Starting phenix.real_space_refine on Wed Mar 4 03:14:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6v_33649/03_2026/7y6v_33649.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6v_33649/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7y6v_33649/03_2026/7y6v_33649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6v_33649/03_2026/7y6v_33649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y6v_33649/03_2026/7y6v_33649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6v_33649/03_2026/7y6v_33649.map" } 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-dev-5986/lib/python3.9/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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.72, per 1000 atoms: 0.27 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: 1.14 Conformation dependent library (CDL) restraints added in 593.5 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: 0.54 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: 2.22 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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 - 23.73: 6150 23.73 - 47.46: 285 47.46 - 71.19: 73 71.19 - 94.92: 43 94.92 - 118.65: 29 Dihedral angle restraints: 6580 sinusoidal: 3032 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 6577 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: 4.630 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.150 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 17.908 118.652 4273 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 covalent geometry : bond 0.00439 (10200) covalent geometry : angle 0.73939 (13900) SS BOND : bond 0.00147 ( 13) SS BOND : angle 1.38427 ( 26) hydrogen bonds : bond 0.14864 ( 368) hydrogen bonds : angle 6.47955 ( 1086) Misc. bond : bond 0.00160 ( 1) link_ALPHA1-3 : bond 0.00281 ( 1) link_ALPHA1-3 : angle 1.53282 ( 3) link_ALPHA1-6 : bond 0.00329 ( 1) link_ALPHA1-6 : angle 1.47685 ( 3) link_BETA1-4 : bond 0.00576 ( 18) link_BETA1-4 : angle 3.34967 ( 54) link_BETA1-6 : bond 0.00535 ( 4) link_BETA1-6 : angle 1.58710 ( 12) link_NAG-ASN : bond 0.01144 ( 20) link_NAG-ASN : angle 5.69594 ( 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 : 0.365 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: 0.0772 time to fit residues: 3.2323 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 : 0.366 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3644 r_free = 0.3644 target = 0.060893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.044632 restraints weight = 56431.699| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 5.32 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10258 Z= 0.154 Angle : 0.778 19.267 14058 Z= 0.350 Chirality : 0.052 0.521 1731 Planarity : 0.004 0.061 1734 Dihedral : 14.728 96.069 2230 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.70 % Rotamer: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % 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: -0.55 (0.25), residues: 1222 helix: 1.70 (0.34), residues: 241 sheet: -1.14 (0.29), residues: 312 loop : -0.70 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.019 0.001 TYR A 984 PHE 0.028 0.001 PHE A 588 TRP 0.007 0.001 TRP A 439 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00330 (10200) covalent geometry : angle 0.67480 (13900) SS BOND : bond 0.00181 ( 13) SS BOND : angle 1.13126 ( 26) hydrogen bonds : bond 0.04353 ( 368) hydrogen bonds : angle 5.20472 ( 1086) Misc. bond : bond 0.00061 ( 1) link_ALPHA1-3 : bond 0.00702 ( 1) link_ALPHA1-3 : angle 3.12543 ( 3) link_ALPHA1-6 : bond 0.00186 ( 1) link_ALPHA1-6 : angle 1.65485 ( 3) link_BETA1-4 : bond 0.00628 ( 18) link_BETA1-4 : angle 3.05100 ( 54) link_BETA1-6 : bond 0.00673 ( 4) link_BETA1-6 : angle 1.67191 ( 12) link_NAG-ASN : bond 0.00915 ( 20) link_NAG-ASN : angle 5.12134 ( 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 21 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 1107 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8601 (tm-30) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0958 time to fit residues: 3.2068 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 : 0.375 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.060264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043830 restraints weight = 56583.962| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 5.40 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10258 Z= 0.174 Angle : 0.750 18.383 14058 Z= 0.338 Chirality : 0.051 0.524 1731 Planarity : 0.004 0.062 1734 Dihedral : 11.968 86.623 2230 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.62 % Rotamer: Outliers : 1.24 % Allowed : 7.82 % Favored : 90.94 % 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: -0.57 (0.25), residues: 1222 helix: 1.67 (0.34), residues: 241 sheet: -1.12 (0.29), residues: 320 loop : -0.71 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1112 TYR 0.016 0.001 TYR A 796 PHE 0.012 0.001 PHE A 588 TRP 0.009 0.001 TRP A 439 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00381 (10200) covalent geometry : angle 0.65870 (13900) SS BOND : bond 0.00175 ( 13) SS BOND : angle 0.96574 ( 26) hydrogen bonds : bond 0.04042 ( 368) hydrogen bonds : angle 4.88785 ( 1086) Misc. bond : bond 0.00111 ( 1) link_ALPHA1-3 : bond 0.01174 ( 1) link_ALPHA1-3 : angle 2.23616 ( 3) link_ALPHA1-6 : bond 0.00018 ( 1) link_ALPHA1-6 : angle 1.79740 ( 3) link_BETA1-4 : bond 0.00621 ( 18) link_BETA1-4 : angle 2.79161 ( 54) link_BETA1-6 : bond 0.00781 ( 4) link_BETA1-6 : angle 1.90742 ( 12) link_NAG-ASN : bond 0.00869 ( 20) link_NAG-ASN : angle 4.75992 ( 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 34 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 619 TYR cc_start: 0.9044 (m-80) cc_final: 0.8790 (m-80) REVERT: A 795 GLU cc_start: 0.8489 (tp30) cc_final: 0.8258 (tp30) REVERT: A 1107 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8587 (tm-30) outliers start: 13 outliers final: 4 residues processed: 31 average time/residue: 0.0782 time to fit residues: 4.0993 Evaluate side-chains 23 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL 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: 0.6980 chunk 78 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 205 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 = 0.3643 r_free = 0.3643 target = 0.060967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.044562 restraints weight = 56370.011| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 5.40 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10258 Z= 0.123 Angle : 0.714 18.203 14058 Z= 0.320 Chirality : 0.051 0.484 1731 Planarity : 0.004 0.057 1734 Dihedral : 10.789 82.199 2230 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.48 % Favored : 94.27 % Rotamer: Outliers : 1.24 % Allowed : 8.87 % Favored : 89.90 % 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: -0.51 (0.25), residues: 1222 helix: 1.70 (0.34), residues: 243 sheet: -1.03 (0.29), residues: 312 loop : -0.71 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1112 TYR 0.009 0.001 TYR A 184 PHE 0.008 0.001 PHE A 549 TRP 0.007 0.001 TRP A 439 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00262 (10200) covalent geometry : angle 0.62211 (13900) SS BOND : bond 0.00272 ( 13) SS BOND : angle 0.84200 ( 26) hydrogen bonds : bond 0.03600 ( 368) hydrogen bonds : angle 4.72630 ( 1086) Misc. bond : bond 0.00038 ( 1) link_ALPHA1-3 : bond 0.01134 ( 1) link_ALPHA1-3 : angle 2.45598 ( 3) link_ALPHA1-6 : bond 0.00248 ( 1) link_ALPHA1-6 : angle 1.77693 ( 3) link_BETA1-4 : bond 0.00623 ( 18) link_BETA1-4 : angle 2.71655 ( 54) link_BETA1-6 : bond 0.00522 ( 4) link_BETA1-6 : angle 2.14559 ( 12) link_NAG-ASN : bond 0.00891 ( 20) link_NAG-ASN : angle 4.63479 ( 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 30 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 17 time to evaluate : 0.385 Fit side-chains REVERT: A 619 TYR cc_start: 0.9093 (m-80) cc_final: 0.8672 (m-80) REVERT: A 795 GLU cc_start: 0.8476 (tp30) cc_final: 0.8185 (tp30) REVERT: A 1107 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8524 (tm-30) outliers start: 13 outliers final: 8 residues processed: 29 average time/residue: 0.0687 time to fit residues: 3.7654 Evaluate side-chains 25 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 991 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 chunk 97 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3570 r_free = 0.3570 target = 0.058614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.042221 restraints weight = 58093.880| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 5.37 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 10258 Z= 0.313 Angle : 0.833 16.873 14058 Z= 0.385 Chirality : 0.052 0.496 1731 Planarity : 0.004 0.052 1734 Dihedral : 10.721 82.466 2230 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.87 % Favored : 92.88 % Rotamer: Outliers : 2.00 % Allowed : 10.87 % Favored : 87.13 % 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: -0.89 (0.25), residues: 1222 helix: 1.31 (0.33), residues: 241 sheet: -1.28 (0.28), residues: 330 loop : -0.89 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1112 TYR 0.023 0.002 TYR A 208 PHE 0.016 0.002 PHE A 36 TRP 0.013 0.002 TRP A 439 HIS 0.007 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00682 (10200) covalent geometry : angle 0.75667 (13900) SS BOND : bond 0.00269 ( 13) SS BOND : angle 1.08034 ( 26) hydrogen bonds : bond 0.04331 ( 368) hydrogen bonds : angle 5.08930 ( 1086) Misc. bond : bond 0.00244 ( 1) link_ALPHA1-3 : bond 0.00950 ( 1) link_ALPHA1-3 : angle 3.15832 ( 3) link_ALPHA1-6 : bond 0.00143 ( 1) link_ALPHA1-6 : angle 1.61890 ( 3) link_BETA1-4 : bond 0.00562 ( 18) link_BETA1-4 : angle 2.58388 ( 54) link_BETA1-6 : bond 0.00192 ( 4) link_BETA1-6 : angle 1.52909 ( 12) link_NAG-ASN : bond 0.00851 ( 20) link_NAG-ASN : angle 4.71014 ( 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 39 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 18 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 619 TYR cc_start: 0.9170 (m-80) cc_final: 0.8891 (m-80) REVERT: A 1107 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8567 (tm-30) outliers start: 21 outliers final: 12 residues processed: 38 average time/residue: 0.0825 time to fit residues: 5.3011 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 : 0.381 ------------------------------------------------------------------------------- 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 620 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 677 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 99 optimal weight: 0.2980 chunk 60 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3615 r_free = 0.3615 target = 0.060159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.043836 restraints weight = 57317.221| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 5.39 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10258 Z= 0.120 Angle : 0.716 17.499 14058 Z= 0.323 Chirality : 0.050 0.495 1731 Planarity : 0.004 0.055 1734 Dihedral : 10.255 79.608 2230 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 1.14 % Allowed : 12.58 % Favored : 86.27 % 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: -0.66 (0.25), residues: 1222 helix: 1.61 (0.34), residues: 243 sheet: -1.18 (0.28), residues: 334 loop : -0.77 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1112 TYR 0.010 0.001 TYR A 184 PHE 0.011 0.001 PHE A 387 TRP 0.006 0.001 TRP A 439 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00255 (10200) covalent geometry : angle 0.63099 (13900) SS BOND : bond 0.00186 ( 13) SS BOND : angle 0.95566 ( 26) hydrogen bonds : bond 0.03632 ( 368) hydrogen bonds : angle 4.76883 ( 1086) Misc. bond : bond 0.00042 ( 1) link_ALPHA1-3 : bond 0.01235 ( 1) link_ALPHA1-3 : angle 2.24580 ( 3) link_ALPHA1-6 : bond 0.00256 ( 1) link_ALPHA1-6 : angle 1.70398 ( 3) link_BETA1-4 : bond 0.00614 ( 18) link_BETA1-4 : angle 2.51857 ( 54) link_BETA1-6 : bond 0.00319 ( 4) link_BETA1-6 : angle 1.43009 ( 12) link_NAG-ASN : bond 0.00866 ( 20) link_NAG-ASN : angle 4.56607 ( 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 30 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8517 (mp) REVERT: A 619 TYR cc_start: 0.9165 (m-80) cc_final: 0.8878 (m-80) REVERT: A 795 GLU cc_start: 0.8316 (tp30) cc_final: 0.8093 (tp30) REVERT: A 1107 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8520 (tm-30) REVERT: A 1244 ASP cc_start: 0.8682 (m-30) cc_final: 0.8453 (t70) outliers start: 12 outliers final: 8 residues processed: 29 average time/residue: 0.0859 time to fit residues: 4.1980 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 : 0.362 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.059506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.043160 restraints weight = 57241.591| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 5.32 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10258 Z= 0.183 Angle : 0.734 16.812 14058 Z= 0.333 Chirality : 0.050 0.502 1731 Planarity : 0.004 0.052 1734 Dihedral : 10.035 77.483 2230 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.30 % Favored : 93.45 % Rotamer: Outliers : 1.53 % Allowed : 12.58 % Favored : 85.89 % 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: -0.69 (0.25), residues: 1222 helix: 1.61 (0.34), residues: 241 sheet: -1.18 (0.28), residues: 329 loop : -0.81 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1112 TYR 0.014 0.001 TYR A1245 PHE 0.010 0.001 PHE A 788 TRP 0.010 0.001 TRP A 439 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00403 (10200) covalent geometry : angle 0.65292 (13900) SS BOND : bond 0.00170 ( 13) SS BOND : angle 1.20911 ( 26) hydrogen bonds : bond 0.03723 ( 368) hydrogen bonds : angle 4.78242 ( 1086) Misc. bond : bond 0.00106 ( 1) link_ALPHA1-3 : bond 0.01036 ( 1) link_ALPHA1-3 : angle 2.51917 ( 3) link_ALPHA1-6 : bond 0.00301 ( 1) link_ALPHA1-6 : angle 1.61172 ( 3) link_BETA1-4 : bond 0.00555 ( 18) link_BETA1-4 : angle 2.49137 ( 54) link_BETA1-6 : bond 0.00198 ( 4) link_BETA1-6 : angle 1.50223 ( 12) link_NAG-ASN : bond 0.00789 ( 20) link_NAG-ASN : angle 4.51424 ( 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 35 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 619 TYR cc_start: 0.9198 (m-80) cc_final: 0.8885 (m-80) REVERT: A 795 GLU cc_start: 0.8406 (tp30) cc_final: 0.8170 (tp30) REVERT: A 1107 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8545 (tm-30) REVERT: A 1244 ASP cc_start: 0.8681 (m-30) cc_final: 0.8476 (t70) outliers start: 16 outliers final: 12 residues processed: 34 average time/residue: 0.0792 time to fit residues: 4.5467 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 : 0.356 ------------------------------------------------------------------------------- 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 874 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.0570 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3613 r_free = 0.3613 target = 0.060023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.043759 restraints weight = 56876.008| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 5.32 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1896 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= 0.131 Angle : 0.706 16.657 14058 Z= 0.318 Chirality : 0.049 0.493 1731 Planarity : 0.003 0.053 1734 Dihedral : 9.743 74.880 2230 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.62 % Rotamer: Outliers : 1.24 % Allowed : 13.25 % 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: -0.64 (0.25), residues: 1222 helix: 1.63 (0.34), residues: 243 sheet: -1.14 (0.28), residues: 334 loop : -0.77 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1112 TYR 0.009 0.001 TYR A 66 PHE 0.009 0.001 PHE A 788 TRP 0.008 0.001 TRP A 439 HIS 0.003 0.001 HIS A1192 Details of bonding type rmsd covalent geometry : bond 0.00282 (10200) covalent geometry : angle 0.62345 (13900) SS BOND : bond 0.00161 ( 13) SS BOND : angle 1.04101 ( 26) hydrogen bonds : bond 0.03501 ( 368) hydrogen bonds : angle 4.68498 ( 1086) Misc. bond : bond 0.00045 ( 1) link_ALPHA1-3 : bond 0.01154 ( 1) link_ALPHA1-3 : angle 2.19529 ( 3) link_ALPHA1-6 : bond 0.00362 ( 1) link_ALPHA1-6 : angle 1.63861 ( 3) link_BETA1-4 : bond 0.00585 ( 18) link_BETA1-4 : angle 2.48771 ( 54) link_BETA1-6 : bond 0.00270 ( 4) link_BETA1-6 : angle 1.41566 ( 12) link_NAG-ASN : bond 0.00820 ( 20) link_NAG-ASN : angle 4.44964 ( 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 32 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.361 Fit side-chains REVERT: A 166 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8515 (mp) REVERT: A 619 TYR cc_start: 0.9206 (m-80) cc_final: 0.8891 (m-80) REVERT: A 795 GLU cc_start: 0.8381 (tp30) cc_final: 0.8087 (tp30) REVERT: A 1107 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8453 (tm-30) REVERT: A 1244 ASP cc_start: 0.8657 (m-30) cc_final: 0.8439 (t70) outliers start: 13 outliers final: 10 residues processed: 31 average time/residue: 0.0733 time to fit residues: 3.8371 Evaluate side-chains 28 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 17 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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: 8.9990 chunk 36 optimal weight: 0.2980 chunk 22 optimal weight: 0.0070 chunk 101 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3631 r_free = 0.3631 target = 0.060635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.044443 restraints weight = 56645.192| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 5.32 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1968 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= 0.110 Angle : 0.696 16.371 14058 Z= 0.313 Chirality : 0.049 0.493 1731 Planarity : 0.004 0.051 1734 Dihedral : 9.482 72.029 2230 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.56 % Favored : 94.19 % Rotamer: Outliers : 1.43 % Allowed : 13.16 % Favored : 85.41 % 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: -0.56 (0.25), residues: 1222 helix: 1.69 (0.34), residues: 243 sheet: -1.03 (0.28), residues: 335 loop : -0.75 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 146 TYR 0.009 0.001 TYR A 184 PHE 0.009 0.001 PHE A 549 TRP 0.006 0.001 TRP A 439 HIS 0.003 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00231 (10200) covalent geometry : angle 0.61542 (13900) SS BOND : bond 0.00134 ( 13) SS BOND : angle 0.96851 ( 26) hydrogen bonds : bond 0.03362 ( 368) hydrogen bonds : angle 4.59852 ( 1086) Misc. bond : bond 0.00028 ( 1) link_ALPHA1-3 : bond 0.01213 ( 1) link_ALPHA1-3 : angle 2.04873 ( 3) link_ALPHA1-6 : bond 0.00466 ( 1) link_ALPHA1-6 : angle 1.55507 ( 3) link_BETA1-4 : bond 0.00594 ( 18) link_BETA1-4 : angle 2.50247 ( 54) link_BETA1-6 : bond 0.00293 ( 4) link_BETA1-6 : angle 1.41175 ( 12) link_NAG-ASN : bond 0.00845 ( 20) link_NAG-ASN : angle 4.37452 ( 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 36 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 21 time to evaluate : 0.339 Fit side-chains REVERT: A 166 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8548 (mp) REVERT: A 619 TYR cc_start: 0.9261 (m-80) cc_final: 0.8936 (m-80) REVERT: A 795 GLU cc_start: 0.8374 (tp30) cc_final: 0.8089 (tp30) REVERT: A 1107 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8399 (tm-30) REVERT: A 1244 ASP cc_start: 0.8707 (m-30) cc_final: 0.8401 (t0) REVERT: A 1245 TYR cc_start: 0.8562 (t80) cc_final: 0.7569 (t80) outliers start: 15 outliers final: 11 residues processed: 35 average time/residue: 0.0654 time to fit residues: 4.1407 Evaluate side-chains 31 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 677 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** 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 = 0.3635 r_free = 0.3635 target = 0.060750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.044549 restraints weight = 56076.340| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 5.29 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10258 Z= 0.115 Angle : 0.701 15.943 14058 Z= 0.314 Chirality : 0.049 0.490 1731 Planarity : 0.004 0.051 1734 Dihedral : 9.279 69.309 2230 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.65 % Favored : 94.11 % Rotamer: Outliers : 1.24 % Allowed : 13.54 % Favored : 85.22 % 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: -0.50 (0.25), residues: 1222 helix: 1.70 (0.34), residues: 244 sheet: -0.92 (0.28), residues: 329 loop : -0.75 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 146 TYR 0.009 0.001 TYR A 184 PHE 0.009 0.001 PHE A 35 TRP 0.007 0.001 TRP A 439 HIS 0.003 0.001 HIS A1192 Details of bonding type rmsd covalent geometry : bond 0.00246 (10200) covalent geometry : angle 0.62286 (13900) SS BOND : bond 0.00136 ( 13) SS BOND : angle 0.98309 ( 26) hydrogen bonds : bond 0.03333 ( 368) hydrogen bonds : angle 4.57322 ( 1086) Misc. bond : bond 0.00027 ( 1) link_ALPHA1-3 : bond 0.01055 ( 1) link_ALPHA1-3 : angle 2.00007 ( 3) link_ALPHA1-6 : bond 0.00549 ( 1) link_ALPHA1-6 : angle 1.47638 ( 3) link_BETA1-4 : bond 0.00587 ( 18) link_BETA1-4 : angle 2.49578 ( 54) link_BETA1-6 : bond 0.00243 ( 4) link_BETA1-6 : angle 1.40007 ( 12) link_NAG-ASN : bond 0.00824 ( 20) link_NAG-ASN : angle 4.31297 ( 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 33 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 20 time to evaluate : 0.304 Fit side-chains REVERT: A 166 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 619 TYR cc_start: 0.9269 (m-80) cc_final: 0.8951 (m-80) REVERT: A 795 GLU cc_start: 0.8381 (tp30) cc_final: 0.8136 (tp30) REVERT: A 1107 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 1244 ASP cc_start: 0.8672 (m-30) cc_final: 0.8389 (t0) REVERT: A 1245 TYR cc_start: 0.8500 (t80) cc_final: 0.7539 (t80) outliers start: 13 outliers final: 11 residues processed: 32 average time/residue: 0.0662 time to fit residues: 3.8631 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 : 0.254 ------------------------------------------------------------------------------- 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 677 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 53 optimal weight: 30.0000 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 73 optimal weight: 0.0050 chunk 24 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 overall best weight: 0.2470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.061652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.045562 restraints weight = 56418.750| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 5.35 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2237 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= 0.103 Angle : 0.691 15.513 14058 Z= 0.308 Chirality : 0.049 0.483 1731 Planarity : 0.003 0.050 1734 Dihedral : 8.905 63.410 2230 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.32 % Favored : 94.44 % Rotamer: Outliers : 1.05 % Allowed : 14.01 % Favored : 84.94 % 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: -0.40 (0.25), residues: 1222 helix: 1.74 (0.34), residues: 244 sheet: -0.80 (0.28), residues: 334 loop : -0.70 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 146 TYR 0.008 0.001 TYR A 953 PHE 0.009 0.001 PHE A 549 TRP 0.005 0.001 TRP A 439 HIS 0.003 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00211 (10200) covalent geometry : angle 0.61426 (13900) SS BOND : bond 0.00125 ( 13) SS BOND : angle 0.93790 ( 26) hydrogen bonds : bond 0.03181 ( 368) hydrogen bonds : angle 4.45237 ( 1086) Misc. bond : bond 0.00009 ( 1) link_ALPHA1-3 : bond 0.00998 ( 1) link_ALPHA1-3 : angle 1.74870 ( 3) link_ALPHA1-6 : bond 0.00660 ( 1) link_ALPHA1-6 : angle 1.43831 ( 3) link_BETA1-4 : bond 0.00626 ( 18) link_BETA1-4 : angle 2.52835 ( 54) link_BETA1-6 : bond 0.00327 ( 4) link_BETA1-6 : angle 1.32307 ( 12) link_NAG-ASN : bond 0.00901 ( 20) link_NAG-ASN : angle 4.22569 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2201.61 seconds wall clock time: 38 minutes 40.48 seconds (2320.48 seconds total)