A 966 ASN cc_start: 0.7884 (t0) cc_final: 0.7642 (t0) REVERT: A 1042 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8602 (mmm) REVERT: A 1074 ARG cc_start: 0.6087 (OUTLIER) cc_final: 0.5279 (tpp-160) REVERT: A 1079 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7706 (tp-100) REVERT: A 1094 PHE cc_start: 0.7953 (t80) cc_final: 0.7702 (t80) REVERT: A 1170 ARG cc_start: 0.7465 (mmt90) cc_final: 0.6947 (ttt90) REVERT: A 1234 ASN cc_start: 0.6778 (m-40) cc_final: 0.6507 (m-40) REVERT: A 1288 LEU cc_start: 0.8931 (tt) cc_final: 0.8677 (tt) REVERT: A 1415 LEU cc_start: 0.8726 (tp) cc_final: 0.8308 (tt) REVERT: A 1429 ASP cc_start: 0.5707 (m-30) cc_final: 0.4943 (m-30) REVERT: A 1432 MET cc_start: 0.6643 (ppp) cc_final: 0.5992 (ppp) REVERT: A 1439 GLN cc_start: 0.8684 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 1449 ARG cc_start: 0.5885 (ttm-80) cc_final: 0.5656 (ttm170) REVERT: A 1473 LYS cc_start: 0.8908 (mmtp) cc_final: 0.8554 (mmtm) outliers start: 68 outliers final: 25 residues processed: 308 average time/residue: 0.2239 time to fit residues: 99.7050 Evaluate side-chains 265 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP 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 318 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 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 909 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain A residue 1079 GLN Chi-restraints excluded: chain A residue 1109 CYS Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1141 MET 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 1456 LEU Chi-restraints excluded: chain A residue 1497 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** A1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.172549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140284 restraints weight = 16082.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140230 restraints weight = 10470.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142127 restraints weight = 8151.368| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.8726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10952 Z= 0.182 Angle : 0.875 23.021 14944 Z= 0.422 Chirality : 0.047 0.230 1765 Planarity : 0.005 0.082 1818 Dihedral : 8.517 56.414 1843 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.79 % Favored : 89.52 % Rotamer: Outliers : 5.03 % Allowed : 25.43 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 6.38 % Twisted General : 0.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.23), residues: 1317 helix: -0.27 (0.17), residues: 876 sheet: -4.43 (1.06), residues: 10 loop : -3.44 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 316 HIS 0.005 0.001 HIS A 192 PHE 0.019 0.002 PHE A 927 TYR 0.025 0.002 TYR A1089 ARG 0.008 0.001 ARG A 386 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 7) link_NAG-ASN : angle 3.76830 ( 21) link_BETA1-4 : bond 0.00739 ( 11) link_BETA1-4 : angle 2.58771 ( 33) hydrogen bonds : bond 0.04280 ( 549) hydrogen bonds : angle 4.89287 ( 1584) link_BETA1-6 : bond 0.00460 ( 1) link_BETA1-6 : angle 2.99795 ( 3) SS BOND : bond 0.01284 ( 5) SS BOND : angle 1.34508 ( 10) link_BETA1-3 : bond 0.00574 ( 1) link_BETA1-3 : angle 2.04702 ( 3) covalent geometry : bond 0.00409 (10927) covalent geometry : angle 0.85477 (14874) *********************** 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: 53 poor density : 263 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7687 (mpp) cc_final: 0.7366 (mpp) REVERT: A 542 ASP cc_start: 0.6890 (m-30) cc_final: 0.5900 (p0) REVERT: A 555 ASN cc_start: 0.7971 (t0) cc_final: 0.7348 (t0) REVERT: A 556 TYR cc_start: 0.7607 (m-10) cc_final: 0.6902 (t80) REVERT: A 580 LYS cc_start: 0.6123 (tptt) cc_final: 0.5419 (ttmm) REVERT: A 710 MET cc_start: 0.8207 (mtm) cc_final: 0.7918 (mtm) REVERT: A 905 MET cc_start: 0.7890 (tpt) cc_final: 0.7078 (tpt) REVERT: A 1094 PHE cc_start: 0.8043 (t80) cc_final: 0.7800 (t80) REVERT: A 1170 ARG cc_start: 0.7634 (mmt90) cc_final: 0.6950 (ttt90) REVERT: A 1380 ASN cc_start: 0.7370 (t0) cc_final: 0.7167 (t0) REVERT: A 1415 LEU cc_start: 0.8852 (tp) cc_final: 0.8237 (tt) REVERT: A 1419 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: A 1429 ASP cc_start: 0.5876 (m-30) cc_final: 0.5237 (m-30) REVERT: A 1432 MET cc_start: 0.6644 (ppp) cc_final: 0.6071 (ppp) REVERT: A 1438 GLN cc_start: 0.8434 (tt0) cc_final: 0.8226 (tm-30) REVERT: A 1439 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8178 (tm-30) REVERT: A 1449 ARG cc_start: 0.5880 (ttm-80) cc_final: 0.5619 (ttm170) REVERT: A 1473 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8606 (mmtm) outliers start: 53 outliers final: 30 residues processed: 298 average time/residue: 0.2082 time to fit residues: 88.9059 Evaluate side-chains 271 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL 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 375 ASP 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 875 LEU Chi-restraints excluded: chain A residue 892 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1032 HIS 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 1143 THR Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1419 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1492 VAL Chi-restraints excluded: chain A residue 1497 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 118 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 HIS A1438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.170224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138023 restraints weight = 16312.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.138654 restraints weight = 10705.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139948 restraints weight = 8730.703| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.9319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10952 Z= 0.195 Angle : 0.864 21.698 14944 Z= 0.419 Chirality : 0.046 0.243 1765 Planarity : 0.005 0.075 1818 Dihedral : 7.829 50.726 1843 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.68 % Allowed : 10.86 % Favored : 88.46 % Rotamer: Outliers : 4.74 % Allowed : 27.51 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.23), residues: 1317 helix: -0.15 (0.17), residues: 879 sheet: -3.78 (1.14), residues: 10 loop : -3.41 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 203 HIS 0.004 0.001 HIS A1227 PHE 0.023 0.002 PHE A 609 TYR 0.022 0.002 TYR A 355 ARG 0.024 0.001 ARG A 616 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 7) link_NAG-ASN : angle 3.49865 ( 21) link_BETA1-4 : bond 0.00604 ( 11) link_BETA1-4 : angle 2.49697 ( 33) hydrogen bonds : bond 0.04195 ( 549) hydrogen bonds : angle 4.76516 ( 1584) link_BETA1-6 : bond 0.00539 ( 1) link_BETA1-6 : angle 2.75249 ( 3) SS BOND : bond 0.01420 ( 5) SS BOND : angle 1.38990 ( 10) link_BETA1-3 : bond 0.00573 ( 1) link_BETA1-3 : angle 1.87802 ( 3) covalent geometry : bond 0.00442 (10927) covalent geometry : angle 0.84625 (14874) *********************** 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 315 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.7724 (mpp) cc_final: 0.7477 (mpp) REVERT: A 556 TYR cc_start: 0.7685 (m-10) cc_final: 0.7114 (t80) REVERT: A 580 LYS cc_start: 0.6217 (tptt) cc_final: 0.5486 (ttmm) REVERT: A 886 LEU cc_start: 0.8723 (mt) cc_final: 0.8306 (mt) REVERT: A 1067 MET cc_start: 0.7983 (mtt) cc_final: 0.7675 (mtt) REVERT: A 1170 ARG cc_start: 0.7800 (mmt90) cc_final: 0.7207 (ttt90) REVERT: A 1283 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6381 (tmm-80) REVERT: A 1294 LYS cc_start: 0.7909 (tttm) cc_final: 0.7676 (tttm) REVERT: A 1380 ASN cc_start: 0.7290 (t0) cc_final: 0.6991 (t0) REVERT: A 1415 LEU cc_start: 0.8913 (tp) cc_final: 0.8270 (tt) REVERT: A 1416 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8029 (tm-30) REVERT: A 1419 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: A 1429 ASP cc_start: 0.5778 (m-30) cc_final: 0.5245 (m-30) REVERT: A 1432 MET cc_start: 0.6661 (ppp) cc_final: 0.6214 (ppp) REVERT: A 1439 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8452 (tm-30) REVERT: A 1449 ARG cc_start: 0.5874 (ttm-80) cc_final: 0.5646 (ttm170) REVERT: A 1473 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8503 (mmtm) outliers start: 50 outliers final: 35 residues processed: 293 average time/residue: 0.1985 time to fit residues: 84.8063 Evaluate side-chains 284 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 283 VAL Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 662 LEU 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 890 THR 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 963 SER Chi-restraints excluded: chain A residue 1032 HIS 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 1143 THR Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1158 HIS Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1419 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1497 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 80 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 33 optimal weight: 0.5980 chunk 126 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.169580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137678 restraints weight = 16594.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139505 restraints weight = 10850.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.140526 restraints weight = 8050.346| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.9739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10952 Z= 0.169 Angle : 0.843 22.516 14944 Z= 0.407 Chirality : 0.045 0.240 1765 Planarity : 0.005 0.122 1818 Dihedral : 7.389 49.038 1843 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.48 % Favored : 88.76 % Rotamer: Outliers : 4.36 % Allowed : 28.75 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.23), residues: 1317 helix: -0.02 (0.17), residues: 882 sheet: -3.26 (1.06), residues: 10 loop : -3.41 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 316 HIS 0.006 0.001 HIS A1227 PHE 0.021 0.001 PHE A 145 TYR 0.021 0.002 TYR A 355 ARG 0.008 0.001 ARG A 616 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 7) link_NAG-ASN : angle 3.34860 ( 21) link_BETA1-4 : bond 0.00588 ( 11) link_BETA1-4 : angle 2.38328 ( 33) hydrogen bonds : bond 0.03999 ( 549) hydrogen bonds : angle 4.64358 ( 1584) link_BETA1-6 : bond 0.00524 ( 1) link_BETA1-6 : angle 2.49826 ( 3) SS BOND : bond 0.00421 ( 5) SS BOND : angle 1.21647 ( 10) link_BETA1-3 : bond 0.00650 ( 1) link_BETA1-3 : angle 1.90740 ( 3) covalent geometry : bond 0.00382 (10927) covalent geometry : angle 0.82580 (14874) *********************** 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 309 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: A 336 MET cc_start: 0.7687 (mpp) cc_final: 0.7429 (mpp) REVERT: A 542 ASP cc_start: 0.6648 (m-30) cc_final: 0.6415 (p0) REVERT: A 556 TYR cc_start: 0.7838 (m-10) cc_final: 0.7201 (t80) REVERT: A 580 LYS cc_start: 0.6261 (tptt) cc_final: 0.5519 (ttmm) REVERT: A 886 LEU cc_start: 0.8759 (mt) cc_final: 0.8299 (mt) REVERT: A 905 MET cc_start: 0.8103 (tpt) cc_final: 0.7537 (tpt) REVERT: A 1067 MET cc_start: 0.8200 (mtt) cc_final: 0.7763 (mtt) REVERT: A 1170 ARG cc_start: 0.7793 (mmt90) cc_final: 0.7223 (ttt90) REVERT: A 1283 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6280 (tmm-80) REVERT: A 1294 LYS cc_start: 0.7955 (tttm) cc_final: 0.7714 (tttm) REVERT: A 1373 HIS cc_start: 0.6269 (t-90) cc_final: 0.6045 (t-90) REVERT: A 1380 ASN cc_start: 0.7347 (t0) cc_final: 0.7124 (t0) REVERT: A 1416 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 1419 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: A 1429 ASP cc_start: 0.5687 (m-30) cc_final: 0.5236 (m-30) REVERT: A 1432 MET cc_start: 0.6619 (ppp) cc_final: 0.6198 (ppp) REVERT: A 1439 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8396 (tm-30) REVERT: A 1449 ARG cc_start: 0.5924 (ttm-80) cc_final: 0.5678 (ttm170) REVERT: A 1473 LYS cc_start: 0.8853 (mmtp) cc_final: 0.8600 (mmtm) REVERT: A 1479 ILE cc_start: 0.8099 (mt) cc_final: 0.7600 (mt) outliers start: 46 outliers final: 33 residues processed: 287 average time/residue: 0.1961 time to fit residues: 82.1351 Evaluate side-chains 281 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 292 PHE Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 662 LEU 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 890 THR 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 1091 TYR 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 1143 THR Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1158 HIS Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1419 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1497 VAL 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 111 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 409 ASN ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 HIS ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1461 GLN A1470 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.167906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136212 restraints weight = 16363.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136890 restraints weight = 10636.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138098 restraints weight = 8585.442| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 1.0327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10952 Z= 0.185 Angle : 0.852 22.107 14944 Z= 0.413 Chirality : 0.045 0.252 1765 Planarity : 0.005 0.122 1818 Dihedral : 7.129 47.690 1843 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.09 % Favored : 88.15 % Rotamer: Outliers : 4.17 % Allowed : 29.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.23), residues: 1317 helix: 0.06 (0.17), residues: 876 sheet: -2.54 (1.26), residues: 10 loop : -3.37 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 922 HIS 0.009 0.001 HIS A 315 PHE 0.018 0.002 PHE A 145 TYR 0.031 0.002 TYR A1489 ARG 0.013 0.001 ARG A1503 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 7) link_NAG-ASN : angle 3.37147 ( 21) link_BETA1-4 : bond 0.00573 ( 11) link_BETA1-4 : angle 2.25326 ( 33) hydrogen bonds : bond 0.04051 ( 549) hydrogen bonds : angle 4.64400 ( 1584) link_BETA1-6 : bond 0.00611 ( 1) link_BETA1-6 : angle 2.38918 ( 3) SS BOND : bond 0.00602 ( 5) SS BOND : angle 1.30825 ( 10) link_BETA1-3 : bond 0.00548 ( 1) link_BETA1-3 : angle 1.81830 ( 3) covalent geometry : bond 0.00418 (10927) covalent geometry : angle 0.83608 (14874) *********************** 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 321 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7564 (m-80) REVERT: A 336 MET cc_start: 0.7718 (mpp) cc_final: 0.7509 (mpp) REVERT: A 556 TYR cc_start: 0.7957 (m-10) cc_final: 0.7292 (t80) REVERT: A 580 LYS cc_start: 0.6337 (tptt) cc_final: 0.5558 (ttmm) REVERT: A 615 LEU cc_start: 0.8973 (tp) cc_final: 0.8612 (tp) REVERT: A 905 MET cc_start: 0.8228 (tpt) cc_final: 0.7844 (tpt) REVERT: A 1049 ASN cc_start: 0.8520 (m-40) cc_final: 0.8228 (m-40) REVERT: A 1067 MET cc_start: 0.8286 (mtt) cc_final: 0.7716 (mtt) REVERT: A 1078 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5777 (ttpt) REVERT: A 1170 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7247 (ttt90) REVERT: A 1198 PHE cc_start: 0.7353 (m-10) cc_final: 0.7142 (m-10) REVERT: A 1231 ASP cc_start: 0.8191 (m-30) cc_final: 0.7871 (t0) REVERT: A 1283 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6548 (tmm-80) REVERT: A 1294 LYS cc_start: 0.7937 (tttm) cc_final: 0.7620 (tttm) REVERT: A 1373 HIS cc_start: 0.6209 (t-90) cc_final: 0.5978 (t-90) REVERT: A 1416 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 1419 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: A 1432 MET cc_start: 0.6789 (ppp) cc_final: 0.6338 (ppp) REVERT: A 1473 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8627 (mptt) outliers start: 44 outliers final: 35 residues processed: 300 average time/residue: 0.1944 time to fit residues: 85.7588 Evaluate side-chains 290 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 283 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 372 VAL 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 733 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE 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 909 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1089 TYR Chi-restraints excluded: chain A residue 1091 TYR 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 1143 THR Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1158 HIS Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1419 GLU Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1497 VAL 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 57 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 GLN A1380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.171059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139121 restraints weight = 16438.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138198 restraints weight = 10612.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.139132 restraints weight = 10148.556| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 1.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10952 Z= 0.164 Angle : 0.853 21.547 14944 Z= 0.410 Chirality : 0.046 0.273 1765 Planarity : 0.005 0.114 1818 Dihedral : 6.934 46.447 1843 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.55 % Favored : 88.69 % Rotamer: Outliers : 4.08 % Allowed : 31.21 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.23), residues: 1317 helix: 0.18 (0.17), residues: 881 sheet: -2.17 (1.47), residues: 10 loop : -3.43 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 922 HIS 0.004 0.001 HIS A 540 PHE 0.026 0.001 PHE A 145 TYR 0.030 0.002 TYR A1489 ARG 0.012 0.001 ARG A1268 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 7) link_NAG-ASN : angle 3.25544 ( 21) link_BETA1-4 : bond 0.00579 ( 11) link_BETA1-4 : angle 2.18965 ( 33) hydrogen bonds : bond 0.03936 ( 549) hydrogen bonds : angle 4.61838 ( 1584) link_BETA1-6 : bond 0.00474 ( 1) link_BETA1-6 : angle 2.17710 ( 3) SS BOND : bond 0.00476 ( 5) SS BOND : angle 1.05220 ( 10) link_BETA1-3 : bond 0.00645 ( 1) link_BETA1-3 : angle 1.85222 ( 3) covalent geometry : bond 0.00368 (10927) covalent geometry : angle 0.83850 (14874) *********************** 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 307 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 264 time to evaluate : 1.138 Fit side-chains REVERT: A 203 TRP cc_start: 0.8103 (t60) cc_final: 0.7786 (m100) REVERT: A 292 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: A 524 PHE cc_start: 0.8294 (t80) cc_final: 0.7812 (t80) REVERT: A 556 TYR cc_start: 0.7912 (m-10) cc_final: 0.7562 (t80) REVERT: A 580 LYS cc_start: 0.6479 (tptt) cc_final: 0.5670 (ttmm) REVERT: A 615 LEU cc_start: 0.9076 (tp) cc_final: 0.8750 (tp) REVERT: A 692 MET cc_start: 0.8262 (mmm) cc_final: 0.7189 (mmm) REVERT: A 902 VAL cc_start: 0.9548 (t) cc_final: 0.9332 (m) REVERT: A 905 MET cc_start: 0.8119 (tpt) cc_final: 0.7532 (tpt) REVERT: A 1049 ASN cc_start: 0.8485 (m-40) cc_final: 0.8207 (m-40) REVERT: A 1078 LYS cc_start: 0.6346 (OUTLIER) cc_final: 0.5928 (ttpt) REVERT: A 1170 ARG cc_start: 0.7928 (mmt90) cc_final: 0.7068 (ttt90) REVERT: A 1198 PHE cc_start: 0.7393 (m-10) cc_final: 0.7186 (m-10) REVERT: A 1231 ASP cc_start: 0.8229 (m-30) cc_final: 0.7891 (t0) REVERT: A 1283 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6567 (tmm-80) REVERT: A 1285 MET cc_start: 0.7478 (tpp) cc_final: 0.6836 (mmp) REVERT: A 1294 LYS cc_start: 0.7933 (tttm) cc_final: 0.7708 (tttm) REVERT: A 1373 HIS cc_start: 0.6241 (t-90) cc_final: 0.6002 (t-90) REVERT: A 1406 TYR cc_start: 0.7877 (m-80) cc_final: 0.7263 (m-80) REVERT: A 1419 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: A 1473 LYS cc_start: 0.8973 (mmtp) cc_final: 0.8607 (mptt) outliers start: 43 outliers final: 29 residues processed: 292 average time/residue: 0.1902 time to fit residues: 83.3299 Evaluate side-chains 281 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 292 PHE Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 372 VAL 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 733 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 891 LEU 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 956 PHE Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1079 GLN Chi-restraints excluded: chain A residue 1091 TYR 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 1147 LYS Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1419 GLU 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 122 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.169087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136807 restraints weight = 16539.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137705 restraints weight = 10458.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.139049 restraints weight = 8179.394| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 1.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.231 10952 Z= 0.314 Angle : 1.242 59.181 14944 Z= 0.688 Chirality : 0.047 0.257 1765 Planarity : 0.006 0.113 1818 Dihedral : 6.960 46.452 1843 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.71 % Favored : 88.46 % Rotamer: Outliers : 3.42 % Allowed : 31.97 % Favored : 64.61 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.23), residues: 1317 helix: 0.17 (0.17), residues: 881 sheet: -2.13 (1.50), residues: 10 loop : -3.43 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 922 HIS 0.004 0.001 HIS A 540 PHE 0.097 0.002 PHE A 521 TYR 0.102 0.002 TYR A1089 ARG 0.014 0.001 ARG A1503 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 7) link_NAG-ASN : angle 3.25803 ( 21) link_BETA1-4 : bond 0.00557 ( 11) link_BETA1-4 : angle 2.23289 ( 33) hydrogen bonds : bond 0.03948 ( 549) hydrogen bonds : angle 4.62739 ( 1584) link_BETA1-6 : bond 0.00459 ( 1) link_BETA1-6 : angle 2.21336 ( 3) SS BOND : bond 0.00154 ( 5) SS BOND : angle 4.21264 ( 10) link_BETA1-3 : bond 0.00635 ( 1) link_BETA1-3 : angle 1.97276 ( 3) covalent geometry : bond 0.00708 (10927) covalent geometry : angle 1.22851 (14874) ********************** 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 286 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 1.209 Fit side-chains REVERT: A 203 TRP cc_start: 0.7997 (t60) cc_final: 0.7782 (m100) REVERT: A 292 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: A 524 PHE cc_start: 0.8253 (t80) cc_final: 0.7799 (t80) REVERT: A 556 TYR cc_start: 0.7862 (m-10) cc_final: 0.7589 (t80) REVERT: A 580 LYS cc_start: 0.6439 (tptt) cc_final: 0.5640 (ttmm) REVERT: A 615 LEU cc_start: 0.9073 (tp) cc_final: 0.8745 (tp) REVERT: A 902 VAL cc_start: 0.9518 (t) cc_final: 0.9313 (m) REVERT: A 905 MET cc_start: 0.8089 (tpt) cc_final: 0.7490 (tpt) REVERT: A 1049 ASN cc_start: 0.8496 (m-40) cc_final: 0.8211 (m-40) REVERT: A 1078 LYS cc_start: 0.6475 (OUTLIER) cc_final: 0.6171 (ttpt) REVERT: A 1170 ARG cc_start: 0.7864 (mmt90) cc_final: 0.7103 (ttt90) REVERT: A 1231 ASP cc_start: 0.8143 (m-30) cc_final: 0.7830 (t0) REVERT: A 1283 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6537 (tmm-80) REVERT: A 1285 MET cc_start: 0.7447 (tpp) cc_final: 0.6826 (mmp) REVERT: A 1294 LYS cc_start: 0.7895 (tttm) cc_final: 0.7688 (tttm) REVERT: A 1373 HIS cc_start: 0.6166 (t-90) cc_final: 0.5960 (t-90) REVERT: A 1406 TYR cc_start: 0.7894 (m-80) cc_final: 0.7261 (m-80) REVERT: A 1419 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: A 1473 LYS cc_start: 0.8909 (mmtp) cc_final: 0.8553 (mmtm) outliers start: 36 outliers final: 28 residues processed: 272 average time/residue: 0.1876 time to fit residues: 77.2874 Evaluate side-chains 281 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 292 PHE Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 372 VAL 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 733 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 891 LEU 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 956 PHE Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1091 TYR 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 1239 LEU Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1322 MET 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 1456 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 10.0000 chunk 113 optimal weight: 0.0070 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 122 optimal weight: 0.0670 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.169033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136860 restraints weight = 16380.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137579 restraints weight = 10568.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139098 restraints weight = 8357.329| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 1.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.231 10952 Z= 0.314 Angle : 1.242 59.181 14944 Z= 0.688 Chirality : 0.047 0.257 1765 Planarity : 0.006 0.113 1818 Dihedral : 6.960 46.452 1843 Min Nonbonded Distance : 1.254 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.71 % Favored : 88.46 % Rotamer: Outliers : 3.04 % Allowed : 32.45 % Favored : 64.52 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.08 % Twisted Proline : 2.13 % Twisted General : 0.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.23), residues: 1317 helix: 0.17 (0.17), residues: 881 sheet: -2.13 (1.50), residues: 10 loop : -3.43 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 922 HIS 0.004 0.001 HIS A 540 PHE 0.097 0.002 PHE A 521 TYR 0.102 0.002 TYR A1089 ARG 0.014 0.001 ARG A1503 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 7) link_NAG-ASN : angle 3.25803 ( 21) link_BETA1-4 : bond 0.00557 ( 11) link_BETA1-4 : angle 2.23289 ( 33) hydrogen bonds : bond 0.03948 ( 549) hydrogen bonds : angle 4.62739 ( 1584) link_BETA1-6 : bond 0.00459 ( 1) link_BETA1-6 : angle 2.21336 ( 3) SS BOND : bond 0.00154 ( 5) SS BOND : angle 4.21264 ( 10) link_BETA1-3 : bond 0.00635 ( 1) link_BETA1-3 : angle 1.97274 ( 3) covalent geometry : bond 0.00708 (10927) covalent geometry : angle 1.22852 (14874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3972.50 seconds wall clock time: 71 minutes 15.95 seconds (4275.95 seconds total)