Starting phenix.real_space_refine on Fri Sep 11 21:27:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6a91_6996/09_2026/6a91_6996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a91_6996/09_2026/6a91_6996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6a91_6996/09_2026/6a91_6996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a91_6996/09_2026/6a91_6996.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6a91_6996/09_2026/6a91_6996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6a91_6996/09_2026/6a91_6996.cif" model { file = "/net/cci-nas-00/data/ceres_data/6a91_6996/09_2026/6a91_6996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a91_6996/09_2026/6a91_6996.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 74 5.16 5 C 7384 2.51 5 N 1788 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11182 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10537 Classifications: {'peptide': 1323} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 1275} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 6, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 6, 'PHE:plan': 7, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 171 Chain: "B" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 449 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 139 Unusual residues: {'9SL': 1, 'NAG': 3, 'PC1': 2} Classifications: {'undetermined': 6, 'water': 2} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.23 Number of scatterers: 11182 At special positions: 0 Unit cell: (133.102, 133.102, 122.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 2 15.00 O 1934 8.00 N 1788 7.00 C 7384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 337 " distance=1.56 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.05 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.03 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 26 " distance=2.02 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 54 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 52 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1605 " - " ASN A1015 " " NAG A1606 " - " ASN A 312 " " NAG A1607 " - " ASN A 308 " " NAG C 1 " - " ASN A 330 " " NAG D 1 " - " ASN A1034 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 431.2 milliseconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2618 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 4 sheets defined 66.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.845A pdb=" N PHE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 139 through 154 removed outlier: 3.997A pdb=" N SER A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.629A pdb=" N ILE A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 159' Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.703A pdb=" N PHE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.779A pdb=" N VAL A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.867A pdb=" N LEU A 207 " --> pdb=" O TRP A 203 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 removed outlier: 3.548A pdb=" N LEU A 226 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 227 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 228 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 230 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 237 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 240 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 removed outlier: 4.211A pdb=" N ALA A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 281 removed outlier: 3.710A pdb=" N LEU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.853A pdb=" N TRP A 316 " --> pdb=" O SER A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 360 through 374 removed outlier: 3.522A pdb=" N LEU A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.586A pdb=" N LEU A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.774A pdb=" N PHE A 396 " --> pdb=" O HIS A 392 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 405 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.744A pdb=" N LEU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 504 through 516 removed outlier: 3.521A pdb=" N GLN A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 537 removed outlier: 3.549A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 573 removed outlier: 3.875A pdb=" N LEU A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 598 removed outlier: 3.776A pdb=" N VAL A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 623 removed outlier: 3.510A pdb=" N PHE A 618 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 622 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.858A pdb=" N VAL A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 664 removed outlier: 3.776A pdb=" N PHE A 641 " --> pdb=" O SER A 637 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.588A pdb=" N ASN A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 678 Proline residue: A 675 - end of helix removed outlier: 3.958A pdb=" N ASP A 678 " --> pdb=" O PRO A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 699 removed outlier: 3.504A pdb=" N MET A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 removed outlier: 3.854A pdb=" N ASP A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 729 removed outlier: 4.003A pdb=" N PHE A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 744 removed outlier: 3.784A pdb=" N LEU A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 855 removed outlier: 4.505A pdb=" N ASN A 844 " --> pdb=" O ARG A 840 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 851 " --> pdb=" O ARG A 847 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 872 removed outlier: 3.701A pdb=" N THR A 863 " --> pdb=" O GLN A 859 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 876 removed outlier: 4.011A pdb=" N GLU A 876 " --> pdb=" O LEU A 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 873 through 876' Processing helix chain 'A' and resid 879 through 882 removed outlier: 3.666A pdb=" N GLN A 882 " --> pdb=" O TYR A 879 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 882' Processing helix chain 'A' and resid 883 through 910 removed outlier: 3.775A pdb=" N ASN A 888 " --> pdb=" O PRO A 884 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP A 894 " --> pdb=" O THR A 890 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 896 " --> pdb=" O TYR A 892 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.231A pdb=" N LYS A 916 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 918 " --> pdb=" O PHE A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 942 removed outlier: 3.567A pdb=" N TRP A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 937 " --> pdb=" O TYR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 958 removed outlier: 3.581A pdb=" N LEU A 953 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 954 " --> pdb=" O ARG A 951 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 955 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 978 removed outlier: 4.114A pdb=" N VAL A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 974 " --> pdb=" O VAL A 970 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1005 removed outlier: 3.751A pdb=" N PHE A 983 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 985 " --> pdb=" O HIS A 981 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN A1002 " --> pdb=" O ILE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1032 Processing helix chain 'A' and resid 1046 through 1057 removed outlier: 3.579A pdb=" N LEU A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1073 removed outlier: 4.026A pdb=" N ILE A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A1072 " --> pdb=" O ASN A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.894A pdb=" N PHE A1092 " --> pdb=" O MET A1088 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A1098 " --> pdb=" O PHE A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1123 removed outlier: 3.502A pdb=" N LEU A1111 " --> pdb=" O PHE A1107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A1117 " --> pdb=" O ASP A1113 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A1120 " --> pdb=" O ARG A1116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A1121 " --> pdb=" O GLN A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1141 removed outlier: 3.598A pdb=" N ALA A1139 " --> pdb=" O ILE A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1165 Processing helix chain 'A' and resid 1169 through 1176 Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1186 through 1190 removed outlier: 3.877A pdb=" N ASP A1190 " --> pdb=" O MET A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1223 removed outlier: 3.750A pdb=" N VAL A1201 " --> pdb=" O GLU A1197 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A1203 " --> pdb=" O SER A1199 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A1206 " --> pdb=" O LEU A1202 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A1209 " --> pdb=" O LEU A1205 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE A1214 " --> pdb=" O ILE A1210 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A1221 " --> pdb=" O CYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1230 Processing helix chain 'A' and resid 1231 through 1249 removed outlier: 3.586A pdb=" N ILE A1236 " --> pdb=" O PRO A1232 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP A1237 " --> pdb=" O TRP A1233 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A1248 " --> pdb=" O ALA A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1270 removed outlier: 3.820A pdb=" N LEU A1264 " --> pdb=" O SER A1260 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1267 " --> pdb=" O LEU A1263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A1269 " --> pdb=" O ARG A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1278 removed outlier: 3.545A pdb=" N ARG A1274 " --> pdb=" O ARG A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1294 removed outlier: 4.284A pdb=" N LEU A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A1291 " --> pdb=" O LEU A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1321 removed outlier: 3.612A pdb=" N ASN A1301 " --> pdb=" O ARG A1297 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A1302 " --> pdb=" O THR A1298 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A1303 " --> pdb=" O LEU A1299 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A1308 " --> pdb=" O PHE A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1349 removed outlier: 3.556A pdb=" N LEU A1345 " --> pdb=" O GLN A1341 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1352 No H-bonds generated for 'chain 'A' and resid 1350 through 1352' Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 3.727A pdb=" N VAL A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A1361 " --> pdb=" O GLY A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1396 removed outlier: 3.632A pdb=" N SER A1393 " --> pdb=" O ALA A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1402 removed outlier: 3.505A pdb=" N VAL A1401 " --> pdb=" O ILE A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1422 removed outlier: 3.806A pdb=" N TYR A1406 " --> pdb=" O VAL A1402 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A1412 " --> pdb=" O ALA A1408 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A1415 " --> pdb=" O LEU A1411 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A1419 " --> pdb=" O LEU A1415 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A1422 " --> pdb=" O TYR A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1438 removed outlier: 3.771A pdb=" N TYR A1430 " --> pdb=" O THR A1426 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A1431 " --> pdb=" O ASP A1427 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A1435 " --> pdb=" O ASP A1431 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A1438 " --> pdb=" O PHE A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1460 removed outlier: 4.045A pdb=" N GLU A1458 " --> pdb=" O SER A1454 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A1460 " --> pdb=" O LEU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1476 removed outlier: 3.599A pdb=" N LEU A1475 " --> pdb=" O LYS A1471 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER A1476 " --> pdb=" O TYR A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1505 removed outlier: 4.091A pdb=" N ALA A1495 " --> pdb=" O ASP A1491 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A1500 " --> pdb=" O LEU A1496 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A1502 " --> pdb=" O LYS A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1521 removed outlier: 3.799A pdb=" N GLN A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A1515 " --> pdb=" O GLY A1511 " (cutoff:3.500A) Proline residue: A1516 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.533A pdb=" N LEU A 344 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1009 through 1012 removed outlier: 3.672A pdb=" N THR A1036 " --> pdb=" O VAL A1012 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1447 through 1449 removed outlier: 3.568A pdb=" N ILE A1487 " --> pdb=" O ILE A1448 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 8 removed outlier: 3.560A pdb=" N LYS B 28 " --> pdb=" O GLU B 8 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1703 1.30 - 1.43: 3332 1.43 - 1.56: 6310 1.56 - 1.69: 5 1.69 - 1.82: 119 Bond restraints: 11469 Sorted by residual: bond pdb=" C12 9SL A1610 " pdb=" N11 9SL A1610 " ideal model delta sigma weight residual 1.284 1.506 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C12 9SL A1610 " pdb=" N13 9SL A1610 " ideal model delta sigma weight residual 1.370 1.490 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C CYS A 337 " pdb=" N PRO A 338 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.18e-02 7.18e+03 2.68e+01 bond pdb=" C02 9SL A1610 " pdb=" N21 9SL A1610 " ideal model delta sigma weight residual 1.345 1.445 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C21 PC1 A1609 " pdb=" O21 PC1 A1609 " ideal model delta sigma weight residual 1.331 1.423 -0.092 2.00e-02 2.50e+03 2.14e+01 ... (remaining 11464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 15082 2.84 - 5.68: 429 5.68 - 8.53: 58 8.53 - 11.37: 11 11.37 - 14.21: 4 Bond angle restraints: 15584 Sorted by residual: angle pdb=" N VAL A1492 " pdb=" CA VAL A1492 " pdb=" C VAL A1492 " ideal model delta sigma weight residual 112.96 107.11 5.85 1.00e+00 1.00e+00 3.42e+01 angle pdb=" C CYS A 337 " pdb=" N PRO A 338 " pdb=" CA PRO A 338 " ideal model delta sigma weight residual 120.38 114.78 5.60 1.03e+00 9.43e-01 2.95e+01 angle pdb=" N LEU A1425 " pdb=" CA LEU A1425 " pdb=" C LEU A1425 " ideal model delta sigma weight residual 110.91 116.47 -5.56 1.17e+00 7.31e-01 2.26e+01 angle pdb=" O12 PC1 A1609 " pdb=" P PC1 A1609 " pdb=" O14 PC1 A1609 " ideal model delta sigma weight residual 123.67 109.46 14.21 3.00e+00 1.11e-01 2.24e+01 angle pdb=" O12 PC1 A1608 " pdb=" P PC1 A1608 " pdb=" O14 PC1 A1608 " ideal model delta sigma weight residual 123.67 109.46 14.21 3.00e+00 1.11e-01 2.24e+01 ... (remaining 15579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 6125 16.07 - 32.14: 354 32.14 - 48.21: 102 48.21 - 64.28: 22 64.28 - 80.35: 15 Dihedral angle restraints: 6618 sinusoidal: 2560 harmonic: 4058 Sorted by residual: dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 164.37 -71.37 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CB CYS A 328 " pdb=" SG CYS A 328 " pdb=" SG CYS A 343 " pdb=" CB CYS A 343 " ideal model delta sinusoidal sigma weight residual -86.00 -156.97 70.97 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CA PHE A 126 " pdb=" C PHE A 126 " pdb=" N THR A 127 " pdb=" CA THR A 127 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 6615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 1750 0.159 - 0.318: 27 0.318 - 0.477: 1 0.477 - 0.636: 1 0.636 - 0.795: 1 Chirality restraints: 1780 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 330 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C1 NAG A1605 " pdb=" ND2 ASN A1015 " pdb=" C2 NAG A1605 " pdb=" O5 NAG A1605 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A1034 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 1777 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 308 " 0.079 2.00e-02 2.50e+03 3.18e-01 1.26e+03 pdb=" CG ASN A 308 " -0.097 2.00e-02 2.50e+03 pdb=" OD1 ASN A 308 " 0.201 2.00e-02 2.50e+03 pdb=" ND2 ASN A 308 " -0.556 2.00e-02 2.50e+03 pdb=" C1 NAG A1607 " 0.374 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 330 " -0.174 2.00e-02 2.50e+03 1.93e-01 4.64e+02 pdb=" CG ASN A 330 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN A 330 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 330 " 0.304 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.237 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1605 " 0.207 2.00e-02 2.50e+03 1.76e-01 3.88e+02 pdb=" C7 NAG A1605 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG A1605 " -0.039 2.00e-02 2.50e+03 pdb=" N2 NAG A1605 " -0.287 2.00e-02 2.50e+03 pdb=" O7 NAG A1605 " 0.162 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2510 2.77 - 3.30: 9827 3.30 - 3.84: 17259 3.84 - 4.37: 20375 4.37 - 4.90: 35176 Nonbonded interactions: 85147 Sorted by model distance: nonbonded pdb=" O TYR A 341 " pdb=" OG1 THR A 342 " model vdw 2.238 3.040 nonbonded pdb=" NH2 ARG A 370 " pdb=" O TYR A 376 " model vdw 2.332 3.120 nonbonded pdb=" OE2 GLU A 701 " pdb=" C04 9SL A1610 " model vdw 2.332 3.440 nonbonded pdb=" O LEU A1460 " pdb=" NE2 GLN A1465 " model vdw 2.346 3.120 nonbonded pdb=" OD1 ASP A1441 " pdb=" OG1 THR A1445 " model vdw 2.349 3.040 ... (remaining 85142 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 0.476 11485 Z= 0.466 Angle : 1.304 43.996 15623 Z= 0.640 Chirality : 0.065 0.795 1780 Planarity : 0.008 0.176 1915 Dihedral : 12.461 80.351 3973 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.80 % Favored : 91.62 % Rotamer: Outliers : 1.22 % Allowed : 5.32 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.38 (0.14), residues: 1372 helix: -4.45 (0.08), residues: 821 sheet: -3.47 (1.12), residues: 20 loop : -3.61 (0.22), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 696 TYR 0.044 0.004 TYR A1313 PHE 0.045 0.003 PHE B 47 TRP 0.059 0.005 TRP A 993 HIS 0.017 0.003 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00903 / 0.41 (11469) covalent geometry : angle 1.14362 / 0.59 (15584) SS BOND : bond 0.15867 / 8.35 ( 9) SS BOND : angle 12.82852 / 7.08 ( 18) hydrogen bonds : bond 0.32553 / 23.86 ( 492) hydrogen bonds : angle 10.25253 / 7.21 ( 1386) link_BETA1-4 : bond 0.00518 / 0.25 ( 2) link_BETA1-4 : angle 6.46518 / 3.72 ( 6) link_NAG-ASN : bond 0.05876 / 4.04 ( 5) link_NAG-ASN : angle 14.11773 / 10.66 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 256 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6542 (tm-30) REVERT: A 424 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7825 (mtpt) REVERT: A 571 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8073 (mm) REVERT: A 587 ASP cc_start: 0.8056 (t70) cc_final: 0.7766 (t0) REVERT: A 665 MET cc_start: 0.7745 (mmm) cc_final: 0.7451 (mmm) REVERT: A 856 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7700 (ptmt) REVERT: A 910 PHE cc_start: 0.7854 (m-10) cc_final: 0.7410 (m-80) REVERT: A 977 GLU cc_start: 0.8136 (tp30) cc_final: 0.7839 (tp30) REVERT: A 1125 LEU cc_start: 0.8336 (mp) cc_final: 0.8095 (mp) REVERT: A 1147 LYS cc_start: 0.8380 (mttm) cc_final: 0.8057 (mtmm) REVERT: A 1173 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7741 (mt-10) REVERT: A 1198 PHE cc_start: 0.8504 (t80) cc_final: 0.8221 (t80) REVERT: A 1235 ILE cc_start: 0.8754 (tt) cc_final: 0.8552 (mt) REVERT: A 1310 MET cc_start: 0.8885 (mtp) cc_final: 0.8685 (mtm) REVERT: B 53 VAL cc_start: 0.9079 (t) cc_final: 0.8801 (m) outliers start: 14 outliers final: 2 residues processed: 266 average time/residue: 0.1119 time to fit residues: 40.8426 Evaluate side-chains 165 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 571 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS A 202 ASN A 291 HIS A 532 ASN A1056 GLN A1085 ASN A1118 GLN A1169 ASN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1470 ASN A1478 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106411 restraints weight = 16123.077| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.04 r_work: 0.3096 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11485 Z= 0.126 Angle : 0.681 10.947 15623 Z= 0.343 Chirality : 0.044 0.420 1780 Planarity : 0.005 0.050 1915 Dihedral : 8.086 65.664 1559 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.92 % Favored : 92.93 % Rotamer: Outliers : 3.23 % Allowed : 9.51 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.18), residues: 1372 helix: -2.55 (0.14), residues: 826 sheet: -3.07 (0.77), residues: 36 loop : -3.10 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1268 TYR 0.018 0.001 TYR A1313 PHE 0.016 0.001 PHE A1095 TRP 0.029 0.002 TRP A1063 HIS 0.006 0.001 HIS A1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (11469) covalent geometry : angle 0.65555 / 0.34 (15584) SS BOND : bond 0.00241 / 0.16 ( 9) SS BOND : angle 1.08171 / 0.80 ( 18) hydrogen bonds : bond 0.05574 / 4.06 ( 492) hydrogen bonds : angle 4.99410 / 3.47 ( 1386) link_BETA1-4 : bond 0.00742 / 0.36 ( 2) link_BETA1-4 : angle 4.03434 / 2.33 ( 6) link_NAG-ASN : bond 0.01111 / 0.64 ( 5) link_NAG-ASN : angle 5.34493 / 3.79 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6611 (tm-30) REVERT: A 197 LEU cc_start: 0.8544 (mm) cc_final: 0.8138 (mm) REVERT: A 324 GLU cc_start: 0.8885 (pm20) cc_final: 0.8240 (tt0) REVERT: A 424 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7903 (mtpt) REVERT: A 546 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7964 (mm-30) REVERT: A 629 ASN cc_start: 0.8760 (m-40) cc_final: 0.8534 (m-40) REVERT: A 631 MET cc_start: 0.8071 (mmm) cc_final: 0.7475 (mtt) REVERT: A 651 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9097 (mt) REVERT: A 856 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7809 (ptmt) REVERT: A 857 TYR cc_start: 0.8348 (m-10) cc_final: 0.8112 (m-10) REVERT: A 926 ASP cc_start: 0.8444 (t0) cc_final: 0.8122 (t70) REVERT: A 977 GLU cc_start: 0.8974 (tp30) cc_final: 0.8709 (tp30) REVERT: A 1125 LEU cc_start: 0.8481 (mp) cc_final: 0.8145 (mp) REVERT: A 1147 LYS cc_start: 0.8478 (mttm) cc_final: 0.8214 (mtmm) REVERT: A 1173 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8050 (mt-10) REVERT: A 1235 ILE cc_start: 0.9053 (tt) cc_final: 0.8835 (mt) REVERT: A 1289 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8445 (mt) REVERT: A 1428 ASP cc_start: 0.8029 (t0) cc_final: 0.7711 (t0) REVERT: A 1432 MET cc_start: 0.9076 (ttp) cc_final: 0.8555 (tmm) REVERT: A 1470 ASN cc_start: 0.5760 (OUTLIER) cc_final: 0.5356 (p0) REVERT: B 31 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8336 (pt) outliers start: 37 outliers final: 16 residues processed: 226 average time/residue: 0.0886 time to fit residues: 30.0861 Evaluate side-chains 175 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1470 ASN Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 50.0000 chunk 98 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 509 GLN A 540 HIS ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 ASN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.137700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101170 restraints weight = 16254.685| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.05 r_work: 0.3016 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11485 Z= 0.187 Angle : 0.683 10.490 15623 Z= 0.340 Chirality : 0.045 0.378 1780 Planarity : 0.004 0.050 1915 Dihedral : 7.545 64.624 1554 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.94 % Favored : 91.91 % Rotamer: Outliers : 2.79 % Allowed : 12.65 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.20), residues: 1372 helix: -1.51 (0.16), residues: 828 sheet: -3.61 (1.00), residues: 20 loop : -2.92 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 696 TYR 0.025 0.002 TYR A1313 PHE 0.017 0.002 PHE B 47 TRP 0.026 0.002 TRP A 624 HIS 0.006 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (11469) covalent geometry : angle 0.66068 / 0.34 (15584) SS BOND : bond 0.00324 / 0.21 ( 9) SS BOND : angle 1.45667 / 1.01 ( 18) hydrogen bonds : bond 0.05149 / 3.71 ( 492) hydrogen bonds : angle 4.47888 / 3.12 ( 1386) link_BETA1-4 : bond 0.00650 / 0.32 ( 2) link_BETA1-4 : angle 3.43118 / 1.96 ( 6) link_NAG-ASN : bond 0.00767 / 0.44 ( 5) link_NAG-ASN : angle 5.03398 / 3.51 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6681 (tm-30) REVERT: A 324 GLU cc_start: 0.8908 (pm20) cc_final: 0.8292 (tt0) REVERT: A 424 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7800 (mtpt) REVERT: A 629 ASN cc_start: 0.8783 (m-40) cc_final: 0.8582 (m-40) REVERT: A 856 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7874 (ptmt) REVERT: A 977 GLU cc_start: 0.8992 (tp30) cc_final: 0.8743 (tp30) REVERT: A 1147 LYS cc_start: 0.8567 (mttm) cc_final: 0.8234 (mtmm) REVERT: A 1163 MET cc_start: 0.7454 (mmt) cc_final: 0.7193 (mmt) REVERT: A 1289 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8562 (mt) REVERT: A 1428 ASP cc_start: 0.8052 (t0) cc_final: 0.7714 (t0) REVERT: A 1432 MET cc_start: 0.9091 (ttp) cc_final: 0.8593 (tmm) REVERT: B 31 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8334 (pp) outliers start: 32 outliers final: 18 residues processed: 181 average time/residue: 0.0852 time to fit residues: 23.0917 Evaluate side-chains 167 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 117 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097348 restraints weight = 16373.932| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.08 r_work: 0.2957 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11485 Z= 0.255 Angle : 0.719 11.737 15623 Z= 0.358 Chirality : 0.048 0.368 1780 Planarity : 0.004 0.041 1915 Dihedral : 7.654 66.239 1554 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.31 % Favored : 91.55 % Rotamer: Outliers : 3.93 % Allowed : 13.35 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.21), residues: 1372 helix: -0.99 (0.17), residues: 835 sheet: -3.02 (0.88), residues: 29 loop : -2.88 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1119 TYR 0.024 0.002 TYR A1313 PHE 0.020 0.002 PHE B 47 TRP 0.028 0.002 TRP A 203 HIS 0.007 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.25 (11469) covalent geometry : angle 0.69899 / 0.35 (15584) SS BOND : bond 0.00577 / 0.35 ( 9) SS BOND : angle 1.89085 / 1.23 ( 18) hydrogen bonds : bond 0.05180 / 3.73 ( 492) hydrogen bonds : angle 4.38797 / 3.07 ( 1386) link_BETA1-4 : bond 0.00626 / 0.30 ( 2) link_BETA1-4 : angle 3.37939 / 1.87 ( 6) link_NAG-ASN : bond 0.00654 / 0.38 ( 5) link_NAG-ASN : angle 4.62962 / 3.25 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6616 (tm-30) REVERT: A 205 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: A 371 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9165 (tt) REVERT: A 374 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8455 (mp) REVERT: A 424 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8031 (mtpt) REVERT: A 678 ASP cc_start: 0.8556 (m-30) cc_final: 0.8259 (m-30) REVERT: A 856 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7868 (ptmt) REVERT: A 857 TYR cc_start: 0.8495 (m-10) cc_final: 0.8285 (m-80) REVERT: A 910 PHE cc_start: 0.8173 (m-10) cc_final: 0.7972 (m-80) REVERT: A 977 GLU cc_start: 0.8975 (tp30) cc_final: 0.8734 (tp30) REVERT: A 1054 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9008 (mp) REVERT: A 1147 LYS cc_start: 0.8567 (mttm) cc_final: 0.8218 (mtmm) REVERT: A 1163 MET cc_start: 0.7533 (mmt) cc_final: 0.7266 (mmt) REVERT: A 1289 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8635 (mt) REVERT: B 31 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8310 (pp) outliers start: 45 outliers final: 25 residues processed: 188 average time/residue: 0.0930 time to fit residues: 26.0766 Evaluate side-chains 178 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 4 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1085 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.101288 restraints weight = 16088.906| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.07 r_work: 0.3016 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11485 Z= 0.119 Angle : 0.597 10.790 15623 Z= 0.297 Chirality : 0.042 0.283 1780 Planarity : 0.003 0.034 1915 Dihedral : 7.324 64.077 1554 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.85 % Favored : 93.00 % Rotamer: Outliers : 2.88 % Allowed : 15.10 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.22), residues: 1372 helix: -0.33 (0.18), residues: 828 sheet: -2.91 (0.87), residues: 29 loop : -2.70 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 960 TYR 0.016 0.001 TYR A 347 PHE 0.014 0.001 PHE A1279 TRP 0.019 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (11469) covalent geometry : angle 0.58273 / 0.29 (15584) SS BOND : bond 0.00310 / 0.23 ( 9) SS BOND : angle 1.25972 / 0.86 ( 18) hydrogen bonds : bond 0.04004 / 2.88 ( 492) hydrogen bonds : angle 4.01783 / 2.82 ( 1386) link_BETA1-4 : bond 0.00528 / 0.27 ( 2) link_BETA1-4 : angle 3.16244 / 1.79 ( 6) link_NAG-ASN : bond 0.00557 / 0.33 ( 5) link_NAG-ASN : angle 3.60272 / 2.51 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6574 (tm-30) REVERT: A 205 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: A 424 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7962 (mtpt) REVERT: A 571 ILE cc_start: 0.8733 (tt) cc_final: 0.8489 (mm) REVERT: A 678 ASP cc_start: 0.8482 (m-30) cc_final: 0.8182 (m-30) REVERT: A 856 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7765 (ptmt) REVERT: A 977 GLU cc_start: 0.8962 (tp30) cc_final: 0.8748 (tp30) REVERT: A 1147 LYS cc_start: 0.8573 (mttm) cc_final: 0.8242 (mtmm) REVERT: A 1405 MET cc_start: 0.8771 (tpp) cc_final: 0.8274 (mmt) REVERT: A 1415 LEU cc_start: 0.9226 (tt) cc_final: 0.8817 (mp) REVERT: B 31 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8192 (pt) outliers start: 33 outliers final: 21 residues processed: 178 average time/residue: 0.0894 time to fit residues: 23.6160 Evaluate side-chains 171 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1504 ARG Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 99 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098141 restraints weight = 16316.485| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.09 r_work: 0.2972 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11485 Z= 0.207 Angle : 0.662 11.262 15623 Z= 0.329 Chirality : 0.045 0.310 1780 Planarity : 0.004 0.032 1915 Dihedral : 7.206 66.707 1554 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.73 % Favored : 92.13 % Rotamer: Outliers : 3.84 % Allowed : 15.01 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.23), residues: 1372 helix: -0.21 (0.18), residues: 835 sheet: -2.93 (0.80), residues: 29 loop : -2.72 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 960 TYR 0.020 0.002 TYR A 381 PHE 0.018 0.002 PHE A 687 TRP 0.022 0.002 TRP A 624 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (11469) covalent geometry : angle 0.64656 / 0.33 (15584) SS BOND : bond 0.00401 / 0.23 ( 9) SS BOND : angle 1.79689 / 1.17 ( 18) hydrogen bonds : bond 0.04561 / 3.28 ( 492) hydrogen bonds : angle 4.09107 / 2.87 ( 1386) link_BETA1-4 : bond 0.00528 / 0.25 ( 2) link_BETA1-4 : angle 3.20832 / 1.78 ( 6) link_NAG-ASN : bond 0.00465 / 0.27 ( 5) link_NAG-ASN : angle 3.67763 / 2.57 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6618 (tm-30) REVERT: A 205 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: A 371 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9090 (tp) REVERT: A 424 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8048 (mtpt) REVERT: A 571 ILE cc_start: 0.8747 (tt) cc_final: 0.8465 (mm) REVERT: A 678 ASP cc_start: 0.8526 (m-30) cc_final: 0.8231 (m-30) REVERT: A 856 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7798 (ptmt) REVERT: A 926 ASP cc_start: 0.8625 (t70) cc_final: 0.8406 (t70) REVERT: A 977 GLU cc_start: 0.8982 (tp30) cc_final: 0.8758 (tp30) REVERT: A 1147 LYS cc_start: 0.8555 (mttm) cc_final: 0.8228 (mtmm) REVERT: A 1163 MET cc_start: 0.7475 (mmt) cc_final: 0.7209 (mmt) REVERT: A 1289 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8579 (mt) REVERT: A 1405 MET cc_start: 0.8923 (tpp) cc_final: 0.8436 (mmt) REVERT: B 31 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8198 (pp) outliers start: 44 outliers final: 32 residues processed: 175 average time/residue: 0.0913 time to fit residues: 23.8383 Evaluate side-chains 176 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1504 ARG Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 135 optimal weight: 2.9990 chunk 5 optimal weight: 40.0000 chunk 108 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.137925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100856 restraints weight = 16157.794| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.09 r_work: 0.3008 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11485 Z= 0.125 Angle : 0.617 10.715 15623 Z= 0.308 Chirality : 0.042 0.261 1780 Planarity : 0.003 0.031 1915 Dihedral : 7.004 64.380 1554 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.92 % Favored : 92.93 % Rotamer: Outliers : 2.97 % Allowed : 16.49 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.23), residues: 1372 helix: 0.17 (0.18), residues: 831 sheet: -2.83 (0.78), residues: 29 loop : -2.66 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 960 TYR 0.014 0.001 TYR A 347 PHE 0.011 0.001 PHE A1095 TRP 0.018 0.001 TRP A 624 HIS 0.006 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (11469) covalent geometry : angle 0.59950 / 0.30 (15584) SS BOND : bond 0.00295 / 0.19 ( 9) SS BOND : angle 2.84629 / 1.37 ( 18) hydrogen bonds : bond 0.03906 / 2.81 ( 492) hydrogen bonds : angle 3.92404 / 2.76 ( 1386) link_BETA1-4 : bond 0.00647 / 0.31 ( 2) link_BETA1-4 : angle 3.14681 / 1.76 ( 6) link_NAG-ASN : bond 0.00489 / 0.29 ( 5) link_NAG-ASN : angle 3.16898 / 2.19 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6573 (tm-30) REVERT: A 205 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: A 371 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9098 (tp) REVERT: A 424 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7978 (mtpt) REVERT: A 571 ILE cc_start: 0.8676 (tt) cc_final: 0.8463 (mm) REVERT: A 678 ASP cc_start: 0.8490 (m-30) cc_final: 0.8185 (m-30) REVERT: A 856 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7786 (ptmt) REVERT: A 926 ASP cc_start: 0.8582 (t70) cc_final: 0.8370 (t70) REVERT: A 977 GLU cc_start: 0.8950 (tp30) cc_final: 0.8724 (tp30) REVERT: A 1147 LYS cc_start: 0.8568 (mttm) cc_final: 0.8258 (mtmm) REVERT: A 1163 MET cc_start: 0.7504 (mmt) cc_final: 0.7265 (mmt) REVERT: A 1170 ARG cc_start: 0.7658 (mmm-85) cc_final: 0.7449 (mmm-85) REVERT: A 1405 MET cc_start: 0.8823 (tpp) cc_final: 0.8327 (mmt) REVERT: A 1415 LEU cc_start: 0.9229 (tt) cc_final: 0.8936 (tp) REVERT: B 31 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8079 (pp) outliers start: 34 outliers final: 24 residues processed: 171 average time/residue: 0.0914 time to fit residues: 23.1688 Evaluate side-chains 170 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1504 ARG Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 112 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 chunk 94 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101224 restraints weight = 16122.857| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.09 r_work: 0.3013 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 11485 Z= 0.136 Angle : 0.644 13.153 15623 Z= 0.318 Chirality : 0.043 0.267 1780 Planarity : 0.003 0.031 1915 Dihedral : 6.881 63.701 1554 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.22 % Favored : 92.64 % Rotamer: Outliers : 2.79 % Allowed : 17.19 % Favored : 80.02 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.23), residues: 1372 helix: 0.37 (0.19), residues: 834 sheet: -2.64 (1.09), residues: 19 loop : -2.63 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 960 TYR 0.014 0.001 TYR A 347 PHE 0.012 0.001 PHE A 687 TRP 0.018 0.001 TRP A 624 HIS 0.008 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (11469) covalent geometry : angle 0.62614 / 0.31 (15584) SS BOND : bond 0.00381 / 0.22 ( 9) SS BOND : angle 3.08404 / 1.60 ( 18) hydrogen bonds : bond 0.03859 / 2.77 ( 492) hydrogen bonds : angle 3.87250 / 2.72 ( 1386) link_BETA1-4 : bond 0.00411 / 0.20 ( 2) link_BETA1-4 : angle 3.11398 / 1.74 ( 6) link_NAG-ASN : bond 0.00441 / 0.26 ( 5) link_NAG-ASN : angle 2.98863 / 2.05 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6582 (tm-30) REVERT: A 205 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: A 371 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9103 (tp) REVERT: A 424 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7907 (mtpt) REVERT: A 651 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9122 (mt) REVERT: A 678 ASP cc_start: 0.8494 (m-30) cc_final: 0.8191 (m-30) REVERT: A 977 GLU cc_start: 0.8944 (tp30) cc_final: 0.8720 (tp30) REVERT: A 1147 LYS cc_start: 0.8495 (mttm) cc_final: 0.8233 (mtmm) REVERT: A 1163 MET cc_start: 0.7502 (mmt) cc_final: 0.7222 (mmt) REVERT: A 1170 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7400 (mmm-85) REVERT: A 1405 MET cc_start: 0.8810 (tpp) cc_final: 0.8302 (mmt) REVERT: A 1415 LEU cc_start: 0.9222 (tt) cc_final: 0.8834 (mp) REVERT: B 31 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8045 (pp) outliers start: 32 outliers final: 23 residues processed: 170 average time/residue: 0.1067 time to fit residues: 26.4893 Evaluate side-chains 168 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1504 ARG Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 109 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101154 restraints weight = 16094.366| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.08 r_work: 0.3011 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 11485 Z= 0.137 Angle : 0.637 11.503 15623 Z= 0.316 Chirality : 0.043 0.271 1780 Planarity : 0.003 0.030 1915 Dihedral : 6.754 63.739 1554 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.14 % Favored : 92.71 % Rotamer: Outliers : 2.79 % Allowed : 17.02 % Favored : 80.19 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.23), residues: 1372 helix: 0.51 (0.19), residues: 832 sheet: -2.67 (1.07), residues: 19 loop : -2.59 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 960 TYR 0.014 0.001 TYR A 381 PHE 0.012 0.001 PHE A 687 TRP 0.018 0.001 TRP A 624 HIS 0.006 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (11469) covalent geometry : angle 0.61980 / 0.31 (15584) SS BOND : bond 0.00375 / 0.24 ( 9) SS BOND : angle 3.02416 / 1.68 ( 18) hydrogen bonds : bond 0.03874 / 2.78 ( 492) hydrogen bonds : angle 3.84850 / 2.70 ( 1386) link_BETA1-4 : bond 0.00530 / 0.26 ( 2) link_BETA1-4 : angle 3.02224 / 1.68 ( 6) link_NAG-ASN : bond 0.00408 / 0.24 ( 5) link_NAG-ASN : angle 2.87875 / 1.97 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6580 (tm-30) REVERT: A 205 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: A 371 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9102 (tp) REVERT: A 424 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7907 (mtpt) REVERT: A 638 TYR cc_start: 0.8429 (p90) cc_final: 0.8037 (p90) REVERT: A 651 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9124 (mt) REVERT: A 678 ASP cc_start: 0.8485 (m-30) cc_final: 0.8179 (m-30) REVERT: A 977 GLU cc_start: 0.8951 (tp30) cc_final: 0.8720 (tp30) REVERT: A 1147 LYS cc_start: 0.8487 (mttm) cc_final: 0.8234 (mtmm) REVERT: A 1163 MET cc_start: 0.7439 (mmt) cc_final: 0.7152 (mmt) REVERT: A 1170 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7497 (mmm-85) REVERT: A 1405 MET cc_start: 0.8823 (tpp) cc_final: 0.8316 (mmt) REVERT: A 1415 LEU cc_start: 0.9221 (tt) cc_final: 0.8797 (mt) REVERT: B 27 GLN cc_start: 0.8236 (mp10) cc_final: 0.7867 (pm20) REVERT: B 31 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8052 (pp) outliers start: 32 outliers final: 24 residues processed: 163 average time/residue: 0.1007 time to fit residues: 24.1165 Evaluate side-chains 169 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1504 ARG Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 0.0060 chunk 135 optimal weight: 0.0370 chunk 118 optimal weight: 0.5980 chunk 122 optimal weight: 0.0000 chunk 77 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS A1056 GLN ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.141256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104848 restraints weight = 16351.435| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.07 r_work: 0.3069 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 11485 Z= 0.102 Angle : 0.590 10.976 15623 Z= 0.292 Chirality : 0.041 0.276 1780 Planarity : 0.003 0.030 1915 Dihedral : 6.463 59.921 1554 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.85 % Favored : 93.00 % Rotamer: Outliers : 1.92 % Allowed : 18.06 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.23), residues: 1372 helix: 0.80 (0.19), residues: 834 sheet: -2.62 (1.08), residues: 19 loop : -2.53 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 960 TYR 0.012 0.001 TYR A1164 PHE 0.010 0.001 PHE A1279 TRP 0.016 0.001 TRP A 624 HIS 0.006 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (11469) covalent geometry : angle 0.57718 / 0.29 (15584) SS BOND : bond 0.00422 / 0.25 ( 9) SS BOND : angle 2.39087 / 1.35 ( 18) hydrogen bonds : bond 0.03344 / 2.41 ( 492) hydrogen bonds : angle 3.70022 / 2.59 ( 1386) link_BETA1-4 : bond 0.00631 / 0.31 ( 2) link_BETA1-4 : angle 2.83872 / 1.61 ( 6) link_NAG-ASN : bond 0.00497 / 0.28 ( 5) link_NAG-ASN : angle 2.49153 / 1.67 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6669 (tm-30) REVERT: A 205 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: A 336 MET cc_start: 0.7686 (ptp) cc_final: 0.6911 (tpt) REVERT: A 424 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7895 (mtpt) REVERT: A 678 ASP cc_start: 0.8446 (m-30) cc_final: 0.8152 (m-30) REVERT: A 977 GLU cc_start: 0.8942 (tp30) cc_final: 0.8719 (tp30) REVERT: A 1125 LEU cc_start: 0.8635 (mt) cc_final: 0.8429 (mp) REVERT: A 1141 MET cc_start: 0.8526 (mtp) cc_final: 0.8275 (mtm) REVERT: A 1147 LYS cc_start: 0.8502 (mttm) cc_final: 0.8261 (mtmm) REVERT: A 1163 MET cc_start: 0.7341 (mmt) cc_final: 0.7099 (mmt) REVERT: A 1170 ARG cc_start: 0.7703 (mmm-85) cc_final: 0.7478 (mmm-85) REVERT: A 1405 MET cc_start: 0.8726 (tpp) cc_final: 0.8429 (mmm) REVERT: A 1415 LEU cc_start: 0.9172 (tt) cc_final: 0.8876 (mp) REVERT: A 1432 MET cc_start: 0.9050 (ttp) cc_final: 0.8652 (tmm) REVERT: B 31 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8129 (pt) outliers start: 22 outliers final: 15 residues processed: 166 average time/residue: 0.1014 time to fit residues: 24.6331 Evaluate side-chains 158 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 82 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 107 optimal weight: 0.0020 chunk 17 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 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 = 0.3678 r_free = 0.3678 target = 0.140501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103945 restraints weight = 16383.069| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.07 r_work: 0.3055 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11485 Z= 0.113 Angle : 0.602 9.620 15623 Z= 0.299 Chirality : 0.042 0.277 1780 Planarity : 0.003 0.030 1915 Dihedral : 6.304 60.223 1554 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.14 % Favored : 92.71 % Rotamer: Outliers : 1.66 % Allowed : 18.06 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1372 helix: 0.91 (0.19), residues: 834 sheet: -2.58 (1.05), residues: 19 loop : -2.45 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 960 TYR 0.014 0.001 TYR A 381 PHE 0.011 0.001 PHE A 577 TRP 0.017 0.001 TRP A 624 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (11469) covalent geometry : angle 0.58937 / 0.29 (15584) SS BOND : bond 0.00337 / 0.22 ( 9) SS BOND : angle 2.34916 / 1.35 ( 18) hydrogen bonds : bond 0.03480 / 2.50 ( 492) hydrogen bonds : angle 3.67720 / 2.58 ( 1386) link_BETA1-4 : bond 0.00530 / 0.26 ( 2) link_BETA1-4 : angle 2.82110 / 1.58 ( 6) link_NAG-ASN : bond 0.00408 / 0.23 ( 5) link_NAG-ASN : angle 2.48667 / 1.67 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3241.98 seconds wall clock time: 56 minutes 2.50 seconds (3362.50 seconds total)