Starting phenix.real_space_refine (version: dev) on Fri Sep 2 02:11:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6v_33649/09_2022/7y6v_33649.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6v_33649/09_2022/7y6v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6v_33649/09_2022/7y6v_33649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6v_33649/09_2022/7y6v_33649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6v_33649/09_2022/7y6v_33649.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6v_33649/09_2022/7y6v_33649.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4709/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: 2 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: 3 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: 1 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.16, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 5.65 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: 0.93 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: 4.45 Time building geometry restraints manager: 5.47 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=" C4 NAG J 1 " pdb=" C5 NAG J 1 " ideal model delta sigma weight residual 1.526 1.547 -0.021 1.30e-02 5.92e+03 2.50e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.426 1.470 -0.044 3.20e-02 9.77e+02 1.90e+00 bond pdb=" CA PHE A 299 " pdb=" C PHE A 299 " ideal model delta sigma weight residual 1.523 1.505 0.018 1.41e-02 5.03e+03 1.54e+00 bond pdb=" C7 NAG N 2 " pdb=" N2 NAG N 2 " ideal model delta sigma weight residual 1.337 1.350 -0.013 1.10e-02 8.26e+03 1.50e+00 bond pdb=" C7 NAG N 1 " pdb=" N2 NAG N 1 " ideal model delta sigma weight residual 1.337 1.350 -0.013 1.10e-02 8.26e+03 1.49e+00 ... (remaining 10195 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.39: 242 106.39 - 113.27: 5798 113.27 - 120.16: 3350 120.16 - 127.04: 4427 127.04 - 133.93: 83 Bond angle restraints: 13900 Sorted by residual: angle pdb=" C2 NAG J 1 " pdb=" N2 NAG J 1 " pdb=" C7 NAG J 1 " ideal model delta sigma weight residual 123.12 129.48 -6.36 1.28e+00 6.08e-01 2.45e+01 angle pdb=" C2 NAG N 1 " pdb=" N2 NAG N 1 " pdb=" C7 NAG N 1 " ideal model delta sigma weight residual 123.12 129.13 -6.01 1.28e+00 6.08e-01 2.19e+01 angle pdb=" C2 NAG K 1 " pdb=" N2 NAG K 1 " pdb=" C7 NAG K 1 " ideal model delta sigma weight residual 123.12 129.03 -5.91 1.28e+00 6.08e-01 2.12e+01 angle pdb=" C2 NAG N 2 " pdb=" N2 NAG N 2 " pdb=" C7 NAG N 2 " ideal model delta sigma weight residual 123.12 128.92 -5.80 1.28e+00 6.08e-01 2.04e+01 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 ... (remaining 13895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.45: 5628 20.45 - 40.90: 291 40.90 - 61.35: 42 61.35 - 81.80: 10 81.80 - 102.25: 10 Dihedral angle restraints: 5981 sinusoidal: 2433 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=" C2 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" C5 NAG E 1 " ideal model delta sinusoidal sigma weight residual 50.00 -52.25 102.25 1 2.00e+01 2.50e-03 2.91e+01 ... (remaining 5978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1705 0.126 - 0.251: 19 0.251 - 0.377: 3 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 2.440 nonbonded pdb=" O THR A 137 " pdb=" ND2 ASN A 140 " model vdw 2.179 2.520 nonbonded pdb=" O GLN A 821 " pdb=" OG1 THR A 824 " model vdw 2.188 2.440 nonbonded pdb=" O PRO A 498 " pdb=" OG1 THR A 650 " model vdw 2.211 2.440 nonbonded pdb=" O4 NAG G 1 " pdb=" O5 FUC G 2 " model vdw 2.224 2.440 ... (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 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 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. 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: 2.600 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: 10.380 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 32.080 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10200 Z= 0.206 Angle : 0.604 8.649 13900 Z= 0.350 Chirality : 0.052 0.628 1731 Planarity : 0.004 0.054 1734 Dihedral : 13.095 102.247 3674 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.166 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1897 time to fit residues: 8.1293 Evaluate side-chains 18 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6205 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 10200 Z= 0.312 Angle : 0.593 6.370 13900 Z= 0.335 Chirality : 0.053 0.766 1731 Planarity : 0.004 0.060 1734 Dihedral : 7.954 101.187 1631 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.96 % Favored : 92.80 % Rotamer Outliers : 0.38 % 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: -0.63 (0.25), residues: 1222 helix: 1.72 (0.35), residues: 241 sheet: -1.23 (0.28), residues: 313 loop : -0.76 (0.25), residues: 668 *********************** 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 23 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 1.093 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 21 average time/residue: 0.1694 time to fit residues: 7.0131 Evaluate side-chains 19 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0927 time to fit residues: 1.9314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 GLN A 996 GLN ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 10200 Z= 0.371 Angle : 0.609 6.311 13900 Z= 0.341 Chirality : 0.053 0.724 1731 Planarity : 0.004 0.066 1734 Dihedral : 8.063 102.703 1631 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.12 % Favored : 92.64 % Rotamer Outliers : 1.43 % 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: -0.80 (0.25), residues: 1222 helix: 1.57 (0.35), residues: 241 sheet: -1.42 (0.28), residues: 315 loop : -0.81 (0.25), residues: 666 *********************** 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 fitting. rotamer outliers: 15 poor density : 18 time to evaluate : 1.224 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 31 average time/residue: 0.1622 time to fit residues: 9.5510 Evaluate side-chains 23 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 16 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0997 time to fit residues: 2.8503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 10200 Z= 0.245 Angle : 0.548 8.350 13900 Z= 0.311 Chirality : 0.051 0.635 1731 Planarity : 0.004 0.060 1734 Dihedral : 7.953 102.432 1631 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.38 % Favored : 93.37 % Rotamer Outliers : 1.05 % 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: -0.70 (0.25), residues: 1222 helix: 1.73 (0.35), residues: 241 sheet: -1.31 (0.27), residues: 340 loop : -0.77 (0.26), residues: 641 *********************** 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 29 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 18 time to evaluate : 1.251 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 28 average time/residue: 0.1723 time to fit residues: 9.3199 Evaluate side-chains 21 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 15 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1097 time to fit residues: 2.8687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 105 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1418 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= 0.185 Angle : 0.527 7.565 13900 Z= 0.299 Chirality : 0.050 0.619 1731 Planarity : 0.004 0.057 1734 Dihedral : 7.828 101.944 1631 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.22 % Favored : 93.54 % Rotamer Outliers : 0.57 % 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: 1.86 (0.35), residues: 241 sheet: -1.20 (0.28), residues: 342 loop : -0.72 (0.26), residues: 639 *********************** 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 24 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 1.163 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 24 average time/residue: 0.2184 time to fit residues: 9.1920 Evaluate side-chains 18 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 118 optimal weight: 0.0470 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 10200 Z= 0.313 Angle : 0.578 7.672 13900 Z= 0.321 Chirality : 0.050 0.624 1731 Planarity : 0.004 0.053 1734 Dihedral : 7.950 103.454 1631 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.87 % Favored : 92.96 % Rotamer Outliers : 1.33 % 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: -0.70 (0.25), residues: 1222 helix: 1.76 (0.35), residues: 241 sheet: -1.24 (0.27), residues: 339 loop : -0.84 (0.26), residues: 642 *********************** 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 32 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 18 time to evaluate : 1.278 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 30 average time/residue: 0.1940 time to fit residues: 10.3813 Evaluate side-chains 22 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 16 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0916 time to fit residues: 2.3919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 73 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1668 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= 0.177 Angle : 0.536 7.943 13900 Z= 0.301 Chirality : 0.049 0.620 1731 Planarity : 0.004 0.052 1734 Dihedral : 7.819 102.456 1631 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.62 % Rotamer Outliers : 0.76 % 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: -0.58 (0.25), residues: 1222 helix: 1.82 (0.35), residues: 243 sheet: -1.10 (0.28), residues: 338 loop : -0.79 (0.26), residues: 641 *********************** 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 25 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 17 time to evaluate : 1.189 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 24 average time/residue: 0.1769 time to fit residues: 8.1957 Evaluate side-chains 18 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1226 time to fit residues: 2.1829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1757 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= 0.220 Angle : 0.535 7.455 13900 Z= 0.300 Chirality : 0.049 0.618 1731 Planarity : 0.004 0.051 1734 Dihedral : 7.813 102.720 1631 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.87 % Favored : 92.88 % Rotamer Outliers : 0.48 % 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: -0.58 (0.25), residues: 1222 helix: 1.89 (0.34), residues: 242 sheet: -1.17 (0.28), residues: 343 loop : -0.76 (0.26), residues: 637 *********************** 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 22 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 17 time to evaluate : 1.048 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 22 average time/residue: 0.1711 time to fit residues: 7.3530 Evaluate side-chains 20 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 16 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1003 time to fit residues: 2.2701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 0.0470 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1776 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= 0.166 Angle : 0.522 7.452 13900 Z= 0.293 Chirality : 0.048 0.611 1731 Planarity : 0.003 0.052 1734 Dihedral : 7.729 102.088 1631 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.73 % Favored : 94.03 % Rotamer Outliers : 0.38 % 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: 1.90 (0.35), residues: 244 sheet: -1.07 (0.28), residues: 344 loop : -0.73 (0.26), residues: 634 *********************** 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 23 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 1.147 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 23 average time/residue: 0.1777 time to fit residues: 7.7968 Evaluate side-chains 18 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.004 0.036 10200 Z= 0.240 Angle : 0.544 8.120 13900 Z= 0.303 Chirality : 0.048 0.612 1731 Planarity : 0.004 0.051 1734 Dihedral : 7.777 102.625 1631 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.71 % Favored : 93.04 % Rotamer Outliers : 0.10 % 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: 1.91 (0.34), residues: 244 sheet: -1.12 (0.28), residues: 348 loop : -0.75 (0.26), residues: 630 ********************** 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 18 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 1.042 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.1768 time to fit residues: 6.3832 Evaluate side-chains 17 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 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 = 0.3628 r_free = 0.3628 target = 0.060675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.044422 restraints weight = 56557.788| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 5.34 r_work: 0.3109 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1912 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= 0.185 Angle : 0.522 7.153 13900 Z= 0.293 Chirality : 0.048 0.609 1731 Planarity : 0.004 0.051 1734 Dihedral : 7.742 102.156 1631 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.30 % Favored : 93.45 % Rotamer Outliers : 0.19 % 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: 1.91 (0.34), residues: 244 sheet: -1.05 (0.28), residues: 345 loop : -0.75 (0.26), residues: 633 =============================================================================== Job complete usr+sys time: 1684.09 seconds wall clock time: 32 minutes 1.75 seconds (1921.75 seconds total)