Starting phenix.real_space_refine on Sun Oct 12 13:50:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0n_42862/10_2025/8v0n_42862_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0n_42862/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v0n_42862/10_2025/8v0n_42862_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0n_42862/10_2025/8v0n_42862_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v0n_42862/10_2025/8v0n_42862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0n_42862/10_2025/8v0n_42862.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 5.64, per 1000 atoms: 0.23 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: 1.90 Conformation dependent library (CDL) restraints added in 964.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.12 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: 5.99 Time building geometry restraints manager: 2.42 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: 0.03 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: 2.250 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.710 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- 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 : 2.89 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.001 ARG C 567 TYR 0.029 0.001 TYR A 495 PHE 0.038 0.002 PHE B 238 TRP 0.033 0.001 TRP B 64 HIS 0.005 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00432 (25233) covalent geometry : angle 0.77326 (34320) SS BOND : bond 0.00587 ( 39) SS BOND : angle 1.92849 ( 78) hydrogen bonds : bond 0.07792 ( 958) hydrogen bonds : angle 5.56084 ( 2637) link_BETA1-4 : bond 0.00708 ( 9) link_BETA1-4 : angle 1.43427 ( 27) link_NAG-ASN : bond 0.01006 ( 36) link_NAG-ASN : angle 4.84769 ( 108) *********************** 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 : 0.938 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: 0.7785 (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: 0.6735 (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: 0.1634 time to fit residues: 65.8509 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 : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN B 30 ASN B 115 GLN B 613 GLN B 901 GLN B1135 ASN C 115 GLN C 394 ASN C 405 ASN C 613 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.160021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113875 restraints weight = 31809.915| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.70 r_work: 0.3060 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25317 Z= 0.182 Angle : 0.598 14.827 34533 Z= 0.299 Chirality : 0.046 0.301 4038 Planarity : 0.004 0.062 4377 Dihedral : 6.943 58.329 4248 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.63 % Allowed : 6.68 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.15), residues: 3042 helix: 1.16 (0.19), residues: 723 sheet: 0.22 (0.18), residues: 726 loop : -1.61 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 567 TYR 0.018 0.001 TYR B1067 PHE 0.018 0.002 PHE A 497 TRP 0.016 0.001 TRP B 64 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00438 (25233) covalent geometry : angle 0.56510 (34320) SS BOND : bond 0.00391 ( 39) SS BOND : angle 1.47299 ( 78) hydrogen bonds : bond 0.05238 ( 958) hydrogen bonds : angle 4.90361 ( 2637) link_BETA1-4 : bond 0.00269 ( 9) link_BETA1-4 : angle 1.11895 ( 27) link_NAG-ASN : bond 0.00468 ( 36) link_NAG-ASN : angle 3.33634 ( 108) *********************** 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 235 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7198 (t80) cc_final: 0.6333 (t80) REVERT: A 498 ARG cc_start: 0.6949 (mmt90) cc_final: 0.6483 (mmt90) REVERT: A 780 GLU cc_start: 0.8575 (tt0) cc_final: 0.8336 (tt0) REVERT: B 360 ASN cc_start: 0.8185 (t0) cc_final: 0.7894 (t0) REVERT: B 568 ASP cc_start: 0.7267 (t0) cc_final: 0.6987 (t0) REVERT: B 574 ASP cc_start: 0.8197 (t0) cc_final: 0.7866 (t0) REVERT: B 591 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8140 (p) REVERT: B 955 ASN cc_start: 0.7503 (m110) cc_final: 0.7123 (m-40) REVERT: C 269 TYR cc_start: 0.7009 (m-10) cc_final: 0.6646 (m-80) REVERT: C 458 LYS cc_start: 0.8430 (mmmm) cc_final: 0.8117 (tppt) REVERT: C 564 GLN cc_start: 0.7750 (mm110) cc_final: 0.7490 (mm110) outliers start: 17 outliers final: 12 residues processed: 230 average time/residue: 0.1691 time to fit residues: 62.6897 Evaluate side-chains 208 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 383 SER 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 231 ILE Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 591 SER 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 267 optimal weight: 0.4980 chunk 124 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 165 optimal weight: 0.4980 chunk 278 optimal weight: 2.9990 chunk 52 optimal weight: 0.0270 chunk 166 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 276 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 280 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS C 394 ASN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.163452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117440 restraints weight = 31588.462| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.66 r_work: 0.3079 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25317 Z= 0.093 Angle : 0.521 14.164 34533 Z= 0.258 Chirality : 0.043 0.272 4038 Planarity : 0.004 0.051 4377 Dihedral : 6.205 56.942 4248 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.63 % Allowed : 9.00 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.15), residues: 3042 helix: 1.74 (0.20), residues: 723 sheet: 0.32 (0.19), residues: 696 loop : -1.38 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.017 0.001 TYR C1067 PHE 0.016 0.001 PHE C 32 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00198 (25233) covalent geometry : angle 0.48946 (34320) SS BOND : bond 0.00321 ( 39) SS BOND : angle 1.10917 ( 78) hydrogen bonds : bond 0.04162 ( 958) hydrogen bonds : angle 4.60636 ( 2637) link_BETA1-4 : bond 0.00322 ( 9) link_BETA1-4 : angle 1.00771 ( 27) link_NAG-ASN : bond 0.00572 ( 36) link_NAG-ASN : angle 3.08102 ( 108) *********************** 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 231 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7144 (t80) cc_final: 0.6258 (t80) REVERT: A 498 ARG cc_start: 0.6903 (mmt90) cc_final: 0.6560 (mmt90) REVERT: A 586 ASP cc_start: 0.8535 (m-30) cc_final: 0.8126 (m-30) REVERT: A 780 GLU cc_start: 0.8482 (tt0) cc_final: 0.8264 (tt0) REVERT: B 360 ASN cc_start: 0.8174 (t0) cc_final: 0.7860 (t0) REVERT: B 420 ASP cc_start: 0.8096 (m-30) cc_final: 0.7604 (t70) REVERT: B 493 GLN cc_start: 0.7668 (tp-100) cc_final: 0.7409 (tp-100) REVERT: B 568 ASP cc_start: 0.7141 (t0) cc_final: 0.6917 (t0) REVERT: B 574 ASP cc_start: 0.8178 (t0) cc_final: 0.7806 (t0) REVERT: B 591 SER cc_start: 0.8720 (m) cc_final: 0.8095 (p) REVERT: B 752 LEU cc_start: 0.9033 (mp) cc_final: 0.8780 (mp) REVERT: B 955 ASN cc_start: 0.7434 (m110) cc_final: 0.7122 (m-40) REVERT: C 32 PHE cc_start: 0.7635 (m-80) cc_final: 0.7397 (m-80) REVERT: C 269 TYR cc_start: 0.6969 (m-10) cc_final: 0.6530 (m-80) REVERT: C 414 GLN cc_start: 0.7063 (mt0) cc_final: 0.6067 (mp10) REVERT: C 458 LYS cc_start: 0.8408 (mmmm) cc_final: 0.8104 (tppt) REVERT: C 564 GLN cc_start: 0.7637 (mm110) cc_final: 0.7362 (mm110) REVERT: C 1050 MET cc_start: 0.9018 (ptt) cc_final: 0.8737 (ptm) outliers start: 17 outliers final: 9 residues processed: 225 average time/residue: 0.1681 time to fit residues: 61.1392 Evaluate side-chains 212 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1125 ASN Chi-restraints excluded: chain B residue 231 ILE 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 195 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 137 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 239 GLN B 563 GLN C 26 GLN C 394 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.157404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110483 restraints weight = 31901.887| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.69 r_work: 0.3029 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25317 Z= 0.215 Angle : 0.602 12.753 34533 Z= 0.302 Chirality : 0.046 0.283 4038 Planarity : 0.004 0.048 4377 Dihedral : 6.213 57.971 4248 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.16 % Allowed : 10.82 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.15), residues: 3042 helix: 1.58 (0.20), residues: 723 sheet: 0.18 (0.19), residues: 696 loop : -1.46 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.020 0.001 TYR B1138 PHE 0.021 0.002 PHE C 92 TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00526 (25233) covalent geometry : angle 0.57630 (34320) SS BOND : bond 0.00427 ( 39) SS BOND : angle 1.43256 ( 78) hydrogen bonds : bond 0.05555 ( 958) hydrogen bonds : angle 4.82556 ( 2637) link_BETA1-4 : bond 0.00373 ( 9) link_BETA1-4 : angle 1.04088 ( 27) link_NAG-ASN : bond 0.00506 ( 36) link_NAG-ASN : angle 2.93385 ( 108) *********************** 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 234 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.834 Fit side-chains REVERT: A 170 TYR cc_start: 0.7337 (t80) cc_final: 0.6370 (t80) REVERT: A 498 ARG cc_start: 0.6948 (mmt90) cc_final: 0.6556 (mmt90) REVERT: A 780 GLU cc_start: 0.8642 (tt0) cc_final: 0.8410 (tt0) REVERT: B 170 TYR cc_start: 0.7200 (t80) cc_final: 0.6987 (t80) REVERT: B 319 ARG cc_start: 0.7408 (mtt90) cc_final: 0.7132 (mtm180) REVERT: B 360 ASN cc_start: 0.8319 (t0) cc_final: 0.8003 (t0) REVERT: B 568 ASP cc_start: 0.7326 (t0) cc_final: 0.7121 (t0) REVERT: B 574 ASP cc_start: 0.8286 (t0) cc_final: 0.7962 (t0) REVERT: B 591 SER cc_start: 0.8793 (m) cc_final: 0.8189 (p) REVERT: B 752 LEU cc_start: 0.9132 (mp) cc_final: 0.8869 (mp) REVERT: B 955 ASN cc_start: 0.7344 (m110) cc_final: 0.7024 (m110) REVERT: C 32 PHE cc_start: 0.7736 (m-80) cc_final: 0.7460 (m-80) REVERT: C 319 ARG cc_start: 0.7634 (ptp-110) cc_final: 0.7114 (ptp-110) REVERT: C 859 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8298 (p) REVERT: C 1050 MET cc_start: 0.9104 (ptt) cc_final: 0.8794 (ptm) outliers start: 31 outliers final: 26 residues processed: 226 average time/residue: 0.1526 time to fit residues: 56.3551 Evaluate side-chains 222 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 747 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 176 LEU 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 305 SER 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 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 307 THR 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 859 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 110 optimal weight: 8.9990 chunk 191 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 235 optimal weight: 0.0070 chunk 5 optimal weight: 5.9990 chunk 147 optimal weight: 0.0770 chunk 277 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 overall best weight: 0.9558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.160084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113373 restraints weight = 31526.165| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.67 r_work: 0.3060 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25317 Z= 0.116 Angle : 0.524 12.331 34533 Z= 0.261 Chirality : 0.044 0.262 4038 Planarity : 0.003 0.044 4377 Dihedral : 5.845 57.234 4248 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.38 % Allowed : 11.72 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.15), residues: 3042 helix: 1.71 (0.20), residues: 738 sheet: 0.31 (0.19), residues: 687 loop : -1.34 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.023 0.001 TYR B1138 PHE 0.026 0.001 PHE C 92 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00267 (25233) covalent geometry : angle 0.49792 (34320) SS BOND : bond 0.00363 ( 39) SS BOND : angle 1.18214 ( 78) hydrogen bonds : bond 0.04555 ( 958) hydrogen bonds : angle 4.60641 ( 2637) link_BETA1-4 : bond 0.00370 ( 9) link_BETA1-4 : angle 0.97278 ( 27) link_NAG-ASN : bond 0.00516 ( 36) link_NAG-ASN : angle 2.79421 ( 108) *********************** 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 248 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.878 Fit side-chains REVERT: A 170 TYR cc_start: 0.7320 (t80) cc_final: 0.6292 (t80) REVERT: A 177 MET cc_start: 0.3663 (mtt) cc_final: 0.2790 (mtm) REVERT: A 498 ARG cc_start: 0.6915 (mmt90) cc_final: 0.6515 (mmt90) REVERT: A 586 ASP cc_start: 0.8595 (m-30) cc_final: 0.8255 (m-30) REVERT: A 780 GLU cc_start: 0.8655 (tt0) cc_final: 0.8429 (tt0) REVERT: B 170 TYR cc_start: 0.7110 (t80) cc_final: 0.6849 (t80) REVERT: B 319 ARG cc_start: 0.7291 (mtt90) cc_final: 0.7041 (mtm180) REVERT: B 360 ASN cc_start: 0.8288 (t0) cc_final: 0.7960 (t0) REVERT: B 420 ASP cc_start: 0.8104 (m-30) cc_final: 0.7548 (t70) REVERT: B 493 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7557 (tp-100) REVERT: B 568 ASP cc_start: 0.7113 (t0) cc_final: 0.6894 (t0) REVERT: B 574 ASP cc_start: 0.8094 (t0) cc_final: 0.7770 (t0) REVERT: B 591 SER cc_start: 0.8765 (m) cc_final: 0.8157 (p) REVERT: B 955 ASN cc_start: 0.7329 (m110) cc_final: 0.6934 (m110) REVERT: C 269 TYR cc_start: 0.7193 (m-10) cc_final: 0.6860 (m-80) REVERT: C 319 ARG cc_start: 0.7716 (ptp-110) cc_final: 0.7314 (ptp-110) REVERT: C 1050 MET cc_start: 0.9223 (ptt) cc_final: 0.9008 (ptm) outliers start: 37 outliers final: 24 residues processed: 236 average time/residue: 0.1653 time to fit residues: 64.2535 Evaluate side-chains 228 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 176 LEU Chi-restraints excluded: chain B residue 231 ILE 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 525 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 38 optimal weight: 0.0970 chunk 255 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 293 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 GLN C 394 ASN ** 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 = 0.3808 r_free = 0.3808 target = 0.159247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112500 restraints weight = 31753.084| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.67 r_work: 0.3025 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25317 Z= 0.148 Angle : 0.547 11.606 34533 Z= 0.273 Chirality : 0.045 0.294 4038 Planarity : 0.004 0.045 4377 Dihedral : 5.804 56.859 4248 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.49 % Allowed : 12.50 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.15), residues: 3042 helix: 1.72 (0.20), residues: 741 sheet: 0.33 (0.19), residues: 687 loop : -1.35 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.023 0.001 TYR B1138 PHE 0.024 0.001 PHE C 92 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00357 (25233) covalent geometry : angle 0.52145 (34320) SS BOND : bond 0.00410 ( 39) SS BOND : angle 1.50254 ( 78) hydrogen bonds : bond 0.04845 ( 958) hydrogen bonds : angle 4.64058 ( 2637) link_BETA1-4 : bond 0.00345 ( 9) link_BETA1-4 : angle 0.98816 ( 27) link_NAG-ASN : bond 0.00437 ( 36) link_NAG-ASN : angle 2.70328 ( 108) *********************** 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 247 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 1.103 Fit side-chains REVERT: A 170 TYR cc_start: 0.7303 (t80) cc_final: 0.6294 (t80) REVERT: A 177 MET cc_start: 0.3851 (mtt) cc_final: 0.2869 (mtm) REVERT: A 498 ARG cc_start: 0.6804 (mmt90) cc_final: 0.6385 (mmt90) REVERT: A 780 GLU cc_start: 0.8865 (tt0) cc_final: 0.8657 (tt0) REVERT: B 170 TYR cc_start: 0.7389 (t80) cc_final: 0.7061 (t80) REVERT: B 319 ARG cc_start: 0.7396 (mtt90) cc_final: 0.7136 (mtm180) REVERT: B 360 ASN cc_start: 0.8421 (t0) cc_final: 0.8096 (t0) REVERT: B 493 GLN cc_start: 0.7775 (tp-100) cc_final: 0.7499 (tp-100) REVERT: B 568 ASP cc_start: 0.7292 (t0) cc_final: 0.7041 (t0) REVERT: B 574 ASP cc_start: 0.8139 (t0) cc_final: 0.7854 (t0) REVERT: B 591 SER cc_start: 0.8755 (m) cc_final: 0.8141 (p) REVERT: B 955 ASN cc_start: 0.7514 (m110) cc_final: 0.7159 (m110) REVERT: C 319 ARG cc_start: 0.7865 (ptp-110) cc_final: 0.7467 (ptp-110) REVERT: C 394 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7934 (m110) REVERT: C 414 GLN cc_start: 0.7212 (mt0) cc_final: 0.6069 (mp10) REVERT: C 859 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8396 (p) REVERT: C 900 MET cc_start: 0.8720 (mtp) cc_final: 0.8449 (mtp) REVERT: C 1050 MET cc_start: 0.9255 (ptt) cc_final: 0.9046 (ptm) outliers start: 40 outliers final: 32 residues processed: 236 average time/residue: 0.1563 time to fit residues: 60.8707 Evaluate side-chains 234 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 176 LEU 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 305 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 394 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 859 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 255 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 191 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.158675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117048 restraints weight = 31681.051| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.96 r_work: 0.3038 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25317 Z= 0.140 Angle : 0.544 11.807 34533 Z= 0.271 Chirality : 0.044 0.293 4038 Planarity : 0.004 0.045 4377 Dihedral : 5.749 56.939 4248 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.68 % Allowed : 12.99 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.15), residues: 3042 helix: 1.75 (0.20), residues: 741 sheet: 0.34 (0.19), residues: 687 loop : -1.32 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.021 0.001 TYR B1138 PHE 0.023 0.001 PHE C 92 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00337 (25233) covalent geometry : angle 0.51906 (34320) SS BOND : bond 0.00415 ( 39) SS BOND : angle 1.58734 ( 78) hydrogen bonds : bond 0.04770 ( 958) hydrogen bonds : angle 4.61850 ( 2637) link_BETA1-4 : bond 0.00345 ( 9) link_BETA1-4 : angle 0.97076 ( 27) link_NAG-ASN : bond 0.00487 ( 36) link_NAG-ASN : angle 2.66243 ( 108) *********************** 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 248 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.954 Fit side-chains REVERT: A 170 TYR cc_start: 0.7267 (t80) cc_final: 0.6256 (t80) REVERT: A 177 MET cc_start: 0.3797 (mtt) cc_final: 0.2836 (mtm) REVERT: A 497 PHE cc_start: 0.6057 (m-10) cc_final: 0.5576 (m-10) REVERT: A 498 ARG cc_start: 0.6831 (mmt90) cc_final: 0.6626 (mmt90) REVERT: A 780 GLU cc_start: 0.8639 (tt0) cc_final: 0.8425 (tt0) REVERT: B 170 TYR cc_start: 0.7151 (t80) cc_final: 0.6739 (t80) REVERT: B 319 ARG cc_start: 0.7324 (mtt90) cc_final: 0.7063 (mtm180) REVERT: B 360 ASN cc_start: 0.8344 (t0) cc_final: 0.8013 (t0) REVERT: B 420 ASP cc_start: 0.8098 (m-30) cc_final: 0.7555 (t70) REVERT: B 574 ASP cc_start: 0.8035 (t0) cc_final: 0.7764 (t0) REVERT: B 591 SER cc_start: 0.8762 (m) cc_final: 0.8150 (p) REVERT: B 955 ASN cc_start: 0.7323 (m110) cc_final: 0.6955 (m110) REVERT: C 319 ARG cc_start: 0.7674 (ptp-110) cc_final: 0.7279 (ptp-110) REVERT: C 414 GLN cc_start: 0.7193 (mt0) cc_final: 0.6061 (mp10) REVERT: C 859 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8349 (p) REVERT: C 900 MET cc_start: 0.8536 (mtp) cc_final: 0.8231 (mtp) outliers start: 45 outliers final: 36 residues processed: 236 average time/residue: 0.1594 time to fit residues: 61.9997 Evaluate side-chains 237 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 ASP 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 305 SER 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 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 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 859 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 193 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 195 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 280 optimal weight: 0.0370 chunk 264 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 GLN C 394 ASN ** 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 = 0.3816 r_free = 0.3816 target = 0.160043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113780 restraints weight = 31500.570| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.64 r_work: 0.3050 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25317 Z= 0.113 Angle : 0.519 11.903 34533 Z= 0.259 Chirality : 0.044 0.291 4038 Planarity : 0.003 0.044 4377 Dihedral : 5.581 57.002 4248 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.49 % Allowed : 13.25 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.15), residues: 3042 helix: 1.88 (0.20), residues: 741 sheet: 0.41 (0.19), residues: 699 loop : -1.30 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.020 0.001 TYR B1138 PHE 0.022 0.001 PHE C 92 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00261 (25233) covalent geometry : angle 0.49535 (34320) SS BOND : bond 0.00330 ( 39) SS BOND : angle 1.31883 ( 78) hydrogen bonds : bond 0.04380 ( 958) hydrogen bonds : angle 4.50663 ( 2637) link_BETA1-4 : bond 0.00350 ( 9) link_BETA1-4 : angle 0.95892 ( 27) link_NAG-ASN : bond 0.00497 ( 36) link_NAG-ASN : angle 2.57760 ( 108) *********************** 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 249 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.942 Fit side-chains REVERT: A 170 TYR cc_start: 0.7335 (t80) cc_final: 0.6329 (t80) REVERT: A 177 MET cc_start: 0.3743 (mtt) cc_final: 0.2736 (mtm) REVERT: A 192 PHE cc_start: 0.7347 (m-10) cc_final: 0.7123 (m-80) REVERT: A 497 PHE cc_start: 0.6191 (m-10) cc_final: 0.5499 (m-10) REVERT: A 498 ARG cc_start: 0.6802 (mmt90) cc_final: 0.6589 (mmt90) REVERT: A 586 ASP cc_start: 0.8693 (m-30) cc_final: 0.8373 (m-30) REVERT: B 170 TYR cc_start: 0.7284 (t80) cc_final: 0.6880 (t80) REVERT: B 319 ARG cc_start: 0.7326 (mtt90) cc_final: 0.7100 (mtm180) REVERT: B 360 ASN cc_start: 0.8411 (t0) cc_final: 0.8051 (t0) REVERT: B 420 ASP cc_start: 0.8152 (m-30) cc_final: 0.7697 (t70) REVERT: B 568 ASP cc_start: 0.7252 (t0) cc_final: 0.7000 (t0) REVERT: B 591 SER cc_start: 0.8701 (m) cc_final: 0.8098 (p) REVERT: B 619 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: B 955 ASN cc_start: 0.7476 (m110) cc_final: 0.7080 (m110) REVERT: C 319 ARG cc_start: 0.7767 (ptp-110) cc_final: 0.7423 (ptp-110) REVERT: C 414 GLN cc_start: 0.7230 (mt0) cc_final: 0.6082 (mp10) outliers start: 40 outliers final: 33 residues processed: 239 average time/residue: 0.1564 time to fit residues: 61.7564 Evaluate side-chains 239 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 ASP 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 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 619 GLU 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 383 SER Chi-restraints excluded: chain C residue 524 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 172 optimal weight: 0.3980 chunk 10 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 112 optimal weight: 0.0980 chunk 77 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 926 GLN B 563 GLN C 394 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 = 0.3801 r_free = 0.3801 target = 0.158627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116605 restraints weight = 31681.163| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.94 r_work: 0.2998 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25317 Z= 0.156 Angle : 0.555 11.779 34533 Z= 0.278 Chirality : 0.045 0.297 4038 Planarity : 0.004 0.046 4377 Dihedral : 5.681 56.708 4248 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.49 % Allowed : 13.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.15), residues: 3042 helix: 1.74 (0.20), residues: 741 sheet: 0.38 (0.19), residues: 699 loop : -1.33 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.025 0.001 TYR B1138 PHE 0.022 0.001 PHE C 92 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00379 (25233) covalent geometry : angle 0.53296 (34320) SS BOND : bond 0.00363 ( 39) SS BOND : angle 1.42061 ( 78) hydrogen bonds : bond 0.04874 ( 958) hydrogen bonds : angle 4.61273 ( 2637) link_BETA1-4 : bond 0.00339 ( 9) link_BETA1-4 : angle 0.96589 ( 27) link_NAG-ASN : bond 0.00479 ( 36) link_NAG-ASN : angle 2.58843 ( 108) *********************** 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 245 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.953 Fit side-chains REVERT: A 106 PHE cc_start: 0.5336 (m-80) cc_final: 0.5081 (m-80) REVERT: A 170 TYR cc_start: 0.7372 (t80) cc_final: 0.6388 (t80) REVERT: A 177 MET cc_start: 0.3870 (mtt) cc_final: 0.2829 (mtm) REVERT: A 281 GLU cc_start: 0.8474 (tt0) cc_final: 0.7979 (tm-30) REVERT: A 498 ARG cc_start: 0.6836 (mmt90) cc_final: 0.6613 (mmt90) REVERT: B 170 TYR cc_start: 0.7399 (t80) cc_final: 0.6979 (t80) REVERT: B 319 ARG cc_start: 0.7323 (mtt90) cc_final: 0.7107 (mtm180) REVERT: B 360 ASN cc_start: 0.8446 (t0) cc_final: 0.8086 (t0) REVERT: B 420 ASP cc_start: 0.8208 (m-30) cc_final: 0.7834 (t70) REVERT: B 591 SER cc_start: 0.8714 (m) cc_final: 0.8123 (p) REVERT: B 955 ASN cc_start: 0.7473 (m110) cc_final: 0.7131 (m110) REVERT: C 319 ARG cc_start: 0.7816 (ptp-110) cc_final: 0.7458 (ptp-110) REVERT: C 394 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7934 (m110) REVERT: C 414 GLN cc_start: 0.7289 (mt0) cc_final: 0.6117 (mp10) REVERT: C 859 THR cc_start: 0.8681 (m) cc_final: 0.8315 (p) outliers start: 40 outliers final: 36 residues processed: 232 average time/residue: 0.1447 time to fit residues: 55.6159 Evaluate side-chains 242 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 ASP 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 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 383 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 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 220 optimal weight: 0.8980 chunk 288 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 294 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 194 optimal weight: 0.3980 chunk 145 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.160127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116153 restraints weight = 31542.919| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.61 r_work: 0.3060 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25317 Z= 0.111 Angle : 0.528 11.927 34533 Z= 0.263 Chirality : 0.044 0.295 4038 Planarity : 0.003 0.045 4377 Dihedral : 5.583 56.970 4248 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.34 % Allowed : 13.81 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.15), residues: 3042 helix: 1.90 (0.20), residues: 741 sheet: 0.44 (0.19), residues: 699 loop : -1.27 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.025 0.001 TYR B1138 PHE 0.023 0.001 PHE C 92 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00254 (25233) covalent geometry : angle 0.50544 (34320) SS BOND : bond 0.00328 ( 39) SS BOND : angle 1.26198 ( 78) hydrogen bonds : bond 0.04451 ( 958) hydrogen bonds : angle 4.52299 ( 2637) link_BETA1-4 : bond 0.00367 ( 9) link_BETA1-4 : angle 0.95788 ( 27) link_NAG-ASN : bond 0.00500 ( 36) link_NAG-ASN : angle 2.55312 ( 108) ********************** 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 240 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7625 (m-10) cc_final: 0.7128 (m-10) REVERT: A 106 PHE cc_start: 0.5345 (m-80) cc_final: 0.5037 (m-80) REVERT: A 170 TYR cc_start: 0.7340 (t80) cc_final: 0.6362 (t80) REVERT: A 177 MET cc_start: 0.4205 (mtt) cc_final: 0.3060 (mtm) REVERT: A 192 PHE cc_start: 0.7397 (m-10) cc_final: 0.7185 (m-80) REVERT: A 497 PHE cc_start: 0.6377 (m-10) cc_final: 0.5756 (m-10) REVERT: A 498 ARG cc_start: 0.6833 (mmt90) cc_final: 0.6616 (mmt90) REVERT: A 586 ASP cc_start: 0.8690 (m-30) cc_final: 0.8382 (m-30) REVERT: B 170 TYR cc_start: 0.7302 (t80) cc_final: 0.6846 (t80) REVERT: B 319 ARG cc_start: 0.7299 (mtt90) cc_final: 0.7092 (mtm180) REVERT: B 360 ASN cc_start: 0.8452 (t0) cc_final: 0.8089 (t0) REVERT: B 420 ASP cc_start: 0.8169 (m-30) cc_final: 0.7725 (t70) REVERT: B 591 SER cc_start: 0.8703 (m) cc_final: 0.8102 (p) REVERT: B 955 ASN cc_start: 0.7434 (m110) cc_final: 0.7055 (m110) REVERT: C 319 ARG cc_start: 0.7786 (ptp-110) cc_final: 0.7442 (ptp-110) REVERT: C 414 GLN cc_start: 0.7259 (mt0) cc_final: 0.6113 (mp10) REVERT: C 859 THR cc_start: 0.8686 (m) cc_final: 0.8334 (p) REVERT: C 900 MET cc_start: 0.8634 (mtp) cc_final: 0.8416 (mtp) outliers start: 36 outliers final: 36 residues processed: 232 average time/residue: 0.1629 time to fit residues: 62.0721 Evaluate side-chains 240 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 ASP 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 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 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 383 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 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 161 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 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 = 0.3776 r_free = 0.3776 target = 0.156292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114651 restraints weight = 31690.682| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.98 r_work: 0.2977 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25317 Z= 0.206 Angle : 0.596 11.774 34533 Z= 0.300 Chirality : 0.046 0.301 4038 Planarity : 0.004 0.046 4377 Dihedral : 5.883 57.620 4248 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.57 % Allowed : 13.74 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.15), residues: 3042 helix: 1.59 (0.20), residues: 741 sheet: 0.29 (0.19), residues: 684 loop : -1.36 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.026 0.001 TYR B1138 PHE 0.020 0.002 PHE C 92 TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00506 (25233) covalent geometry : angle 0.57376 (34320) SS BOND : bond 0.00401 ( 39) SS BOND : angle 1.53779 ( 78) hydrogen bonds : bond 0.05454 ( 958) hydrogen bonds : angle 4.76248 ( 2637) link_BETA1-4 : bond 0.00368 ( 9) link_BETA1-4 : angle 0.98784 ( 27) link_NAG-ASN : bond 0.00483 ( 36) link_NAG-ASN : angle 2.64035 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6209.39 seconds wall clock time: 107 minutes 4.43 seconds (6424.43 seconds total)