Starting phenix.real_space_refine on Thu May 1 08:21:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6v_33649/05_2025/7y6v_33649.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6v_33649/05_2025/7y6v_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_33649/05_2025/7y6v_33649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6v_33649/05_2025/7y6v_33649.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6v_33649/05_2025/7y6v_33649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6v_33649/05_2025/7y6v_33649.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.50, per 1000 atoms: 0.75 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: 3.54 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.57 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: 4.83 Time building geometry restraints manager: 3.98 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: 4.740 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.870 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP A 259 HIS 0.004 0.001 HIS A 110 PHE 0.020 0.001 PHE A 375 TYR 0.023 0.001 TYR A 555 ARG 0.001 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.01144 ( 20) link_NAG-ASN : angle 5.69594 ( 60) 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_ALPHA1-3 : bond 0.00281 ( 1) link_ALPHA1-3 : angle 1.53282 ( 3) hydrogen bonds : bond 0.14864 ( 368) hydrogen bonds : angle 6.47955 ( 1086) link_BETA1-6 : bond 0.00535 ( 4) link_BETA1-6 : angle 1.58710 ( 12) SS BOND : bond 0.00147 ( 13) SS BOND : angle 1.38427 ( 26) covalent geometry : bond 0.00439 (10200) covalent geometry : angle 0.73939 (13900) Misc. bond : bond 0.00160 ( 1) *********************** 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 : 1.171 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: 0.1930 time to fit residues: 8.2662 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 : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.0570 chunk 71 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.4104 ------------------------------------------------------------------------------- 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 A1051 GLN A1055 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.059969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.043539 restraints weight = 56534.763| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 5.38 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0995 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= 0.220 Angle : 0.817 18.974 14058 Z= 0.370 Chirality : 0.052 0.527 1731 Planarity : 0.004 0.062 1734 Dihedral : 14.533 95.043 2230 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.79 % Favored : 92.96 % Rotamer: Outliers : 0.29 % Allowed : 5.72 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1222 helix: 1.59 (0.34), residues: 241 sheet: -1.22 (0.29), residues: 307 loop : -0.71 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 439 HIS 0.005 0.001 HIS A 510 PHE 0.033 0.001 PHE A 588 TYR 0.021 0.002 TYR A 984 ARG 0.004 0.000 ARG A1112 Details of bonding type rmsd link_NAG-ASN : bond 0.00845 ( 20) link_NAG-ASN : angle 5.13626 ( 60) link_ALPHA1-6 : bond 0.00011 ( 1) link_ALPHA1-6 : angle 1.67148 ( 3) link_BETA1-4 : bond 0.00593 ( 18) link_BETA1-4 : angle 3.05272 ( 54) link_ALPHA1-3 : bond 0.00561 ( 1) link_ALPHA1-3 : angle 3.57684 ( 3) hydrogen bonds : bond 0.04365 ( 368) hydrogen bonds : angle 5.24795 ( 1086) link_BETA1-6 : bond 0.00611 ( 4) link_BETA1-6 : angle 1.72134 ( 12) SS BOND : bond 0.00204 ( 13) SS BOND : angle 1.21496 ( 26) covalent geometry : bond 0.00482 (10200) covalent geometry : angle 0.71812 (13900) Misc. bond : bond 0.00132 ( 1) *********************** 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: 3 poor density : 19 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 1107 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8600 (tm-30) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.2396 time to fit residues: 8.3766 Evaluate side-chains 21 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 1204 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 0.8980 chunk 99 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 10 optimal weight: 0.0010 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7566 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.061121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.044805 restraints weight = 56231.005| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 5.40 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1162 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= 0.119 Angle : 0.727 18.738 14058 Z= 0.325 Chirality : 0.051 0.513 1731 Planarity : 0.004 0.064 1734 Dihedral : 12.013 86.865 2230 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.89 % Favored : 93.78 % Rotamer: Outliers : 1.05 % Allowed : 7.63 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1222 helix: 1.69 (0.34), residues: 243 sheet: -1.10 (0.28), residues: 316 loop : -0.71 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 439 HIS 0.004 0.001 HIS A 110 PHE 0.009 0.001 PHE A 375 TYR 0.012 0.001 TYR A1245 ARG 0.002 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00962 ( 20) link_NAG-ASN : angle 4.74660 ( 60) link_ALPHA1-6 : bond 0.00088 ( 1) link_ALPHA1-6 : angle 1.89340 ( 3) link_BETA1-4 : bond 0.00705 ( 18) link_BETA1-4 : angle 2.82938 ( 54) link_ALPHA1-3 : bond 0.01278 ( 1) link_ALPHA1-3 : angle 1.99067 ( 3) hydrogen bonds : bond 0.03860 ( 368) hydrogen bonds : angle 4.84312 ( 1086) link_BETA1-6 : bond 0.00796 ( 4) link_BETA1-6 : angle 1.88104 ( 12) SS BOND : bond 0.00154 ( 13) SS BOND : angle 0.82906 ( 26) covalent geometry : bond 0.00248 (10200) covalent geometry : angle 0.63257 (13900) Misc. bond : bond 0.00027 ( 1) *********************** 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 33 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 1.235 Fit side-chains REVERT: A 619 TYR cc_start: 0.9013 (m-80) cc_final: 0.8617 (m-80) REVERT: A 795 GLU cc_start: 0.8512 (tp30) cc_final: 0.8254 (tp30) REVERT: A 1107 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8583 (tm-30) outliers start: 11 outliers final: 3 residues processed: 31 average time/residue: 0.1653 time to fit residues: 9.6848 Evaluate side-chains 20 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 0.0980 chunk 36 optimal weight: 0.0370 chunk 47 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.6264 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.060582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.044279 restraints weight = 55752.417| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 5.31 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10258 Z= 0.162 Angle : 0.730 18.069 14058 Z= 0.329 Chirality : 0.051 0.482 1731 Planarity : 0.004 0.058 1734 Dihedral : 10.891 82.847 2230 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.30 % Favored : 93.45 % Rotamer: Outliers : 1.53 % Allowed : 8.39 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1222 helix: 1.66 (0.34), residues: 243 sheet: -1.10 (0.29), residues: 317 loop : -0.68 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 439 HIS 0.004 0.001 HIS A 157 PHE 0.008 0.001 PHE A 36 TYR 0.014 0.001 TYR A1245 ARG 0.002 0.000 ARG A1112 Details of bonding type rmsd link_NAG-ASN : bond 0.00840 ( 20) link_NAG-ASN : angle 4.65950 ( 60) link_ALPHA1-6 : bond 0.00212 ( 1) link_ALPHA1-6 : angle 1.78963 ( 3) link_BETA1-4 : bond 0.00591 ( 18) link_BETA1-4 : angle 2.73927 ( 54) link_ALPHA1-3 : bond 0.01105 ( 1) link_ALPHA1-3 : angle 2.61512 ( 3) hydrogen bonds : bond 0.03728 ( 368) hydrogen bonds : angle 4.77444 ( 1086) link_BETA1-6 : bond 0.00563 ( 4) link_BETA1-6 : angle 2.15642 ( 12) SS BOND : bond 0.00220 ( 13) SS BOND : angle 0.85618 ( 26) covalent geometry : bond 0.00357 (10200) covalent geometry : angle 0.63894 (13900) Misc. bond : bond 0.00086 ( 1) *********************** 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 35 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 1.074 Fit side-chains REVERT: A 619 TYR cc_start: 0.9110 (m-80) cc_final: 0.8705 (m-80) REVERT: A 795 GLU cc_start: 0.8482 (tp30) cc_final: 0.8281 (tp30) REVERT: A 1107 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8575 (tm-30) outliers start: 16 outliers final: 11 residues processed: 32 average time/residue: 0.1919 time to fit residues: 10.6407 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 : 1.141 ------------------------------------------------------------------------------- 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 961 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.061186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.044759 restraints weight = 56098.383| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 5.41 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1497 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= 0.113 Angle : 0.700 17.837 14058 Z= 0.315 Chirality : 0.050 0.484 1731 Planarity : 0.004 0.055 1734 Dihedral : 10.395 80.002 2230 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 1.43 % Allowed : 10.30 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1222 helix: 1.66 (0.34), residues: 243 sheet: -0.95 (0.28), residues: 331 loop : -0.71 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 439 HIS 0.003 0.001 HIS A 110 PHE 0.009 0.001 PHE A 128 TYR 0.008 0.001 TYR A 184 ARG 0.004 0.000 ARG A 146 Details of bonding type rmsd link_NAG-ASN : bond 0.00890 ( 20) link_NAG-ASN : angle 4.55061 ( 60) link_ALPHA1-6 : bond 0.00254 ( 1) link_ALPHA1-6 : angle 1.78568 ( 3) link_BETA1-4 : bond 0.00614 ( 18) link_BETA1-4 : angle 2.62769 ( 54) link_ALPHA1-3 : bond 0.01170 ( 1) link_ALPHA1-3 : angle 2.09137 ( 3) hydrogen bonds : bond 0.03505 ( 368) hydrogen bonds : angle 4.66662 ( 1086) link_BETA1-6 : bond 0.00329 ( 4) link_BETA1-6 : angle 1.34786 ( 12) SS BOND : bond 0.00205 ( 13) SS BOND : angle 0.86552 ( 26) covalent geometry : bond 0.00238 (10200) covalent geometry : angle 0.61161 (13900) Misc. bond : bond 0.00032 ( 1) *********************** 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 35 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 619 TYR cc_start: 0.9132 (m-80) cc_final: 0.8711 (m-80) REVERT: A 795 GLU cc_start: 0.8459 (tp30) cc_final: 0.8259 (tp30) REVERT: A 1107 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8485 (tm-30) outliers start: 15 outliers final: 10 residues processed: 33 average time/residue: 0.1829 time to fit residues: 10.5042 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 : 1.023 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 28 optimal weight: 0.1980 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 548 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 = 0.3662 r_free = 0.3662 target = 0.061663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.045465 restraints weight = 55676.665| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 5.34 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1718 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= 0.105 Angle : 0.684 17.123 14058 Z= 0.306 Chirality : 0.049 0.494 1731 Planarity : 0.003 0.051 1734 Dihedral : 9.788 74.807 2230 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.32 % Favored : 94.44 % Rotamer: Outliers : 1.33 % Allowed : 11.63 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1222 helix: 1.76 (0.34), residues: 243 sheet: -0.88 (0.28), residues: 327 loop : -0.72 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 439 HIS 0.006 0.001 HIS A 157 PHE 0.009 0.001 PHE A 549 TYR 0.009 0.001 TYR A 184 ARG 0.004 0.000 ARG A 146 Details of bonding type rmsd link_NAG-ASN : bond 0.00900 ( 20) link_NAG-ASN : angle 4.41696 ( 60) link_ALPHA1-6 : bond 0.00356 ( 1) link_ALPHA1-6 : angle 1.68779 ( 3) link_BETA1-4 : bond 0.00597 ( 18) link_BETA1-4 : angle 2.58851 ( 54) link_ALPHA1-3 : bond 0.01075 ( 1) link_ALPHA1-3 : angle 1.95705 ( 3) hydrogen bonds : bond 0.03296 ( 368) hydrogen bonds : angle 4.49485 ( 1086) link_BETA1-6 : bond 0.00310 ( 4) link_BETA1-6 : angle 1.40942 ( 12) SS BOND : bond 0.00165 ( 13) SS BOND : angle 0.86230 ( 26) covalent geometry : bond 0.00214 (10200) covalent geometry : angle 0.59809 (13900) Misc. bond : bond 0.00009 ( 1) *********************** 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 37 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8611 (mp) REVERT: A 619 TYR cc_start: 0.9164 (m-80) cc_final: 0.8708 (m-80) REVERT: A 1107 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8386 (tm-30) REVERT: A 1245 TYR cc_start: 0.8575 (t80) cc_final: 0.7783 (t80) outliers start: 14 outliers final: 7 residues processed: 37 average time/residue: 0.1743 time to fit residues: 11.1786 Evaluate side-chains 27 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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 92 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 95 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 548 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 = 0.3659 r_free = 0.3659 target = 0.061536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.045229 restraints weight = 57036.128| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 5.42 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10258 Z= 0.115 Angle : 0.689 16.574 14058 Z= 0.308 Chirality : 0.049 0.492 1731 Planarity : 0.003 0.050 1734 Dihedral : 9.527 71.682 2230 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.40 % Favored : 94.35 % Rotamer: Outliers : 1.24 % Allowed : 12.39 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1222 helix: 1.75 (0.34), residues: 243 sheet: -0.84 (0.29), residues: 327 loop : -0.68 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 439 HIS 0.003 0.000 HIS A1192 PHE 0.012 0.001 PHE A 615 TYR 0.009 0.001 TYR A 66 ARG 0.003 0.000 ARG A1073 Details of bonding type rmsd link_NAG-ASN : bond 0.00851 ( 20) link_NAG-ASN : angle 4.34088 ( 60) link_ALPHA1-6 : bond 0.00350 ( 1) link_ALPHA1-6 : angle 1.67606 ( 3) link_BETA1-4 : bond 0.00582 ( 18) link_BETA1-4 : angle 2.55817 ( 54) link_ALPHA1-3 : bond 0.01110 ( 1) link_ALPHA1-3 : angle 2.07744 ( 3) hydrogen bonds : bond 0.03341 ( 368) hydrogen bonds : angle 4.48544 ( 1086) link_BETA1-6 : bond 0.00281 ( 4) link_BETA1-6 : angle 1.37949 ( 12) SS BOND : bond 0.00163 ( 13) SS BOND : angle 0.83710 ( 26) covalent geometry : bond 0.00244 (10200) covalent geometry : angle 0.60786 (13900) Misc. bond : bond 0.00026 ( 1) *********************** 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 31 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 1.087 Fit side-chains REVERT: A 619 TYR cc_start: 0.9190 (m-80) cc_final: 0.8766 (m-80) REVERT: A 1107 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8390 (tm-30) REVERT: A 1245 TYR cc_start: 0.8582 (t80) cc_final: 0.7778 (t80) outliers start: 13 outliers final: 9 residues processed: 31 average time/residue: 0.1909 time to fit residues: 10.1716 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 : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 65 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 96 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 548 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 = 0.3657 r_free = 0.3657 target = 0.061477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.045084 restraints weight = 56584.574| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 5.43 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10258 Z= 0.122 Angle : 0.695 16.165 14058 Z= 0.312 Chirality : 0.049 0.492 1731 Planarity : 0.003 0.048 1734 Dihedral : 9.329 69.505 2230 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.32 % Favored : 94.44 % Rotamer: Outliers : 1.05 % Allowed : 12.49 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1222 helix: 1.84 (0.34), residues: 243 sheet: -0.85 (0.28), residues: 327 loop : -0.66 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 439 HIS 0.003 0.000 HIS A1192 PHE 0.008 0.001 PHE A 549 TYR 0.009 0.001 TYR A 66 ARG 0.007 0.000 ARG A 146 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 20) link_NAG-ASN : angle 4.28745 ( 60) link_ALPHA1-6 : bond 0.00380 ( 1) link_ALPHA1-6 : angle 1.64741 ( 3) link_BETA1-4 : bond 0.00572 ( 18) link_BETA1-4 : angle 2.53914 ( 54) link_ALPHA1-3 : bond 0.01057 ( 1) link_ALPHA1-3 : angle 2.05542 ( 3) hydrogen bonds : bond 0.03321 ( 368) hydrogen bonds : angle 4.46710 ( 1086) link_BETA1-6 : bond 0.00275 ( 4) link_BETA1-6 : angle 1.37020 ( 12) SS BOND : bond 0.00132 ( 13) SS BOND : angle 1.14848 ( 26) covalent geometry : bond 0.00264 (10200) covalent geometry : angle 0.61580 (13900) Misc. bond : bond 0.00028 ( 1) *********************** 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 29 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 18 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 619 TYR cc_start: 0.9208 (m-80) cc_final: 0.8781 (m-80) REVERT: A 1107 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8391 (tm-30) REVERT: A 1245 TYR cc_start: 0.8588 (t80) cc_final: 0.7859 (t80) outliers start: 11 outliers final: 9 residues processed: 28 average time/residue: 0.1837 time to fit residues: 9.0124 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 : 1.031 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 79 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 44 optimal weight: 0.0980 chunk 16 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 548 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 = 0.3639 r_free = 0.3639 target = 0.061111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.044795 restraints weight = 56946.982| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 5.36 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1928 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= 0.158 Angle : 0.712 15.581 14058 Z= 0.321 Chirality : 0.049 0.487 1731 Planarity : 0.003 0.048 1734 Dihedral : 9.223 67.899 2230 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.65 % Favored : 94.11 % Rotamer: Outliers : 1.05 % Allowed : 12.58 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1222 helix: 1.87 (0.35), residues: 243 sheet: -0.90 (0.28), residues: 333 loop : -0.66 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 439 HIS 0.004 0.001 HIS A1192 PHE 0.008 0.001 PHE A 36 TYR 0.013 0.001 TYR A 66 ARG 0.005 0.000 ARG A 146 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 20) link_NAG-ASN : angle 4.25223 ( 60) link_ALPHA1-6 : bond 0.00413 ( 1) link_ALPHA1-6 : angle 1.59849 ( 3) link_BETA1-4 : bond 0.00552 ( 18) link_BETA1-4 : angle 2.50873 ( 54) link_ALPHA1-3 : bond 0.01041 ( 1) link_ALPHA1-3 : angle 2.27239 ( 3) hydrogen bonds : bond 0.03444 ( 368) hydrogen bonds : angle 4.52581 ( 1086) link_BETA1-6 : bond 0.00225 ( 4) link_BETA1-6 : angle 1.40066 ( 12) SS BOND : bond 0.00178 ( 13) SS BOND : angle 1.12382 ( 26) covalent geometry : bond 0.00347 (10200) covalent geometry : angle 0.63576 (13900) Misc. bond : bond 0.00064 ( 1) *********************** 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 : 1.102 Fit side-chains revert: symmetry clash REVERT: A 619 TYR cc_start: 0.9284 (m-80) cc_final: 0.8879 (m-80) REVERT: A 1107 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8500 (tm-30) REVERT: A 1245 TYR cc_start: 0.8626 (t80) cc_final: 0.7843 (t80) outliers start: 11 outliers final: 9 residues processed: 28 average time/residue: 0.1966 time to fit residues: 9.5983 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 : 1.143 ------------------------------------------------------------------------------- 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 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 548 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 = 0.3646 r_free = 0.3646 target = 0.061325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.044975 restraints weight = 56590.865| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 5.34 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1996 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= 0.127 Angle : 0.690 15.423 14058 Z= 0.311 Chirality : 0.049 0.485 1731 Planarity : 0.003 0.048 1734 Dihedral : 9.087 67.091 2230 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.48 % Favored : 94.27 % Rotamer: Outliers : 1.14 % Allowed : 12.39 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1222 helix: 1.83 (0.34), residues: 243 sheet: -0.87 (0.28), residues: 331 loop : -0.67 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 439 HIS 0.003 0.001 HIS A 157 PHE 0.008 0.001 PHE A 788 TYR 0.009 0.001 TYR A 66 ARG 0.003 0.000 ARG A 146 Details of bonding type rmsd link_NAG-ASN : bond 0.00808 ( 20) link_NAG-ASN : angle 4.21393 ( 60) link_ALPHA1-6 : bond 0.00492 ( 1) link_ALPHA1-6 : angle 1.55082 ( 3) link_BETA1-4 : bond 0.00580 ( 18) link_BETA1-4 : angle 2.49696 ( 54) link_ALPHA1-3 : bond 0.01092 ( 1) link_ALPHA1-3 : angle 2.07973 ( 3) hydrogen bonds : bond 0.03363 ( 368) hydrogen bonds : angle 4.46937 ( 1086) link_BETA1-6 : bond 0.00267 ( 4) link_BETA1-6 : angle 1.35187 ( 12) SS BOND : bond 0.00131 ( 13) SS BOND : angle 1.02214 ( 26) covalent geometry : bond 0.00275 (10200) covalent geometry : angle 0.61310 (13900) Misc. bond : bond 0.00038 ( 1) ********************** 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 31 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8531 (mp) REVERT: A 619 TYR cc_start: 0.9289 (m-80) cc_final: 0.8903 (m-80) REVERT: A 1107 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8442 (tm-30) REVERT: A 1245 TYR cc_start: 0.8633 (t80) cc_final: 0.7877 (t80) outliers start: 12 outliers final: 9 residues processed: 29 average time/residue: 0.2035 time to fit residues: 10.7199 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 : 1.146 ------------------------------------------------------------------------------- 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 418 LEU 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 72 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 12 optimal weight: 0.0670 chunk 1 optimal weight: 0.2980 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 205 GLN ** 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 = 0.3676 r_free = 0.3676 target = 0.062493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.046230 restraints weight = 56410.725| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 5.42 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2181 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= 0.102 Angle : 0.681 15.213 14058 Z= 0.305 Chirality : 0.049 0.491 1731 Planarity : 0.003 0.048 1734 Dihedral : 8.832 64.222 2230 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.32 % Favored : 94.44 % Rotamer: Outliers : 0.95 % Allowed : 12.49 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1222 helix: 1.93 (0.34), residues: 242 sheet: -0.78 (0.28), residues: 336 loop : -0.62 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 439 HIS 0.009 0.001 HIS A 157 PHE 0.010 0.001 PHE A 549 TYR 0.009 0.001 TYR A 796 ARG 0.002 0.000 ARG A 146 Details of bonding type rmsd link_NAG-ASN : bond 0.00902 ( 20) link_NAG-ASN : angle 4.13790 ( 60) link_ALPHA1-6 : bond 0.00622 ( 1) link_ALPHA1-6 : angle 1.47079 ( 3) link_BETA1-4 : bond 0.00620 ( 18) link_BETA1-4 : angle 2.51574 ( 54) link_ALPHA1-3 : bond 0.01030 ( 1) link_ALPHA1-3 : angle 1.75572 ( 3) hydrogen bonds : bond 0.03124 ( 368) hydrogen bonds : angle 4.32357 ( 1086) link_BETA1-6 : bond 0.00317 ( 4) link_BETA1-6 : angle 1.29704 ( 12) SS BOND : bond 0.00117 ( 13) SS BOND : angle 1.02838 ( 26) covalent geometry : bond 0.00208 (10200) covalent geometry : angle 0.60529 (13900) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4547.94 seconds wall clock time: 80 minutes 10.97 seconds (4810.97 seconds total)