Starting phenix.real_space_refine on Fri May 23 23:24:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0n_42862/05_2025/8v0n_42862_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0n_42862/05_2025/8v0n_42862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0n_42862/05_2025/8v0n_42862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0n_42862/05_2025/8v0n_42862.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0n_42862/05_2025/8v0n_42862_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0n_42862/05_2025/8v0n_42862_neut.cif" } resolution = 3.4 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= 0.038 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 111 5.16 5 C 15735 2.51 5 N 4056 2.21 5 O 4788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24690 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8020 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 51, 'TRANS': 976} Chain breaks: 6 Chain: "B" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8020 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 51, 'TRANS': 976} Chain breaks: 6 Chain: "C" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8020 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 51, 'TRANS': 976} Chain breaks: 6 Chain: "D" 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: "E" 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: "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: 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: "H" 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: "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: 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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.22, per 1000 atoms: 0.62 Number of scatterers: 24690 At special positions: 0 Unit cell: (135, 127.44, 176.04, 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 111 16.00 O 4788 8.00 N 4056 7.00 C 15735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 616 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 234 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 234 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C1098 " " NAG L 1 " - " ASN C 801 " Time building additional restraints: 6.05 Conformation dependent library (CDL) restraints added in 3.5 seconds 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 43 sheets defined 26.2% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.015A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.727A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.629A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 841 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.588A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.097A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.803A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.965A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.667A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.894A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.742A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.660A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.816A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 841 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.596A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.013A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.188A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.716A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.592A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.168A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.022A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.542A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.633A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 835 through 841 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.704A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.764A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.625A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.093A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 4.416A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.358A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.098A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.962A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.723A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.636A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.572A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.116A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.492A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.599A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.056A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.674A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.729A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.868A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.727A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.117A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.553A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.431A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.277A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.813A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 722 removed outlier: 6.798A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.675A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.053A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.035A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.954A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.602A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.076A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.916A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 958 hydrogen bonds defined for protein. 2637 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: 10.27 Time building geometry restraints manager: 7.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7854 1.35 - 1.48: 6562 1.48 - 1.61: 10679 1.61 - 1.74: 0 1.74 - 1.86: 138 Bond restraints: 25233 Sorted by residual: bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.326 1.382 -0.056 1.44e-02 4.82e+03 1.49e+01 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" C1 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" CA VAL C 620 " pdb=" C VAL C 620 " ideal model delta sigma weight residual 1.520 1.543 -0.023 8.80e-03 1.29e+04 7.04e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.54e+00 ... (remaining 25228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 33757 2.63 - 5.25: 490 5.25 - 7.88: 58 7.88 - 10.51: 12 10.51 - 13.14: 3 Bond angle restraints: 34320 Sorted by residual: angle pdb=" N ASP B 198 " pdb=" CA ASP B 198 " pdb=" CB ASP B 198 " ideal model delta sigma weight residual 114.17 108.10 6.07 1.14e+00 7.69e-01 2.83e+01 angle pdb=" N ILE C 235 " pdb=" CA ILE C 235 " pdb=" C ILE C 235 " ideal model delta sigma weight residual 113.47 108.18 5.29 1.01e+00 9.80e-01 2.75e+01 angle pdb=" C ASP B 198 " pdb=" CA ASP B 198 " pdb=" CB ASP B 198 " ideal model delta sigma weight residual 110.06 117.00 -6.94 1.44e+00 4.82e-01 2.32e+01 angle pdb=" C GLY C 744 " pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 121.54 130.45 -8.91 1.91e+00 2.74e-01 2.18e+01 angle pdb=" CG1 ILE B 119 " pdb=" CB ILE B 119 " pdb=" CG2 ILE B 119 " ideal model delta sigma weight residual 110.70 97.56 13.14 3.00e+00 1.11e-01 1.92e+01 ... (remaining 34315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.20: 14073 18.20 - 36.40: 1278 36.40 - 54.61: 233 54.61 - 72.81: 49 72.81 - 91.01: 24 Dihedral angle restraints: 15657 sinusoidal: 6678 harmonic: 8979 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -15.02 -70.98 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -19.75 -66.25 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 143.16 36.84 0 5.00e+00 4.00e-02 5.43e+01 ... (remaining 15654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3781 0.107 - 0.214: 242 0.214 - 0.321: 9 0.321 - 0.428: 5 0.428 - 0.536: 1 Chirality restraints: 4038 Sorted by residual: chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" CB ILE B 119 " pdb=" CA ILE B 119 " pdb=" CG1 ILE B 119 " pdb=" CG2 ILE B 119 " both_signs ideal model delta sigma weight residual False 2.64 3.05 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 4035 not shown) Planarity restraints: 4413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.008 2.00e-02 2.50e+03 3.52e-02 1.55e+01 pdb=" CG ASN A 234 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.043 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 808 " 0.061 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO B 809 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 809 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 809 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 198 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ASP B 198 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP B 198 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY B 199 " 0.017 2.00e-02 2.50e+03 ... (remaining 4410 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6432 2.81 - 3.33: 19910 3.33 - 3.85: 39427 3.85 - 4.38: 43552 4.38 - 4.90: 79280 Nonbonded interactions: 188601 Sorted by model distance: nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.286 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.304 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.312 3.040 nonbonded pdb=" OG SER C 31 " pdb=" OG SER C 60 " model vdw 2.319 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.322 3.040 ... (remaining 188596 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.960 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: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 57.840 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.110 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 0.059 25317 Z= 0.219 Angle : 0.823 24.282 34533 Z= 0.417 Chirality : 0.056 0.536 4038 Planarity : 0.006 0.093 4377 Dihedral : 14.359 91.012 9762 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.17 (0.14), residues: 3042 helix: 0.08 (0.18), residues: 696 sheet: 0.41 (0.20), residues: 621 loop : -1.66 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 64 HIS 0.005 0.001 HIS C 339 PHE 0.038 0.002 PHE B 238 TYR 0.029 0.001 TYR A 495 ARG 0.017 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.01006 ( 36) link_NAG-ASN : angle 4.84769 ( 108) link_BETA1-4 : bond 0.00708 ( 9) link_BETA1-4 : angle 1.43427 ( 27) hydrogen bonds : bond 0.07792 ( 958) hydrogen bonds : angle 5.56084 ( 2637) SS BOND : bond 0.00587 ( 39) SS BOND : angle 1.92849 ( 78) covalent geometry : bond 0.00432 (25233) covalent geometry : angle 0.77326 (34320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.6944 (t80) cc_final: 0.6239 (t80) REVERT: A 586 ASP cc_start: 0.8263 (m-30) cc_final: 0.7989 (m-30) REVERT: A 780 GLU cc_start: 0.7808 (tt0) cc_final: 0.7496 (tt0) REVERT: B 460 LYS cc_start: 0.7403 (mttt) cc_final: 0.6736 (mttm) REVERT: B 574 ASP cc_start: 0.7936 (t0) cc_final: 0.7730 (t0) REVERT: B 955 ASN cc_start: 0.7266 (m110) cc_final: 0.6905 (m-40) REVERT: C 32 PHE cc_start: 0.6975 (m-80) cc_final: 0.6704 (m-80) REVERT: C 564 GLN cc_start: 0.7600 (mm110) cc_final: 0.7392 (mm110) REVERT: C 574 ASP cc_start: 0.7203 (t70) cc_final: 0.6917 (m-30) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.3581 time to fit residues: 144.7520 Evaluate side-chains 195 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 145 optimal weight: 0.0370 chunk 178 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN B 30 ASN B 115 GLN B 613 GLN C 115 GLN C 394 ASN C 405 ASN C 613 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.163399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116848 restraints weight = 31671.999| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.67 r_work: 0.3114 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25317 Z= 0.120 Angle : 0.553 15.547 34533 Z= 0.274 Chirality : 0.044 0.294 4038 Planarity : 0.004 0.063 4377 Dihedral : 6.887 57.613 4248 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.60 % Allowed : 5.64 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3042 helix: 1.25 (0.19), residues: 726 sheet: 0.45 (0.19), residues: 663 loop : -1.53 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.005 0.001 HIS C1048 PHE 0.013 0.001 PHE A 192 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 36) link_NAG-ASN : angle 3.42104 ( 108) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 1.11376 ( 27) hydrogen bonds : bond 0.04448 ( 958) hydrogen bonds : angle 4.78772 ( 2637) SS BOND : bond 0.00416 ( 39) SS BOND : angle 1.26260 ( 78) covalent geometry : bond 0.00276 (25233) covalent geometry : angle 0.51652 (34320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7111 (t80) cc_final: 0.6247 (t80) REVERT: A 498 ARG cc_start: 0.6918 (mmt90) cc_final: 0.6474 (mmt90) REVERT: A 586 ASP cc_start: 0.8595 (m-30) cc_final: 0.8283 (m-30) REVERT: A 780 GLU cc_start: 0.8424 (tt0) cc_final: 0.8160 (tt0) REVERT: B 360 ASN cc_start: 0.8117 (t0) cc_final: 0.7837 (t0) REVERT: B 568 ASP cc_start: 0.7179 (t0) cc_final: 0.6916 (t0) REVERT: B 574 ASP cc_start: 0.8065 (t0) cc_final: 0.7740 (t0) REVERT: B 591 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8175 (p) REVERT: B 955 ASN cc_start: 0.7464 (m110) cc_final: 0.7031 (m-40) REVERT: B 964 LYS cc_start: 0.8636 (tptm) cc_final: 0.8019 (ttmt) REVERT: C 32 PHE cc_start: 0.6976 (m-80) cc_final: 0.6655 (m-80) REVERT: C 269 TYR cc_start: 0.7020 (m-10) cc_final: 0.6757 (m-80) REVERT: C 458 LYS cc_start: 0.8401 (mmmm) cc_final: 0.8114 (tppt) REVERT: C 564 GLN cc_start: 0.7712 (mm110) cc_final: 0.7467 (mm110) outliers start: 16 outliers final: 11 residues processed: 231 average time/residue: 0.3515 time to fit residues: 130.9864 Evaluate side-chains 214 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 198 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 218 GLN B 901 GLN B1135 ASN C 26 GLN C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.157864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116065 restraints weight = 31712.652| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.01 r_work: 0.2992 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25317 Z= 0.199 Angle : 0.609 13.709 34533 Z= 0.306 Chirality : 0.046 0.276 4038 Planarity : 0.004 0.054 4377 Dihedral : 6.477 57.625 4248 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.90 % Allowed : 9.11 % Favored : 90.00 % 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: -0.53 (0.15), residues: 3042 helix: 1.45 (0.20), residues: 726 sheet: 0.16 (0.19), residues: 693 loop : -1.49 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.006 0.001 HIS C1048 PHE 0.022 0.002 PHE C 92 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 36) link_NAG-ASN : angle 3.06881 ( 108) link_BETA1-4 : bond 0.00330 ( 9) link_BETA1-4 : angle 1.04243 ( 27) hydrogen bonds : bond 0.05674 ( 958) hydrogen bonds : angle 4.89424 ( 2637) SS BOND : bond 0.00445 ( 39) SS BOND : angle 1.57919 ( 78) covalent geometry : bond 0.00486 (25233) covalent geometry : angle 0.58025 (34320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 2.759 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7318 (t80) cc_final: 0.6332 (t80) REVERT: A 498 ARG cc_start: 0.6922 (mmt90) cc_final: 0.6554 (mmt90) REVERT: A 780 GLU cc_start: 0.8670 (tt0) cc_final: 0.8429 (tt0) REVERT: B 360 ASN cc_start: 0.8289 (t0) cc_final: 0.7986 (t0) REVERT: B 568 ASP cc_start: 0.7325 (t0) cc_final: 0.7104 (t0) REVERT: B 574 ASP cc_start: 0.8238 (t0) cc_final: 0.7886 (t0) REVERT: B 591 SER cc_start: 0.8774 (m) cc_final: 0.8190 (p) REVERT: B 752 LEU cc_start: 0.9094 (mp) cc_final: 0.8831 (mp) REVERT: B 955 ASN cc_start: 0.7343 (m110) cc_final: 0.7034 (m110) REVERT: B 1138 TYR cc_start: 0.7807 (t80) cc_final: 0.7528 (t80) REVERT: C 319 ARG cc_start: 0.7712 (ttm110) cc_final: 0.7447 (ptp-110) REVERT: C 414 GLN cc_start: 0.7299 (mt0) cc_final: 0.6171 (mp10) REVERT: C 564 GLN cc_start: 0.7674 (mm110) cc_final: 0.7469 (mm110) REVERT: C 900 MET cc_start: 0.8531 (mtp) cc_final: 0.8246 (mtp) outliers start: 24 outliers final: 14 residues processed: 229 average time/residue: 0.3270 time to fit residues: 123.2606 Evaluate side-chains 214 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 225 optimal weight: 0.5980 chunk 302 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 296 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 274 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 926 GLN B 563 GLN C 30 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113309 restraints weight = 31717.918| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.70 r_work: 0.3054 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25317 Z= 0.135 Angle : 0.543 12.581 34533 Z= 0.271 Chirality : 0.044 0.270 4038 Planarity : 0.004 0.047 4377 Dihedral : 6.088 57.265 4248 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.12 % Allowed : 10.94 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3042 helix: 1.61 (0.20), residues: 741 sheet: 0.26 (0.19), residues: 687 loop : -1.41 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS B1048 PHE 0.024 0.001 PHE C 92 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 36) link_NAG-ASN : angle 2.86322 ( 108) link_BETA1-4 : bond 0.00351 ( 9) link_BETA1-4 : angle 0.99115 ( 27) hydrogen bonds : bond 0.04846 ( 958) hydrogen bonds : angle 4.70978 ( 2637) SS BOND : bond 0.00408 ( 39) SS BOND : angle 1.32751 ( 78) covalent geometry : bond 0.00322 (25233) covalent geometry : angle 0.51551 (34320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 2.924 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7311 (t80) cc_final: 0.6307 (t80) REVERT: A 498 ARG cc_start: 0.6852 (mmt90) cc_final: 0.6474 (mmt90) REVERT: A 780 GLU cc_start: 0.8618 (tt0) cc_final: 0.8387 (tt0) REVERT: B 360 ASN cc_start: 0.8272 (t0) cc_final: 0.7937 (t0) REVERT: B 420 ASP cc_start: 0.8134 (m-30) cc_final: 0.7731 (t70) REVERT: B 493 GLN cc_start: 0.7737 (tp-100) cc_final: 0.7472 (tp-100) REVERT: B 568 ASP cc_start: 0.7132 (t0) cc_final: 0.6914 (t0) REVERT: B 574 ASP cc_start: 0.8139 (t0) cc_final: 0.7850 (t0) REVERT: B 591 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8123 (p) REVERT: B 752 LEU cc_start: 0.9073 (mp) cc_final: 0.8823 (mp) REVERT: B 902 MET cc_start: 0.8927 (mmm) cc_final: 0.8656 (mmt) REVERT: B 955 ASN cc_start: 0.7320 (m110) cc_final: 0.6937 (m110) REVERT: B 1138 TYR cc_start: 0.7779 (t80) cc_final: 0.7463 (t80) REVERT: C 319 ARG cc_start: 0.7677 (ttm110) cc_final: 0.7413 (ptp-110) REVERT: C 564 GLN cc_start: 0.7632 (mm110) cc_final: 0.7431 (mm110) outliers start: 30 outliers final: 22 residues processed: 224 average time/residue: 0.3345 time to fit residues: 124.0993 Evaluate side-chains 222 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 42 optimal weight: 0.8980 chunk 285 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 23 optimal weight: 0.0070 chunk 266 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 176 optimal weight: 0.0050 chunk 209 optimal weight: 6.9990 overall best weight: 0.4612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1088 HIS B 474 GLN C 30 ASN C 394 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116134 restraints weight = 31675.592| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.67 r_work: 0.3085 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25317 Z= 0.093 Angle : 0.501 12.482 34533 Z= 0.249 Chirality : 0.043 0.263 4038 Planarity : 0.003 0.045 4377 Dihedral : 5.583 57.002 4248 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.05 % Allowed : 11.76 % Favored : 87.20 % 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: -0.11 (0.15), residues: 3042 helix: 1.92 (0.20), residues: 741 sheet: 0.40 (0.19), residues: 699 loop : -1.32 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS C 519 PHE 0.026 0.001 PHE C 92 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 36) link_NAG-ASN : angle 2.69198 ( 108) link_BETA1-4 : bond 0.00351 ( 9) link_BETA1-4 : angle 0.99023 ( 27) hydrogen bonds : bond 0.04037 ( 958) hydrogen bonds : angle 4.46979 ( 2637) SS BOND : bond 0.00329 ( 39) SS BOND : angle 1.04777 ( 78) covalent geometry : bond 0.00200 (25233) covalent geometry : angle 0.47584 (34320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 2.900 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7260 (t80) cc_final: 0.6280 (t80) REVERT: A 177 MET cc_start: 0.3551 (mtt) cc_final: 0.2735 (mtm) REVERT: A 498 ARG cc_start: 0.6859 (mmt90) cc_final: 0.6460 (mmt90) REVERT: A 586 ASP cc_start: 0.8490 (m-30) cc_final: 0.8170 (m-30) REVERT: A 780 GLU cc_start: 0.8564 (tt0) cc_final: 0.8232 (tt0) REVERT: B 360 ASN cc_start: 0.8279 (t0) cc_final: 0.7935 (t0) REVERT: B 420 ASP cc_start: 0.8092 (m-30) cc_final: 0.7714 (t0) REVERT: B 568 ASP cc_start: 0.7032 (t0) cc_final: 0.6815 (t0) REVERT: B 574 ASP cc_start: 0.8024 (t0) cc_final: 0.7686 (t0) REVERT: B 591 SER cc_start: 0.8703 (m) cc_final: 0.8107 (p) REVERT: B 955 ASN cc_start: 0.7394 (m110) cc_final: 0.6930 (m110) REVERT: B 1138 TYR cc_start: 0.7729 (t80) cc_final: 0.7387 (t80) REVERT: C 269 TYR cc_start: 0.7091 (m-10) cc_final: 0.6706 (m-80) REVERT: C 394 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7846 (m110) REVERT: C 564 GLN cc_start: 0.7576 (mm110) cc_final: 0.7370 (mm110) REVERT: C 900 MET cc_start: 0.8411 (mtp) cc_final: 0.8157 (mtp) outliers start: 28 outliers final: 21 residues processed: 236 average time/residue: 0.3439 time to fit residues: 132.9208 Evaluate side-chains 231 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 106 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 280 optimal weight: 0.8980 chunk 284 optimal weight: 0.7980 chunk 281 optimal weight: 0.5980 chunk 32 optimal weight: 0.0470 chunk 83 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN B 563 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116391 restraints weight = 31453.324| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.66 r_work: 0.3050 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25317 Z= 0.098 Angle : 0.505 12.315 34533 Z= 0.252 Chirality : 0.043 0.295 4038 Planarity : 0.003 0.044 4377 Dihedral : 5.502 56.895 4248 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.19 % Allowed : 12.24 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.03 (0.15), residues: 3042 helix: 1.95 (0.20), residues: 744 sheet: 0.46 (0.19), residues: 699 loop : -1.25 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.000 HIS C 519 PHE 0.026 0.001 PHE C 92 TYR 0.016 0.001 TYR A1067 ARG 0.006 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 36) link_NAG-ASN : angle 2.65001 ( 108) link_BETA1-4 : bond 0.00360 ( 9) link_BETA1-4 : angle 0.98244 ( 27) hydrogen bonds : bond 0.04053 ( 958) hydrogen bonds : angle 4.44587 ( 2637) SS BOND : bond 0.00367 ( 39) SS BOND : angle 1.41223 ( 78) covalent geometry : bond 0.00222 (25233) covalent geometry : angle 0.47910 (34320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 2.470 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7331 (t80) cc_final: 0.6346 (t80) REVERT: A 177 MET cc_start: 0.3551 (mtt) cc_final: 0.2706 (mtm) REVERT: A 498 ARG cc_start: 0.6813 (mmt90) cc_final: 0.6607 (mmt90) REVERT: A 586 ASP cc_start: 0.8628 (m-30) cc_final: 0.8320 (m-30) REVERT: A 780 GLU cc_start: 0.8763 (tt0) cc_final: 0.8449 (tt0) REVERT: B 360 ASN cc_start: 0.8358 (t0) cc_final: 0.8024 (t0) REVERT: B 420 ASP cc_start: 0.8126 (m-30) cc_final: 0.7777 (t0) REVERT: B 493 GLN cc_start: 0.7715 (tp-100) cc_final: 0.7512 (tp-100) REVERT: B 568 ASP cc_start: 0.7148 (t0) cc_final: 0.6909 (t0) REVERT: B 574 ASP cc_start: 0.8088 (t0) cc_final: 0.7748 (t0) REVERT: B 591 SER cc_start: 0.8698 (m) cc_final: 0.8099 (p) REVERT: B 955 ASN cc_start: 0.7548 (m110) cc_final: 0.7077 (m110) REVERT: B 1138 TYR cc_start: 0.7757 (t80) cc_final: 0.7394 (t80) REVERT: C 269 TYR cc_start: 0.7196 (m-10) cc_final: 0.6898 (m-80) REVERT: C 564 GLN cc_start: 0.7646 (mm110) cc_final: 0.7437 (mm110) REVERT: C 900 MET cc_start: 0.8618 (mtp) cc_final: 0.8380 (mtp) outliers start: 32 outliers final: 25 residues processed: 243 average time/residue: 0.3161 time to fit residues: 126.2615 Evaluate side-chains 238 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 252 optimal weight: 4.9990 chunk 201 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 225 optimal weight: 0.0010 chunk 145 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 chunk 271 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN A1135 ASN B 563 GLN C 26 GLN C 394 ASN C 414 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.163597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122889 restraints weight = 31605.416| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.97 r_work: 0.3077 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25317 Z= 0.088 Angle : 0.487 11.849 34533 Z= 0.243 Chirality : 0.043 0.296 4038 Planarity : 0.003 0.044 4377 Dihedral : 5.285 56.756 4248 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.16 % Allowed : 12.77 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.10 (0.15), residues: 3042 helix: 2.06 (0.20), residues: 744 sheet: 0.53 (0.19), residues: 699 loop : -1.17 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS C 519 PHE 0.026 0.001 PHE C 92 TYR 0.016 0.001 TYR A1067 ARG 0.006 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 36) link_NAG-ASN : angle 2.53353 ( 108) link_BETA1-4 : bond 0.00361 ( 9) link_BETA1-4 : angle 0.96482 ( 27) hydrogen bonds : bond 0.03758 ( 958) hydrogen bonds : angle 4.35158 ( 2637) SS BOND : bond 0.00281 ( 39) SS BOND : angle 1.06134 ( 78) covalent geometry : bond 0.00192 (25233) covalent geometry : angle 0.46425 (34320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 2.476 Fit side-chains revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7530 (m-10) cc_final: 0.7062 (m-10) REVERT: A 170 TYR cc_start: 0.7268 (t80) cc_final: 0.6259 (t80) REVERT: A 177 MET cc_start: 0.3860 (mtt) cc_final: 0.2835 (mtm) REVERT: A 465 GLU cc_start: 0.8419 (pt0) cc_final: 0.8149 (pt0) REVERT: A 586 ASP cc_start: 0.8431 (m-30) cc_final: 0.8157 (m-30) REVERT: A 780 GLU cc_start: 0.8544 (tt0) cc_final: 0.8233 (tt0) REVERT: B 360 ASN cc_start: 0.8291 (t0) cc_final: 0.7918 (t0) REVERT: B 420 ASP cc_start: 0.8024 (m-30) cc_final: 0.7532 (t70) REVERT: B 493 GLN cc_start: 0.7634 (tp-100) cc_final: 0.7366 (tp-100) REVERT: B 574 ASP cc_start: 0.7942 (t0) cc_final: 0.7731 (t0) REVERT: B 591 SER cc_start: 0.8673 (m) cc_final: 0.8064 (p) REVERT: B 955 ASN cc_start: 0.7358 (m110) cc_final: 0.6994 (m110) REVERT: B 1138 TYR cc_start: 0.7758 (t80) cc_final: 0.7375 (t80) REVERT: C 269 TYR cc_start: 0.7177 (m-10) cc_final: 0.6835 (m-80) REVERT: C 319 ARG cc_start: 0.7807 (ptp-110) cc_final: 0.7185 (ptp-110) REVERT: C 394 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7681 (m110) REVERT: C 564 GLN cc_start: 0.7512 (mm110) cc_final: 0.7297 (mm110) outliers start: 31 outliers final: 24 residues processed: 255 average time/residue: 0.3293 time to fit residues: 137.6081 Evaluate side-chains 248 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 110 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 222 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN B 563 GLN C 394 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.159213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114096 restraints weight = 31507.550| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.78 r_work: 0.3055 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25317 Z= 0.177 Angle : 0.556 11.936 34533 Z= 0.280 Chirality : 0.045 0.299 4038 Planarity : 0.004 0.044 4377 Dihedral : 5.547 56.813 4248 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.27 % Allowed : 13.21 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.10 (0.15), residues: 3042 helix: 1.81 (0.20), residues: 741 sheet: 0.42 (0.19), residues: 699 loop : -1.25 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS C1048 PHE 0.022 0.001 PHE C 92 TYR 0.018 0.001 TYR B1067 ARG 0.007 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 36) link_NAG-ASN : angle 2.58352 ( 108) link_BETA1-4 : bond 0.00350 ( 9) link_BETA1-4 : angle 0.98768 ( 27) hydrogen bonds : bond 0.04890 ( 958) hydrogen bonds : angle 4.57423 ( 2637) SS BOND : bond 0.00360 ( 39) SS BOND : angle 1.34354 ( 78) covalent geometry : bond 0.00432 (25233) covalent geometry : angle 0.53455 (34320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 2.603 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7382 (t80) cc_final: 0.6354 (t80) REVERT: A 177 MET cc_start: 0.4159 (mtt) cc_final: 0.3050 (mtm) REVERT: A 497 PHE cc_start: 0.6066 (m-10) cc_final: 0.5669 (m-10) REVERT: A 586 ASP cc_start: 0.8520 (m-30) cc_final: 0.8262 (m-30) REVERT: A 780 GLU cc_start: 0.8702 (tt0) cc_final: 0.8473 (tt0) REVERT: B 360 ASN cc_start: 0.8347 (t0) cc_final: 0.7988 (t0) REVERT: B 420 ASP cc_start: 0.8104 (m-30) cc_final: 0.7724 (t0) REVERT: B 493 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7470 (tp-100) REVERT: B 574 ASP cc_start: 0.8133 (t0) cc_final: 0.7874 (t0) REVERT: B 591 SER cc_start: 0.8759 (m) cc_final: 0.8178 (p) REVERT: B 902 MET cc_start: 0.8926 (mmm) cc_final: 0.8648 (mmm) REVERT: B 955 ASN cc_start: 0.7297 (m110) cc_final: 0.6941 (m110) REVERT: B 1138 TYR cc_start: 0.8016 (t80) cc_final: 0.7683 (t80) REVERT: C 319 ARG cc_start: 0.7980 (ptp-110) cc_final: 0.7372 (ptp-110) REVERT: C 414 GLN cc_start: 0.7160 (mt0) cc_final: 0.6126 (mp10) outliers start: 34 outliers final: 31 residues processed: 239 average time/residue: 0.3219 time to fit residues: 127.3564 Evaluate side-chains 242 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 179 optimal weight: 0.6980 chunk 286 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 123 optimal weight: 0.0040 chunk 159 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 253 optimal weight: 0.9980 chunk 304 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 GLN ** C 414 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 = 0.3825 r_free = 0.3825 target = 0.160748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114603 restraints weight = 31571.278| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.68 r_work: 0.3026 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25317 Z= 0.115 Angle : 0.526 12.068 34533 Z= 0.262 Chirality : 0.043 0.294 4038 Planarity : 0.003 0.045 4377 Dihedral : 5.463 56.906 4248 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.27 % Allowed : 13.77 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.02 (0.15), residues: 3042 helix: 1.94 (0.20), residues: 741 sheet: 0.45 (0.19), residues: 699 loop : -1.22 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS C1048 PHE 0.023 0.001 PHE C 92 TYR 0.017 0.001 TYR A1067 ARG 0.005 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 36) link_NAG-ASN : angle 2.53270 ( 108) link_BETA1-4 : bond 0.00351 ( 9) link_BETA1-4 : angle 0.94956 ( 27) hydrogen bonds : bond 0.04370 ( 958) hydrogen bonds : angle 4.48012 ( 2637) SS BOND : bond 0.00378 ( 39) SS BOND : angle 1.79388 ( 78) covalent geometry : bond 0.00267 (25233) covalent geometry : angle 0.50067 (34320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 2.524 Fit side-chains revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7572 (m-10) cc_final: 0.7097 (m-10) REVERT: A 170 TYR cc_start: 0.7427 (t80) cc_final: 0.6391 (t80) REVERT: A 177 MET cc_start: 0.4068 (mtt) cc_final: 0.2909 (mtm) REVERT: A 497 PHE cc_start: 0.6216 (m-10) cc_final: 0.5516 (m-10) REVERT: A 586 ASP cc_start: 0.8611 (m-30) cc_final: 0.8352 (m-30) REVERT: A 780 GLU cc_start: 0.8759 (tt0) cc_final: 0.8548 (tt0) REVERT: B 173 GLN cc_start: 0.7532 (tm-30) cc_final: 0.7266 (tm-30) REVERT: B 360 ASN cc_start: 0.8421 (t0) cc_final: 0.8053 (t0) REVERT: B 420 ASP cc_start: 0.8122 (m-30) cc_final: 0.7777 (t0) REVERT: B 493 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7517 (tp-100) REVERT: B 574 ASP cc_start: 0.8147 (t0) cc_final: 0.7905 (t0) REVERT: B 591 SER cc_start: 0.8684 (m) cc_final: 0.8076 (p) REVERT: B 902 MET cc_start: 0.8919 (mmm) cc_final: 0.8671 (mmm) REVERT: B 955 ASN cc_start: 0.7424 (m110) cc_final: 0.7022 (m110) REVERT: B 1138 TYR cc_start: 0.7828 (t80) cc_final: 0.7459 (t80) REVERT: C 319 ARG cc_start: 0.8140 (ptp-110) cc_final: 0.7473 (ptp-110) REVERT: C 414 GLN cc_start: 0.7168 (mt0) cc_final: 0.6060 (mp10) outliers start: 34 outliers final: 32 residues processed: 241 average time/residue: 0.3160 time to fit residues: 126.4850 Evaluate side-chains 244 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 49 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 chunk 235 optimal weight: 0.7980 chunk 176 optimal weight: 0.3980 chunk 100 optimal weight: 0.9980 chunk 136 optimal weight: 0.0040 chunk 303 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 GLN ** C 414 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 = 0.3846 r_free = 0.3846 target = 0.162649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121858 restraints weight = 31404.751| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.93 r_work: 0.3060 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25317 Z= 0.093 Angle : 0.499 12.084 34533 Z= 0.248 Chirality : 0.043 0.293 4038 Planarity : 0.003 0.047 4377 Dihedral : 5.267 56.862 4248 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.16 % Allowed : 13.92 % Favored : 84.92 % 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: 0.05 (0.15), residues: 3042 helix: 1.97 (0.20), residues: 759 sheet: 0.52 (0.19), residues: 699 loop : -1.21 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS C 339 PHE 0.025 0.001 PHE C 92 TYR 0.016 0.001 TYR A1067 ARG 0.006 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 36) link_NAG-ASN : angle 2.46915 ( 108) link_BETA1-4 : bond 0.00347 ( 9) link_BETA1-4 : angle 0.94635 ( 27) hydrogen bonds : bond 0.03840 ( 958) hydrogen bonds : angle 4.35000 ( 2637) SS BOND : bond 0.00281 ( 39) SS BOND : angle 1.29499 ( 78) covalent geometry : bond 0.00206 (25233) covalent geometry : angle 0.47644 (34320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 2.720 Fit side-chains revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7552 (m-10) cc_final: 0.7101 (m-10) REVERT: A 170 TYR cc_start: 0.7348 (t80) cc_final: 0.6292 (t80) REVERT: A 177 MET cc_start: 0.4526 (mtt) cc_final: 0.3229 (mtm) REVERT: A 586 ASP cc_start: 0.8409 (m-30) cc_final: 0.8145 (m-30) REVERT: A 780 GLU cc_start: 0.8526 (tt0) cc_final: 0.8228 (tt0) REVERT: B 173 GLN cc_start: 0.7421 (tm-30) cc_final: 0.7134 (tm-30) REVERT: B 360 ASN cc_start: 0.8376 (t0) cc_final: 0.8010 (t0) REVERT: B 420 ASP cc_start: 0.8039 (m-30) cc_final: 0.7683 (t0) REVERT: B 493 GLN cc_start: 0.7799 (tp-100) cc_final: 0.7545 (tp-100) REVERT: B 529 LYS cc_start: 0.7516 (mmmt) cc_final: 0.7248 (mmmt) REVERT: B 574 ASP cc_start: 0.8007 (t0) cc_final: 0.7742 (t0) REVERT: B 591 SER cc_start: 0.8679 (m) cc_final: 0.8068 (p) REVERT: B 955 ASN cc_start: 0.7359 (m110) cc_final: 0.7002 (m110) REVERT: B 1138 TYR cc_start: 0.7837 (t80) cc_final: 0.7462 (t80) REVERT: C 269 TYR cc_start: 0.7179 (m-10) cc_final: 0.6789 (m-10) REVERT: C 319 ARG cc_start: 0.7938 (ptp-110) cc_final: 0.7306 (ptp-110) REVERT: C 414 GLN cc_start: 0.7005 (mt0) cc_final: 0.6114 (mp10) REVERT: C 859 THR cc_start: 0.8636 (m) cc_final: 0.8292 (p) outliers start: 31 outliers final: 30 residues processed: 242 average time/residue: 0.3271 time to fit residues: 131.1704 Evaluate side-chains 243 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 112 optimal weight: 1.9990 chunk 170 optimal weight: 0.3980 chunk 282 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 262 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 GLN ** C 414 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 = 0.3832 r_free = 0.3832 target = 0.161321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116226 restraints weight = 31543.399| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.79 r_work: 0.3049 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25317 Z= 0.107 Angle : 0.513 12.077 34533 Z= 0.255 Chirality : 0.043 0.297 4038 Planarity : 0.003 0.045 4377 Dihedral : 5.259 56.714 4248 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.12 % Allowed : 14.15 % Favored : 84.73 % 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: 0.07 (0.15), residues: 3042 helix: 1.95 (0.20), residues: 759 sheet: 0.55 (0.19), residues: 699 loop : -1.19 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS C 339 PHE 0.023 0.001 PHE C 92 TYR 0.017 0.001 TYR A1067 ARG 0.006 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 36) link_NAG-ASN : angle 2.46686 ( 108) link_BETA1-4 : bond 0.00337 ( 9) link_BETA1-4 : angle 0.94957 ( 27) hydrogen bonds : bond 0.04028 ( 958) hydrogen bonds : angle 4.36530 ( 2637) SS BOND : bond 0.00297 ( 39) SS BOND : angle 1.24885 ( 78) covalent geometry : bond 0.00248 (25233) covalent geometry : angle 0.49161 (34320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11216.37 seconds wall clock time: 195 minutes 21.17 seconds (11721.17 seconds total)