Starting phenix.real_space_refine on Fri Sep 11 16:45:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y6v_33649/09_2026/7y6v_33649.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6v_33649/09_2026/7y6v_33649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6v_33649/09_2026/7y6v_33649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6v_33649/09_2026/7y6v_33649.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6v_33649/09_2026/7y6v_33649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6v_33649/09_2026/7y6v_33649.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y6v_33649/09_2026/7y6v_33649.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y6v_33649/09_2026/7y6v_33649.cif" } resolution = 3.3 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 6308 2.51 5 N 1589 2.21 5 O 2050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 9988 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 9398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9398 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 47, 'TRANS': 1176} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 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: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.24, per 1000 atoms: 0.22 Number of scatterers: 9988 At special positions: 0 Unit cell: (124.02, 108.12, 193.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 2050 8.00 N 1589 7.00 C 6308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " BETA1-6 " NAG B 1 " - " FUC B 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG D 1 " - " FUC D 2 " " NAG G 1 " - " FUC G 2 " " NAG O 1 " - " FUC O 3 " NAG-ASN " NAG A1501 " - " ASN A 118 " " NAG A1502 " - " ASN A 381 " " NAG A1504 " - " ASN A 556 " " NAG A1505 " - " ASN A 667 " " NAG A1506 " - " ASN A 787 " " NAG A1507 " - " ASN A1009 " " NAG B 1 " - " ASN A 216 " " NAG C 1 " - " ASN A 264 " " NAG D 1 " - " ASN A 300 " " NAG E 1 " - " ASN A 324 " " NAG F 1 " - " ASN A 344 " " NAG G 1 " - " ASN A 351 " " NAG H 1 " - " ASN A 425 " " NAG I 1 " - " ASN A 514 " " NAG J 1 " - " ASN A 726 " " NAG K 1 " - " ASN A 688 " " NAG L 1 " - " ASN A 743 " " NAG M 1 " - " ASN A 781 " " NAG N 1 " - " ASN A 873 " " NAG O 1 " - " ASN A1232 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 396.6 milliseconds 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 18 sheets defined 22.5% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.520A pdb=" N LYS A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.761A pdb=" N GLY A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 238 " --> pdb=" O CYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.902A pdb=" N VAL A 328 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 575 through 583 removed outlier: 4.347A pdb=" N ASN A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 825 through 827 No H-bonds generated for 'chain 'A' and resid 825 through 827' Processing helix chain 'A' and resid 828 through 852 Processing helix chain 'A' and resid 855 through 861 removed outlier: 3.517A pdb=" N LEU A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.537A pdb=" N LYS A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 914 Processing helix chain 'A' and resid 928 through 935 Processing helix chain 'A' and resid 946 through 961 Processing helix chain 'A' and resid 967 through 971 removed outlier: 3.672A pdb=" N ALA A 971 " --> pdb=" O ALA A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.658A pdb=" N LEU A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1016 removed outlier: 3.724A pdb=" N LEU A 999 " --> pdb=" O ASN A 995 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1055 removed outlier: 4.008A pdb=" N GLN A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY A1046 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1058 No H-bonds generated for 'chain 'A' and resid 1056 through 1058' Processing helix chain 'A' and resid 1066 through 1074 Processing helix chain 'A' and resid 1075 through 1122 removed outlier: 3.560A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A1086 " --> pdb=" O GLN A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1237 through 1242 Processing helix chain 'A' and resid 1247 through 1253 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 184 Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 150 removed outlier: 4.129A pdb=" N ASN A 147 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 125 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 150 removed outlier: 4.129A pdb=" N ASN A 147 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 125 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 288 removed outlier: 7.388A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS A 283 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL A 408 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLY A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 288 removed outlier: 7.388A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS A 283 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 460 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN A 454 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ILE A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 298 removed outlier: 4.956A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 344 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 483 through 488 removed outlier: 4.181A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 709 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 499 through 502 removed outlier: 4.507A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 528 through 535 removed outlier: 4.468A pdb=" N LEU A 529 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLY A 522 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR A 619 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 590 " --> pdb=" O TYR A 619 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN A 621 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE A 588 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR A 623 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY A 625 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER A 584 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 528 through 535 removed outlier: 4.468A pdb=" N LEU A 529 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLY A 522 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 568 removed outlier: 3.936A pdb=" N VAL A 613 " --> pdb=" O GLY A 605 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB5, first strand: chain 'A' and resid 780 through 786 removed outlier: 4.315A pdb=" N GLY A 780 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A1167 " --> pdb=" O THR A1191 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A1191 " --> pdb=" O ILE A1167 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 789 through 798 removed outlier: 6.955A pdb=" N GLY A1150 " --> pdb=" O ALA A1146 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA A1146 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A1152 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL A1144 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A1154 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER A1142 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A1156 " --> pdb=" O ILE A1140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB8, first strand: chain 'A' and resid 881 through 882 Processing sheet with id=AB9, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 4.095A pdb=" N ALA A1179 " --> pdb=" O ILE A1223 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1086 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: 2.30 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3130 1.34 - 1.46: 2552 1.46 - 1.58: 4467 1.58 - 1.70: 0 1.70 - 1.81: 51 Bond restraints: 10200 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.69e+00 bond pdb=" C1 BMA K 3 " pdb=" C2 BMA K 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.43e+00 bond pdb=" C1 MAN C 4 " pdb=" C2 MAN C 4 " ideal model delta sigma weight residual 1.526 1.562 -0.036 2.00e-02 2.50e+03 3.15e+00 ... (remaining 10195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 13395 1.73 - 3.46: 395 3.46 - 5.19: 79 5.19 - 6.92: 29 6.92 - 8.65: 2 Bond angle restraints: 13900 Sorted by residual: angle pdb=" C ASN A 556 " pdb=" CA ASN A 556 " pdb=" CB ASN A 556 " ideal model delta sigma weight residual 110.42 101.77 8.65 1.99e+00 2.53e-01 1.89e+01 angle pdb=" C GLN A 368 " pdb=" N VAL A 369 " pdb=" CA VAL A 369 " ideal model delta sigma weight residual 122.13 129.66 -7.53 1.85e+00 2.92e-01 1.66e+01 angle pdb=" CA ASN A 556 " pdb=" CB ASN A 556 " pdb=" CG ASN A 556 " ideal model delta sigma weight residual 112.60 116.14 -3.54 1.00e+00 1.00e+00 1.25e+01 angle pdb=" C TYR A 555 " pdb=" N ASN A 556 " pdb=" CA ASN A 556 " ideal model delta sigma weight residual 121.54 114.98 6.56 1.91e+00 2.74e-01 1.18e+01 angle pdb=" N TYR A 555 " pdb=" CA TYR A 555 " pdb=" C TYR A 555 " ideal model delta sigma weight residual 109.54 113.36 -3.82 1.37e+00 5.33e-01 7.77e+00 ... (remaining 13895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 5240 18.07 - 36.14: 346 36.14 - 54.22: 58 54.22 - 72.29: 13 72.29 - 90.36: 10 Dihedral angle restraints: 5667 sinusoidal: 2119 harmonic: 3548 Sorted by residual: dihedral pdb=" CB CYS A 920 " pdb=" SG CYS A 920 " pdb=" SG CYS A 931 " pdb=" CB CYS A 931 " ideal model delta sinusoidal sigma weight residual -86.00 -176.36 90.36 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS A 808 " pdb=" SG CYS A 808 " pdb=" SG CYS A 830 " pdb=" CB CYS A 830 " ideal model delta sinusoidal sigma weight residual -86.00 -153.17 67.17 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CA SER A 554 " pdb=" C SER A 554 " pdb=" N TYR A 555 " pdb=" CA TYR A 555 " ideal model delta harmonic sigma weight residual -180.00 -153.74 -26.26 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 5664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1691 0.126 - 0.251: 28 0.251 - 0.377: 8 0.377 - 0.503: 2 0.503 - 0.628: 2 Chirality restraints: 1731 Sorted by residual: chirality pdb=" C1 NAG A1504 " pdb=" ND2 ASN A 556 " pdb=" C2 NAG A1504 " pdb=" O5 NAG A1504 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 726 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.43e+00 chirality pdb=" C1 NAG A1505 " pdb=" ND2 ASN A 667 " pdb=" C2 NAG A1505 " pdb=" O5 NAG A1505 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1728 not shown) Planarity restraints: 1754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 556 " 0.047 2.00e-02 2.50e+03 4.46e-02 2.49e+01 pdb=" CG ASN A 556 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A 556 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 556 " -0.058 2.00e-02 2.50e+03 pdb=" C1 NAG A1504 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 351 " 0.038 2.00e-02 2.50e+03 3.52e-02 1.55e+01 pdb=" CG ASN A 351 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 351 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 351 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 351 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" CG ASN A 351 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 351 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 351 " 0.015 2.00e-02 2.50e+03 ... (remaining 1751 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 334 2.70 - 3.25: 10316 3.25 - 3.80: 15948 3.80 - 4.35: 19817 4.35 - 4.90: 32537 Nonbonded interactions: 78952 Sorted by model distance: nonbonded pdb=" OG SER A 83 " pdb=" O CYS A 202 " model vdw 2.149 3.040 nonbonded pdb=" O THR A 137 " pdb=" ND2 ASN A 140 " model vdw 2.179 3.120 nonbonded pdb=" O GLN A 821 " pdb=" OG1 THR A 824 " model vdw 2.188 3.040 nonbonded pdb=" O PRO A 498 " pdb=" OG1 THR A 650 " model vdw 2.211 3.040 nonbonded pdb=" O4 NAG G 1 " pdb=" O5 FUC G 2 " model vdw 2.224 3.040 ... (remaining 78947 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 'D' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'N' and resid 1) } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.250 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10258 Z= 0.217 Angle : 0.854 20.119 14058 Z= 0.383 Chirality : 0.057 0.628 1731 Planarity : 0.004 0.054 1734 Dihedral : 12.943 89.875 3360 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.73 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.25), residues: 1222 helix: 1.78 (0.36), residues: 233 sheet: -0.97 (0.29), residues: 311 loop : -0.68 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 460 TYR 0.023 0.001 TYR A 555 PHE 0.020 0.001 PHE A 375 TRP 0.007 0.001 TRP A 259 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.22 (10200) covalent geometry : angle 0.73939 / 0.36 (13900) SS BOND : bond 0.00147 / 0.11 ( 13) SS BOND : angle 1.38427 / 0.87 ( 26) hydrogen bonds : bond 0.14864 / 9.71 ( 368) hydrogen bonds : angle 6.47955 / 4.38 ( 1086) Misc. bond : bond 0.00160 / 0.08 ( 1) link_ALPHA1-3 : bond 0.00281 / 0.15 ( 1) link_ALPHA1-3 : angle 1.53282 / 1.09 ( 3) link_ALPHA1-6 : bond 0.00329 / 0.17 ( 1) link_ALPHA1-6 : angle 1.47685 / 1.24 ( 3) link_BETA1-4 : bond 0.00576 / 0.35 ( 18) link_BETA1-4 : angle 3.34967 / 2.16 ( 54) link_BETA1-6 : bond 0.00535 / 0.26 ( 4) link_BETA1-6 : angle 1.58710 / 1.08 ( 12) link_NAG-ASN : bond 0.01144 / 0.68 ( 20) link_NAG-ASN : angle 5.69594 / 4.74 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.367 Fit side-chains REVERT: A 1107 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8510 (tm-30) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0770 time to fit residues: 3.1589 Evaluate side-chains 18 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN A1055 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.060936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.044660 restraints weight = 56369.127| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 5.33 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10258 Z= 0.151 Angle : 0.748 19.278 14058 Z= 0.342 Chirality : 0.050 0.500 1731 Planarity : 0.004 0.062 1734 Dihedral : 5.123 27.600 1317 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.38 % Favored : 93.37 % Rotamer: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.25), residues: 1222 helix: 1.72 (0.34), residues: 241 sheet: -1.14 (0.29), residues: 312 loop : -0.69 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1112 TYR 0.021 0.001 TYR A 984 PHE 0.029 0.001 PHE A 588 TRP 0.008 0.001 TRP A 439 HIS 0.004 0.001 HIS A1192 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (10200) covalent geometry : angle 0.64807 / 0.32 (13900) SS BOND : bond 0.00179 / 0.11 ( 13) SS BOND : angle 1.11870 / 0.68 ( 26) hydrogen bonds : bond 0.04403 / 2.94 ( 368) hydrogen bonds : angle 5.24332 / 3.58 ( 1086) Misc. bond : bond 0.00072 / 0.04 ( 1) link_ALPHA1-3 : bond 0.00291 / 0.15 ( 1) link_ALPHA1-3 : angle 2.02976 / 1.55 ( 3) link_ALPHA1-6 : bond 0.00360 / 0.19 ( 1) link_ALPHA1-6 : angle 1.49046 / 1.18 ( 3) link_BETA1-4 : bond 0.00579 / 0.34 ( 18) link_BETA1-4 : angle 2.67056 / 1.80 ( 54) link_BETA1-6 : bond 0.00479 / 0.23 ( 4) link_BETA1-6 : angle 1.28275 / 0.87 ( 12) link_NAG-ASN : bond 0.00912 / 0.56 ( 20) link_NAG-ASN : angle 5.11314 / 4.41 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 795 GLU cc_start: 0.8346 (tp30) cc_final: 0.8112 (tp30) REVERT: A 1107 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8607 (tm-30) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.0967 time to fit residues: 3.2937 Evaluate side-chains 17 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 11 optimal weight: 0.0870 chunk 2 optimal weight: 0.2980 chunk 97 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 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 = 0.3660 r_free = 0.3660 target = 0.061476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.045235 restraints weight = 56169.028| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 5.37 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10258 Z= 0.113 Angle : 0.689 18.549 14058 Z= 0.313 Chirality : 0.049 0.486 1731 Planarity : 0.004 0.062 1734 Dihedral : 4.868 26.022 1317 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.06 % Favored : 93.62 % Rotamer: Outliers : 0.95 % Allowed : 7.53 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.25), residues: 1222 helix: 1.71 (0.34), residues: 243 sheet: -0.98 (0.29), residues: 314 loop : -0.71 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1207 TYR 0.023 0.001 TYR A 984 PHE 0.011 0.001 PHE A 375 TRP 0.007 0.001 TRP A 439 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (10200) covalent geometry : angle 0.59879 / 0.29 (13900) SS BOND : bond 0.00154 / 0.09 ( 13) SS BOND : angle 0.82906 / 0.50 ( 26) hydrogen bonds : bond 0.03755 / 2.52 ( 368) hydrogen bonds : angle 4.81674 / 3.29 ( 1086) Misc. bond : bond 0.00042 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00576 / 0.30 ( 1) link_ALPHA1-3 : angle 1.42909 / 1.08 ( 3) link_ALPHA1-6 : bond 0.00330 / 0.17 ( 1) link_ALPHA1-6 : angle 1.50156 / 1.17 ( 3) link_BETA1-4 : bond 0.00610 / 0.35 ( 18) link_BETA1-4 : angle 2.47049 / 1.63 ( 54) link_BETA1-6 : bond 0.00485 / 0.24 ( 4) link_BETA1-6 : angle 1.09815 / 0.70 ( 12) link_NAG-ASN : bond 0.00969 / 0.56 ( 20) link_NAG-ASN : angle 4.68480 / 4.14 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.322 Fit side-chains REVERT: A 158 MET cc_start: 0.9186 (pmm) cc_final: 0.8968 (pmm) REVERT: A 619 TYR cc_start: 0.9010 (m-80) cc_final: 0.8630 (m-80) REVERT: A 1107 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8567 (tm-30) outliers start: 10 outliers final: 3 residues processed: 30 average time/residue: 0.0707 time to fit residues: 3.8939 Evaluate side-chains 22 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 620 PHE Chi-restraints excluded: chain A residue 639 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.060341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.044049 restraints weight = 56518.697| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 5.32 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10258 Z= 0.180 Angle : 0.710 17.829 14058 Z= 0.325 Chirality : 0.049 0.475 1731 Planarity : 0.004 0.057 1734 Dihedral : 4.928 25.111 1317 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.70 % Rotamer: Outliers : 1.33 % Allowed : 8.20 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1222 helix: 1.70 (0.34), residues: 243 sheet: -1.09 (0.29), residues: 322 loop : -0.70 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1112 TYR 0.014 0.001 TYR A 66 PHE 0.009 0.001 PHE A 36 TRP 0.010 0.001 TRP A 439 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (10200) covalent geometry : angle 0.62631 / 0.31 (13900) SS BOND : bond 0.00198 / 0.13 ( 13) SS BOND : angle 0.88864 / 0.53 ( 26) hydrogen bonds : bond 0.03781 / 2.53 ( 368) hydrogen bonds : angle 4.77991 / 3.26 ( 1086) Misc. bond : bond 0.00106 / 0.06 ( 1) link_ALPHA1-3 : bond 0.00371 / 0.20 ( 1) link_ALPHA1-3 : angle 1.72054 / 1.27 ( 3) link_ALPHA1-6 : bond 0.00233 / 0.12 ( 1) link_ALPHA1-6 : angle 1.44402 / 1.18 ( 3) link_BETA1-4 : bond 0.00540 / 0.31 ( 18) link_BETA1-4 : angle 2.39739 / 1.59 ( 54) link_BETA1-6 : bond 0.00348 / 0.17 ( 4) link_BETA1-6 : angle 1.22394 / 0.84 ( 12) link_NAG-ASN : bond 0.00822 / 0.49 ( 20) link_NAG-ASN : angle 4.59920 / 4.07 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 0.381 Fit side-chains REVERT: A 619 TYR cc_start: 0.9095 (m-80) cc_final: 0.8690 (m-80) REVERT: A 795 GLU cc_start: 0.8450 (tp30) cc_final: 0.8206 (tp30) REVERT: A 1107 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8586 (tm-30) outliers start: 14 outliers final: 9 residues processed: 31 average time/residue: 0.0803 time to fit residues: 4.2296 Evaluate side-chains 26 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 17 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 620 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 97 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** 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 = 0.3599 r_free = 0.3599 target = 0.059517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.043193 restraints weight = 57783.880| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 5.35 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10258 Z= 0.225 Angle : 0.736 17.250 14058 Z= 0.341 Chirality : 0.049 0.480 1731 Planarity : 0.004 0.064 1734 Dihedral : 5.099 26.778 1317 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.62 % Rotamer: Outliers : 1.81 % Allowed : 9.82 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.25), residues: 1222 helix: 1.66 (0.34), residues: 241 sheet: -1.16 (0.28), residues: 336 loop : -0.72 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 146 TYR 0.016 0.001 TYR A 66 PHE 0.012 0.001 PHE A 36 TRP 0.011 0.001 TRP A 439 HIS 0.005 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (10200) covalent geometry : angle 0.65879 / 0.32 (13900) SS BOND : bond 0.00434 / 0.31 ( 13) SS BOND : angle 0.89056 / 0.55 ( 26) hydrogen bonds : bond 0.03904 / 2.61 ( 368) hydrogen bonds : angle 4.86313 / 3.31 ( 1086) Misc. bond : bond 0.00129 / 0.07 ( 1) link_ALPHA1-3 : bond 0.00213 / 0.11 ( 1) link_ALPHA1-3 : angle 1.77261 / 1.26 ( 3) link_ALPHA1-6 : bond 0.00213 / 0.11 ( 1) link_ALPHA1-6 : angle 1.47185 / 1.23 ( 3) link_BETA1-4 : bond 0.00517 / 0.30 ( 18) link_BETA1-4 : angle 2.32134 / 1.54 ( 54) link_BETA1-6 : bond 0.00332 / 0.16 ( 4) link_BETA1-6 : angle 1.25458 / 0.87 ( 12) link_NAG-ASN : bond 0.00792 / 0.48 ( 20) link_NAG-ASN : angle 4.55106 / 4.03 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 19 time to evaluate : 0.464 Fit side-chains REVERT: A 158 MET cc_start: 0.9077 (pmm) cc_final: 0.8873 (pmm) REVERT: A 427 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9092 (p) REVERT: A 619 TYR cc_start: 0.9126 (m-80) cc_final: 0.8787 (m-80) REVERT: A 795 GLU cc_start: 0.8441 (tp30) cc_final: 0.8241 (tp30) REVERT: A 1107 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8534 (tm-30) outliers start: 19 outliers final: 11 residues processed: 35 average time/residue: 0.0796 time to fit residues: 4.7680 Evaluate side-chains 30 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 620 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1204 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.059307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.043009 restraints weight = 57865.863| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 5.30 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 10258 Z= 0.206 Angle : 0.725 16.841 14058 Z= 0.335 Chirality : 0.049 0.490 1731 Planarity : 0.004 0.053 1734 Dihedral : 5.144 24.937 1317 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.46 % Favored : 93.29 % Rotamer: Outliers : 2.19 % Allowed : 11.06 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.25), residues: 1222 helix: 1.58 (0.34), residues: 241 sheet: -1.17 (0.28), residues: 327 loop : -0.81 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 146 TYR 0.016 0.001 TYR A1245 PHE 0.011 0.001 PHE A 36 TRP 0.010 0.001 TRP A 439 HIS 0.004 0.001 HIS A1192 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (10200) covalent geometry : angle 0.64808 / 0.32 (13900) SS BOND : bond 0.00353 / 0.25 ( 13) SS BOND : angle 0.98846 / 0.59 ( 26) hydrogen bonds : bond 0.03858 / 2.59 ( 368) hydrogen bonds : angle 4.84318 / 3.29 ( 1086) Misc. bond : bond 0.00110 / 0.06 ( 1) link_ALPHA1-3 : bond 0.00255 / 0.13 ( 1) link_ALPHA1-3 : angle 1.75266 / 1.28 ( 3) link_ALPHA1-6 : bond 0.00215 / 0.11 ( 1) link_ALPHA1-6 : angle 1.45073 / 1.21 ( 3) link_BETA1-4 : bond 0.00520 / 0.30 ( 18) link_BETA1-4 : angle 2.26253 / 1.49 ( 54) link_BETA1-6 : bond 0.00341 / 0.17 ( 4) link_BETA1-6 : angle 1.25414 / 0.86 ( 12) link_NAG-ASN : bond 0.00783 / 0.47 ( 20) link_NAG-ASN : angle 4.49771 / 4.00 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 17 time to evaluate : 0.386 Fit side-chains REVERT: A 427 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9117 (p) REVERT: A 619 TYR cc_start: 0.9180 (m-80) cc_final: 0.8834 (m-80) REVERT: A 1107 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8557 (tm-30) outliers start: 23 outliers final: 13 residues processed: 38 average time/residue: 0.0626 time to fit residues: 4.2954 Evaluate side-chains 31 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 17 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 620 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1204 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** 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 = 0.3626 r_free = 0.3626 target = 0.060425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.044267 restraints weight = 56532.165| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 5.32 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10258 Z= 0.111 Angle : 0.695 16.892 14058 Z= 0.317 Chirality : 0.048 0.485 1731 Planarity : 0.003 0.053 1734 Dihedral : 4.931 23.705 1317 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.73 % Favored : 94.03 % Rotamer: Outliers : 1.14 % Allowed : 12.77 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.25), residues: 1222 helix: 1.67 (0.34), residues: 243 sheet: -1.09 (0.28), residues: 326 loop : -0.76 (0.26), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1112 TYR 0.008 0.001 TYR A 184 PHE 0.008 0.001 PHE A 549 TRP 0.006 0.001 TRP A 439 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10200) covalent geometry : angle 0.61775 / 0.30 (13900) SS BOND : bond 0.00146 / 0.10 ( 13) SS BOND : angle 1.11474 / 0.81 ( 26) hydrogen bonds : bond 0.03525 / 2.37 ( 368) hydrogen bonds : angle 4.66083 / 3.18 ( 1086) Misc. bond : bond 0.00037 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00412 / 0.22 ( 1) link_ALPHA1-3 : angle 1.49212 / 1.16 ( 3) link_ALPHA1-6 : bond 0.00318 / 0.17 ( 1) link_ALPHA1-6 : angle 1.41836 / 1.18 ( 3) link_BETA1-4 : bond 0.00568 / 0.32 ( 18) link_BETA1-4 : angle 2.23458 / 1.45 ( 54) link_BETA1-6 : bond 0.00432 / 0.21 ( 4) link_BETA1-6 : angle 1.17626 / 0.77 ( 12) link_NAG-ASN : bond 0.00874 / 0.50 ( 20) link_NAG-ASN : angle 4.40346 / 3.95 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 0.365 Fit side-chains REVERT: A 166 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8562 (mp) REVERT: A 619 TYR cc_start: 0.9167 (m-80) cc_final: 0.8794 (m-80) REVERT: A 1107 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8475 (tm-30) REVERT: A 1244 ASP cc_start: 0.8669 (m-30) cc_final: 0.8424 (t70) REVERT: A 1245 TYR cc_start: 0.8611 (t80) cc_final: 0.8212 (t80) outliers start: 12 outliers final: 8 residues processed: 28 average time/residue: 0.0844 time to fit residues: 4.0284 Evaluate side-chains 27 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 620 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1143 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 5.9990 chunk 60 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.905 > 50:) chunk 46 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** 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 = 0.3598 r_free = 0.3598 target = 0.059420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.043127 restraints weight = 57543.047| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 5.33 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10258 Z= 0.200 Angle : 0.720 16.030 14058 Z= 0.331 Chirality : 0.048 0.492 1731 Planarity : 0.004 0.049 1734 Dihedral : 5.032 24.619 1317 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.22 % Favored : 93.54 % Rotamer: Outliers : 1.33 % Allowed : 12.87 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.25), residues: 1222 helix: 1.65 (0.34), residues: 241 sheet: -1.16 (0.28), residues: 328 loop : -0.78 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1112 TYR 0.015 0.001 TYR A 66 PHE 0.010 0.001 PHE A 36 TRP 0.011 0.001 TRP A 439 HIS 0.004 0.001 HIS A1192 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (10200) covalent geometry : angle 0.64612 / 0.31 (13900) SS BOND : bond 0.00175 / 0.11 ( 13) SS BOND : angle 1.14280 / 0.83 ( 26) hydrogen bonds : bond 0.03723 / 2.50 ( 368) hydrogen bonds : angle 4.75448 / 3.23 ( 1086) Misc. bond : bond 0.00113 / 0.06 ( 1) link_ALPHA1-3 : bond 0.00228 / 0.12 ( 1) link_ALPHA1-3 : angle 1.67907 / 1.25 ( 3) link_ALPHA1-6 : bond 0.00239 / 0.13 ( 1) link_ALPHA1-6 : angle 1.44506 / 1.22 ( 3) link_BETA1-4 : bond 0.00510 / 0.29 ( 18) link_BETA1-4 : angle 2.20093 / 1.45 ( 54) link_BETA1-6 : bond 0.00311 / 0.15 ( 4) link_BETA1-6 : angle 1.27513 / 0.90 ( 12) link_NAG-ASN : bond 0.00765 / 0.45 ( 20) link_NAG-ASN : angle 4.38019 / 3.89 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 0.370 Fit side-chains REVERT: A 619 TYR cc_start: 0.9211 (m-80) cc_final: 0.8854 (m-80) REVERT: A 795 GLU cc_start: 0.8348 (tp30) cc_final: 0.8113 (tp30) REVERT: A 1107 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 1244 ASP cc_start: 0.8684 (m-30) cc_final: 0.8468 (t70) REVERT: A 1245 TYR cc_start: 0.8591 (t80) cc_final: 0.8184 (t80) outliers start: 14 outliers final: 11 residues processed: 32 average time/residue: 0.0648 time to fit residues: 3.8219 Evaluate side-chains 29 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 18 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 620 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1143 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** 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 = 0.3620 r_free = 0.3620 target = 0.060227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.044022 restraints weight = 56896.831| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 5.31 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10258 Z= 0.116 Angle : 0.685 16.195 14058 Z= 0.311 Chirality : 0.048 0.483 1731 Planarity : 0.003 0.051 1734 Dihedral : 4.872 24.151 1317 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 1.05 % Allowed : 13.44 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.25), residues: 1222 helix: 1.67 (0.34), residues: 243 sheet: -1.10 (0.28), residues: 332 loop : -0.72 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.010 0.001 TYR A 953 PHE 0.008 0.001 PHE A 549 TRP 0.006 0.001 TRP A 439 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10200) covalent geometry : angle 0.60910 / 0.29 (13900) SS BOND : bond 0.00151 / 0.10 ( 13) SS BOND : angle 1.01734 / 0.68 ( 26) hydrogen bonds : bond 0.03471 / 2.33 ( 368) hydrogen bonds : angle 4.62343 / 3.15 ( 1086) Misc. bond : bond 0.00038 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00348 / 0.18 ( 1) link_ALPHA1-3 : angle 1.50480 / 1.17 ( 3) link_ALPHA1-6 : bond 0.00254 / 0.13 ( 1) link_ALPHA1-6 : angle 1.40430 / 1.17 ( 3) link_BETA1-4 : bond 0.00569 / 0.32 ( 18) link_BETA1-4 : angle 2.17924 / 1.42 ( 54) link_BETA1-6 : bond 0.00412 / 0.20 ( 4) link_BETA1-6 : angle 1.19157 / 0.79 ( 12) link_NAG-ASN : bond 0.00834 / 0.48 ( 20) link_NAG-ASN : angle 4.32456 / 3.87 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 18 time to evaluate : 0.374 Fit side-chains REVERT: A 619 TYR cc_start: 0.9235 (m-80) cc_final: 0.8880 (m-80) REVERT: A 795 GLU cc_start: 0.8381 (tp30) cc_final: 0.8108 (tp30) REVERT: A 1107 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8442 (tm-30) REVERT: A 1244 ASP cc_start: 0.8734 (m-30) cc_final: 0.8492 (t70) REVERT: A 1245 TYR cc_start: 0.8613 (t80) cc_final: 0.8245 (t80) outliers start: 11 outliers final: 10 residues processed: 28 average time/residue: 0.0673 time to fit residues: 3.5775 Evaluate side-chains 28 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 620 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 0.0270 chunk 85 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 0.3980 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** 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 = 0.3624 r_free = 0.3624 target = 0.060356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.044230 restraints weight = 56368.476| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 5.31 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10258 Z= 0.119 Angle : 0.679 15.688 14058 Z= 0.308 Chirality : 0.048 0.479 1731 Planarity : 0.003 0.050 1734 Dihedral : 4.818 24.416 1317 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 0.95 % Allowed : 13.44 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.25), residues: 1222 helix: 1.74 (0.34), residues: 243 sheet: -1.01 (0.28), residues: 330 loop : -0.73 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.009 0.001 TYR A 66 PHE 0.008 0.001 PHE A 549 TRP 0.008 0.001 TRP A 439 HIS 0.003 0.000 HIS A1192 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (10200) covalent geometry : angle 0.60468 / 0.29 (13900) SS BOND : bond 0.00142 / 0.09 ( 13) SS BOND : angle 1.02146 / 0.66 ( 26) hydrogen bonds : bond 0.03370 / 2.26 ( 368) hydrogen bonds : angle 4.56456 / 3.11 ( 1086) Misc. bond : bond 0.00041 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00364 / 0.19 ( 1) link_ALPHA1-3 : angle 1.50161 / 1.17 ( 3) link_ALPHA1-6 : bond 0.00309 / 0.16 ( 1) link_ALPHA1-6 : angle 1.40658 / 1.17 ( 3) link_BETA1-4 : bond 0.00548 / 0.31 ( 18) link_BETA1-4 : angle 2.15071 / 1.41 ( 54) link_BETA1-6 : bond 0.00372 / 0.18 ( 4) link_BETA1-6 : angle 1.19656 / 0.81 ( 12) link_NAG-ASN : bond 0.00815 / 0.47 ( 20) link_NAG-ASN : angle 4.25663 / 3.80 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.396 Fit side-chains REVERT: A 619 TYR cc_start: 0.9263 (m-80) cc_final: 0.8893 (m-80) REVERT: A 795 GLU cc_start: 0.8384 (tp30) cc_final: 0.8119 (tp30) REVERT: A 1107 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 1244 ASP cc_start: 0.8746 (m-30) cc_final: 0.8529 (t70) REVERT: A 1245 TYR cc_start: 0.8621 (t80) cc_final: 0.8256 (t80) outliers start: 10 outliers final: 9 residues processed: 28 average time/residue: 0.0720 time to fit residues: 3.7681 Evaluate side-chains 27 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 620 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 53 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 24 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.060839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.044655 restraints weight = 56957.843| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 5.37 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10258 Z= 0.109 Angle : 0.666 15.291 14058 Z= 0.302 Chirality : 0.047 0.467 1731 Planarity : 0.003 0.050 1734 Dihedral : 4.661 24.086 1317 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.65 % Favored : 94.11 % Rotamer: Outliers : 0.95 % Allowed : 13.44 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.25), residues: 1222 helix: 1.82 (0.34), residues: 243 sheet: -0.95 (0.28), residues: 332 loop : -0.73 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 146 TYR 0.009 0.001 TYR A 953 PHE 0.008 0.001 PHE A 549 TRP 0.007 0.001 TRP A 439 HIS 0.003 0.000 HIS A1192 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (10200) covalent geometry : angle 0.59326 / 0.28 (13900) SS BOND : bond 0.00130 / 0.09 ( 13) SS BOND : angle 0.96030 / 0.60 ( 26) hydrogen bonds : bond 0.03250 / 2.18 ( 368) hydrogen bonds : angle 4.44833 / 3.04 ( 1086) Misc. bond : bond 0.00021 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00381 / 0.20 ( 1) link_ALPHA1-3 : angle 1.47528 / 1.16 ( 3) link_ALPHA1-6 : bond 0.00319 / 0.17 ( 1) link_ALPHA1-6 : angle 1.40508 / 1.16 ( 3) link_BETA1-4 : bond 0.00565 / 0.32 ( 18) link_BETA1-4 : angle 2.12062 / 1.39 ( 54) link_BETA1-6 : bond 0.00389 / 0.19 ( 4) link_BETA1-6 : angle 1.20281 / 0.82 ( 12) link_NAG-ASN : bond 0.00850 / 0.48 ( 20) link_NAG-ASN : angle 4.16645 / 3.72 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2114.53 seconds wall clock time: 37 minutes 19.24 seconds (2239.24 seconds total)