Starting phenix.real_space_refine on Fri Feb 14 16:18:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6v_33649/02_2025/7y6v_33649.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6v_33649/02_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_33649/02_2025/7y6v_33649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6v_33649/02_2025/7y6v_33649.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6v_33649/02_2025/7y6v_33649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6v_33649/02_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-5592/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: 6.48, per 1000 atoms: 0.65 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: 3.25 Conformation dependent library (CDL) restraints added in 1.4 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: 1.39 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: 4.52 Time building geometry restraints manager: 3.59 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: 2.840 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.760 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.250 ------------------------------------------------------------------------------- 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 10200 Z= 0.277 Angle : 0.739 8.649 13900 Z= 0.356 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 *********************** 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 : 1.085 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: 0.1846 time to fit residues: 7.8459 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 : 1.232 ------------------------------------------------------------------------------- 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: 7.9990 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 = 0.043538 restraints weight = 56534.669| |-----------------------------------------------------------------------------| 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 10200 Z= 0.321 Angle : 0.718 9.458 13900 Z= 0.348 Chirality : 0.052 0.527 1731 Planarity : 0.004 0.062 1734 Dihedral : 14.532 95.036 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 *********************** 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 : 1.103 Fit side-chains revert: symmetry clash REVERT: A 1107 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8598 (tm-30) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.2374 time to fit residues: 8.3473 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 : 1.164 ------------------------------------------------------------------------------- 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: 5.9990 chunk 99 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 29 optimal weight: 0.9980 overall best weight: 0.8592 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.060952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.044617 restraints weight = 56308.711| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 5.40 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10200 Z= 0.171 Angle : 0.636 9.935 13900 Z= 0.304 Chirality : 0.051 0.520 1731 Planarity : 0.004 0.064 1734 Dihedral : 12.230 87.419 2230 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.81 % Favored : 93.86 % Rotamer: Outliers : 1.05 % Allowed : 7.82 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.68 (0.34), residues: 243 sheet: -1.07 (0.29), residues: 312 loop : -0.71 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 439 HIS 0.004 0.001 HIS A 110 PHE 0.009 0.001 PHE A 387 TYR 0.013 0.001 TYR A1245 ARG 0.002 0.000 ARG A 793 *********************** 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 31 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 1.134 Fit side-chains REVERT: A 158 MET cc_start: 0.9186 (pmm) cc_final: 0.8982 (pmm) REVERT: A 619 TYR cc_start: 0.9026 (m-80) cc_final: 0.8638 (m-80) REVERT: A 1107 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8570 (tm-30) outliers start: 11 outliers final: 3 residues processed: 29 average time/residue: 0.1872 time to fit residues: 9.6038 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 : 1.038 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 33 optimal weight: 0.0000 chunk 16 optimal weight: 4.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.059817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.043507 restraints weight = 57094.150| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 5.34 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10200 Z= 0.300 Angle : 0.671 10.191 13900 Z= 0.324 Chirality : 0.051 0.484 1731 Planarity : 0.004 0.058 1734 Dihedral : 10.943 83.072 2230 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.22 % Favored : 93.54 % Rotamer: Outliers : 1.72 % Allowed : 9.15 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.61 (0.25), residues: 1222 helix: 1.64 (0.34), residues: 241 sheet: -1.19 (0.29), residues: 317 loop : -0.72 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 439 HIS 0.004 0.001 HIS A1192 PHE 0.012 0.001 PHE A 36 TYR 0.028 0.001 TYR A1245 ARG 0.003 0.000 ARG A1112 *********************** 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 36 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 18 time to evaluate : 1.053 Fit side-chains REVERT: A 619 TYR cc_start: 0.9141 (m-80) cc_final: 0.8865 (m-80) REVERT: A 795 GLU cc_start: 0.8453 (tp30) cc_final: 0.8219 (tp30) REVERT: A 1107 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8548 (tm-30) outliers start: 18 outliers final: 11 residues processed: 33 average time/residue: 0.1524 time to fit residues: 9.3779 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 : 1.080 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 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 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 = 0.3615 r_free = 0.3615 target = 0.060096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043857 restraints weight = 57019.822| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 5.32 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10200 Z= 0.228 Angle : 0.630 10.164 13900 Z= 0.305 Chirality : 0.050 0.488 1731 Planarity : 0.004 0.056 1734 Dihedral : 10.495 80.950 2230 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.62 % Rotamer: Outliers : 1.81 % Allowed : 10.68 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.68 (0.34), residues: 241 sheet: -1.13 (0.28), residues: 332 loop : -0.76 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 439 HIS 0.004 0.001 HIS A1192 PHE 0.009 0.001 PHE A 788 TYR 0.011 0.001 TYR A 66 ARG 0.002 0.000 ARG A 146 *********************** 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 36 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 17 time to evaluate : 1.125 Fit side-chains REVERT: A 619 TYR cc_start: 0.9143 (m-80) cc_final: 0.8839 (m-80) REVERT: A 1107 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8519 (tm-30) outliers start: 19 outliers final: 11 residues processed: 34 average time/residue: 0.1884 time to fit residues: 11.4954 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 : 1.026 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 9.9990 chunk 3 optimal weight: 0.0470 chunk 2 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.8682 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.060667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.044497 restraints weight = 56646.254| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 5.33 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10200 Z= 0.165 Angle : 0.612 10.244 13900 Z= 0.293 Chirality : 0.050 0.498 1731 Planarity : 0.003 0.053 1734 Dihedral : 10.002 77.092 2230 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.40 % Favored : 94.35 % Rotamer: Outliers : 1.33 % Allowed : 12.01 % Favored : 86.65 % 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: -0.57 (0.25), residues: 1222 helix: 1.73 (0.34), residues: 243 sheet: -1.11 (0.28), residues: 328 loop : -0.75 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 439 HIS 0.003 0.001 HIS A 110 PHE 0.008 0.001 PHE A 549 TYR 0.018 0.001 TYR A1245 ARG 0.004 0.000 ARG A 146 *********************** 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 33 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 1.107 Fit side-chains REVERT: A 166 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8587 (mp) REVERT: A 619 TYR cc_start: 0.9196 (m-80) cc_final: 0.8862 (m-80) REVERT: A 1107 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8447 (tm-30) outliers start: 14 outliers final: 9 residues processed: 32 average time/residue: 0.1661 time to fit residues: 9.8805 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 : 1.068 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.060419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044140 restraints weight = 57751.731| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 5.36 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10200 Z= 0.198 Angle : 0.620 10.265 13900 Z= 0.296 Chirality : 0.049 0.493 1731 Planarity : 0.003 0.051 1734 Dihedral : 9.761 74.436 2230 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 1.53 % Allowed : 12.30 % Favored : 86.18 % 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: 1.73 (0.34), residues: 243 sheet: -1.03 (0.28), residues: 328 loop : -0.73 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 439 HIS 0.003 0.001 HIS A1192 PHE 0.008 0.001 PHE A 788 TYR 0.011 0.001 TYR A 66 ARG 0.003 0.000 ARG A 146 *********************** 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 : 1.131 Fit side-chains REVERT: A 619 TYR cc_start: 0.9210 (m-80) cc_final: 0.8851 (m-80) REVERT: A 1107 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8432 (tm-30) outliers start: 16 outliers final: 11 residues processed: 33 average time/residue: 0.1575 time to fit residues: 9.6215 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 : 1.049 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 102 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 overall best weight: 1.4164 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.060368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044094 restraints weight = 57007.371| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 5.32 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10200 Z= 0.206 Angle : 0.619 10.263 13900 Z= 0.297 Chirality : 0.049 0.493 1731 Planarity : 0.003 0.050 1734 Dihedral : 9.525 71.608 2230 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.89 % Favored : 93.86 % Rotamer: Outliers : 1.43 % Allowed : 12.77 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.25), residues: 1222 helix: 1.75 (0.34), residues: 243 sheet: -1.09 (0.28), residues: 330 loop : -0.76 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 439 HIS 0.003 0.001 HIS A1192 PHE 0.008 0.001 PHE A 788 TYR 0.011 0.001 TYR A 66 ARG 0.003 0.000 ARG A 146 *********************** 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 34 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 1.031 Fit side-chains REVERT: A 158 MET cc_start: 0.9163 (pmm) cc_final: 0.8872 (pmm) REVERT: A 619 TYR cc_start: 0.9249 (m-80) cc_final: 0.8867 (m-80) REVERT: A 795 GLU cc_start: 0.8398 (tp30) cc_final: 0.8192 (tp30) REVERT: A 1107 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8433 (tm-30) outliers start: 15 outliers final: 12 residues processed: 32 average time/residue: 0.1576 time to fit residues: 9.2892 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 : 1.030 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 79 optimal weight: 4.9990 chunk 120 optimal weight: 0.4980 chunk 21 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** ** 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 = 0.3613 r_free = 0.3613 target = 0.060053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.043741 restraints weight = 56912.420| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 5.34 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10200 Z= 0.231 Angle : 0.631 10.264 13900 Z= 0.303 Chirality : 0.049 0.490 1731 Planarity : 0.003 0.049 1734 Dihedral : 9.368 68.846 2230 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.70 % Rotamer: Outliers : 1.33 % Allowed : 13.16 % 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 (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: -0.56 (0.25), residues: 1222 helix: 1.75 (0.34), residues: 241 sheet: -1.07 (0.28), residues: 330 loop : -0.76 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 439 HIS 0.004 0.001 HIS A1192 PHE 0.009 0.001 PHE A 788 TYR 0.012 0.001 TYR A 66 ARG 0.002 0.000 ARG A 146 *********************** 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 32 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 1.161 Fit side-chains REVERT: A 158 MET cc_start: 0.9156 (pmm) cc_final: 0.8947 (pmm) REVERT: A 619 TYR cc_start: 0.9255 (m-80) cc_final: 0.8874 (m-80) REVERT: A 1107 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8477 (tm-30) outliers start: 14 outliers final: 12 residues processed: 31 average time/residue: 0.1608 time to fit residues: 9.4034 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 : 1.138 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 20 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 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 = 0.3629 r_free = 0.3629 target = 0.060543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.044336 restraints weight = 56646.591| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 5.31 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10200 Z= 0.169 Angle : 0.616 10.292 13900 Z= 0.294 Chirality : 0.049 0.491 1731 Planarity : 0.003 0.050 1734 Dihedral : 9.202 66.899 2230 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.56 % Favored : 94.19 % Rotamer: Outliers : 1.14 % Allowed : 13.54 % Favored : 85.32 % 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: 1.72 (0.34), residues: 243 sheet: -1.01 (0.28), residues: 331 loop : -0.77 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 439 HIS 0.003 0.001 HIS A1192 PHE 0.008 0.001 PHE A 549 TYR 0.008 0.001 TYR A 66 ARG 0.003 0.000 ARG A 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 1.107 Fit side-chains REVERT: A 158 MET cc_start: 0.9153 (pmm) cc_final: 0.8943 (pmm) REVERT: A 166 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8591 (mp) REVERT: A 619 TYR cc_start: 0.9272 (m-80) cc_final: 0.8904 (m-80) REVERT: A 1107 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8416 (tm-30) REVERT: A 1245 TYR cc_start: 0.8501 (t80) cc_final: 0.7655 (t80) outliers start: 12 outliers final: 9 residues processed: 28 average time/residue: 0.1671 time to fit residues: 8.8674 Evaluate side-chains 27 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 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 72 optimal weight: 0.0370 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 1 optimal weight: 0.3980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 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 = 0.3643 r_free = 0.3643 target = 0.061075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.044884 restraints weight = 56587.001| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 5.33 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10200 Z= 0.147 Angle : 0.606 10.332 13900 Z= 0.290 Chirality : 0.049 0.487 1731 Planarity : 0.003 0.050 1734 Dihedral : 9.010 64.462 2230 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.32 % Favored : 94.44 % Rotamer: Outliers : 1.14 % Allowed : 13.44 % 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 (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: -0.49 (0.25), residues: 1222 helix: 1.76 (0.34), residues: 243 sheet: -0.95 (0.28), residues: 334 loop : -0.73 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 439 HIS 0.003 0.000 HIS A 110 PHE 0.009 0.001 PHE A 549 TYR 0.008 0.001 TYR A 184 ARG 0.003 0.000 ARG A 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3929.41 seconds wall clock time: 71 minutes 11.88 seconds (4271.88 seconds total)