Starting phenix.real_space_refine on Mon Aug 25 01:57:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cn9_30419/08_2025/7cn9_30419.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cn9_30419/08_2025/7cn9_30419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cn9_30419/08_2025/7cn9_30419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cn9_30419/08_2025/7cn9_30419.map" model { file = "/net/cci-nas-00/data/ceres_data/7cn9_30419/08_2025/7cn9_30419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cn9_30419/08_2025/7cn9_30419.cif" } resolution = 4.7 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= 0.001 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 106 5.16 5 C 15304 2.51 5 N 3942 2.21 5 O 4700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24052 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 7727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7727 Classifications: {'peptide': 1011} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 48, 'TRANS': 962} Chain breaks: 7 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'HIS:plan': 2, 'GLN:plan1': 5, 'PHE:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 8, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 7674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7674 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 48, 'TRANS': 961} Chain breaks: 10 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 8, 'ARG:plan': 4, 'GLN:plan1': 5, 'PHE:plan': 2, 'TYR:plan': 6, 'ASP:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 164 Chain: "C" Number of atoms: 7889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 7889 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 49, 'TRANS': 987} Chain breaks: 6 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 7, 'GLN:plan1': 6, 'PHE:plan': 3, 'ASP:plan': 10, 'GLU:plan': 5, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 152 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: "X" 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" 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: "Z" 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: "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: "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: "h" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.18, per 1000 atoms: 0.26 Number of scatterers: 24052 At special positions: 0 Unit cell: (152.52, 159.08, 167.28, 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 106 16.00 O 4700 8.00 N 3942 7.00 C 15304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.08 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=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 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 131 " - pdb=" SG CYS B 166 " distance=1.89 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=1.93 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.26 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM23770 O5 NAG A1203 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA h 3 " - " MAN h 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG f 1 " - " NAG f 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG k 1 " - " NAG k 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " BETA1-6 " NAG k 1 " - " FUC k 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1201 " - " ASN A 616 " " NAG A1202 " - " ASN A 657 " " NAG A1203 " - " ASN A1074 " " NAG A1204 " - " ASN A1098 " " NAG A1205 " - " ASN A1134 " " NAG A1206 " - " ASN A 122 " " NAG A1207 " - " ASN A 282 " " NAG B1201 " - " ASN B 331 " " NAG B1202 " - " ASN B 603 " " NAG B1203 " - " ASN B 616 " " NAG B1204 " - " ASN B 657 " " NAG B1205 " - " ASN B 709 " " NAG B1206 " - " ASN B1098 " " NAG B1207 " - " ASN B 234 " " NAG B1208 " - " ASN B 165 " " NAG B1209 " - " ASN B 74 " " NAG C1201 " - " ASN C1134 " " NAG C1202 " - " ASN C 709 " " NAG C1203 " - " ASN C 657 " " NAG C1204 " - " ASN C 616 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 61 " " NAG C1207 " - " ASN C 331 " " NAG E 1 " - " ASN C1074 " " NAG H 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 165 " " NAG Q 1 " - " ASN A 801 " " NAG V 1 " - " ASN A 331 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN C 717 " " NAG Z 1 " - " ASN B1134 " " NAG d 1 " - " ASN B1074 " " NAG f 1 " - " ASN B 801 " " NAG h 1 " - " ASN B 282 " " NAG k 1 " - " ASN C 165 " " NAG p 1 " - " ASN C 801 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5730 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 47 sheets defined 23.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.541A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.021A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.736A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.714A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.664A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 940 removed outlier: 6.068A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.512A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 4.586A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.785A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.456A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.195A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.081A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.485A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.540A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.767A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.290A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.866A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 940 removed outlier: 6.380A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.883A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1034 removed outlier: 6.078A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.062A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.513A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 removed outlier: 3.901A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA6, first strand: chain 'A' and resid 204 through 205 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.012A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 651 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AB1, first strand: chain 'A' and resid 572 through 573 removed outlier: 7.000A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.546A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AB4, first strand: chain 'A' and resid 724 through 728 removed outlier: 3.629A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A1049 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.604A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1086 through 1090 removed outlier: 5.419A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.745A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 192 through 194 removed outlier: 3.876A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.842A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 201 through 205 removed outlier: 3.644A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.879A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 566 through 567 Processing sheet with id=AC7, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC8, first strand: chain 'B' and resid 612 through 613 removed outlier: 3.703A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 659 through 660 removed outlier: 3.528A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.162A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1086 through 1088 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AD6, first strand: chain 'C' and resid 49 through 55 removed outlier: 4.236A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 90 through 94 removed outlier: 4.299A pdb=" N PHE C 92 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE C 192 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 104 through 107 Processing sheet with id=AD9, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.710A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 326 through 328 removed outlier: 7.313A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.831A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE6, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AE7, first strand: chain 'C' and resid 644 through 645 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.700A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 727 removed outlier: 3.712A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 5.272A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1096 698 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7598 1.34 - 1.47: 6253 1.47 - 1.59: 10581 1.59 - 1.72: 3 1.72 - 1.85: 135 Bond restraints: 24570 Sorted by residual: bond pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 1.469 1.700 -0.232 1.28e-02 6.10e+03 3.28e+02 bond pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 1.469 1.700 -0.232 1.28e-02 6.10e+03 3.28e+02 bond pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.34e-02 1.83e+03 2.59e+01 bond pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.34e-02 1.83e+03 2.59e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.09e+01 ... (remaining 24565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 33146 4.15 - 8.30: 317 8.30 - 12.45: 17 12.45 - 16.60: 1 16.60 - 20.76: 2 Bond angle restraints: 33483 Sorted by residual: angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 119.84 140.60 -20.76 1.25e+00 6.40e-01 2.76e+02 angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 119.84 139.73 -19.89 1.25e+00 6.40e-01 2.53e+02 angle pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 112.00 98.17 13.83 1.40e+00 5.10e-01 9.76e+01 angle pdb=" CA PRO C 330 " pdb=" N PRO C 330 " pdb=" CD PRO C 330 " ideal model delta sigma weight residual 112.00 99.76 12.24 1.40e+00 5.10e-01 7.64e+01 angle pdb=" C SER B 172 " pdb=" N GLN B 173 " pdb=" CA GLN B 173 " ideal model delta sigma weight residual 122.89 115.80 7.09 1.12e+00 7.97e-01 4.00e+01 ... (remaining 33478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.59: 14012 22.59 - 45.17: 1026 45.17 - 67.76: 176 67.76 - 90.34: 61 90.34 - 112.93: 16 Dihedral angle restraints: 15291 sinusoidal: 6407 harmonic: 8884 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 173.62 -80.62 1 1.00e+01 1.00e-02 8.04e+01 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 -5.55 -80.45 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -6.43 -79.57 1 1.00e+01 1.00e-02 7.86e+01 ... (remaining 15288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 4004 0.199 - 0.397: 26 0.397 - 0.596: 0 0.596 - 0.794: 3 0.794 - 0.993: 2 Chirality restraints: 4035 Sorted by residual: chirality pdb=" C1 BMA p 3 " pdb=" O4 NAG p 2 " pdb=" C2 BMA p 3 " pdb=" O5 BMA p 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.75e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.38e+01 ... (remaining 4032 not shown) Planarity restraints: 4286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " -0.332 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG V 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " 0.507 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " 0.275 2.00e-02 2.50e+03 2.30e-01 6.59e+02 pdb=" C7 NAG X 1 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " -0.386 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " -0.257 2.00e-02 2.50e+03 2.15e-01 5.76e+02 pdb=" C7 NAG p 1 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " 0.358 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " 0.006 2.00e-02 2.50e+03 ... (remaining 4283 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 570 2.52 - 3.12: 22695 3.12 - 3.71: 37724 3.71 - 4.31: 50734 4.31 - 4.90: 76530 Nonbonded interactions: 188253 Sorted by model distance: nonbonded pdb=" O LEU C 455 " pdb=" CD1 PHE C 456 " model vdw 1.927 3.340 nonbonded pdb=" CZ PHE B 86 " pdb=" N GLY B 89 " model vdw 1.988 3.420 nonbonded pdb=" O SER C1003 " pdb=" OG1 THR C1006 " model vdw 2.004 3.040 nonbonded pdb=" O SER B1003 " pdb=" OG1 THR B1006 " model vdw 2.021 3.040 nonbonded pdb=" NE2 GLN B 613 " pdb=" OD1 ASP B 614 " model vdw 2.026 3.120 ... (remaining 188248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 83 through 95 or (resid 96 throu \ gh 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (r \ esid 99 through 100 and (name N or name CA or name C or name O or name CB )) or \ resid 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) \ or resid 103 through 104 or (resid 105 and (name N or name CA or name C or name \ O or name CB )) or resid 106 through 128 or (resid 129 and (name N or name CA o \ r name C or name O or name CB )) or resid 130 through 140 or (resid 141 and (nam \ e N or name CA or name C or name O or name CB )) or resid 142 through 155 or (re \ sid 156 and (name N or name CA or name C or name O or name CB )) or resid 157 th \ rough 159 or resid 165 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB )) or (resid 187 and (name N or name CA or name C or name \ O or name CB )) or resid 188 through 194 or (resid 195 through 198 and (name N \ or name CA or name C or name O or name CB )) or resid 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 236 or (re \ sid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 or \ (resid 239 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 0 through 243 or resid 264 through 331 or (resid 332 through 333 and (name N or \ name CA or name C or name O or name CB )) or resid 334 or (resid 335 and (name N \ or name CA or name C or name O or name CB )) or resid 336 through 343 or resid \ 355 through 363 or (resid 364 and (name N or name CA or name C or name O or name \ CB )) or resid 365 through 368 or (resid 369 and (name N or name CA or name C o \ r name O or name CB )) or resid 370 through 373 or (resid 374 and (name N or nam \ e CA or name C or name O or name CB )) or resid 375 through 407 or (resid 408 an \ d (name N or name CA or name C or name O or name CB )) or resid 409 through 442 \ or resid 455 or (resid 457 and (name N or name CA or name C or name O or name CB \ )) or resid 458 through 496 or (resid 497 through 498 and (name N or name CA or \ name C or name O or name CB )) or resid 499 through 500 or resid 503 through 50 \ 4 or (resid 505 and (name N or name CA or name C or name O or name CB )) or resi \ d 506 through 508 or (resid 509 and (name N or name CA or name C or name O or na \ me CB )) or resid 510 through 620 or resid 640 through 672 or resid 687 through \ 1207)) selection = (chain 'B' and (resid 27 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 159 or resid 165 t \ hrough 175 or (resid 176 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 187 and (name N or name CA or name C or name O or name CB )) or resi \ d 188 through 189 or (resid 190 and (name N or name CA or name C or name O or na \ me CB )) or resid 191 through 209 or (resid 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 or (resid 212 through 215 and (name N or n \ ame CA or name C or name O or name CB )) or resid 216 through 236 or (resid 237 \ and (name N or name CA or name C or name O or name CB )) or resid 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throug \ h 289 or (resid 290 and (name N or name CA or name C or name O or name CB )) or \ resid 291 through 363 or (resid 364 and (name N or name CA or name C or name O o \ r name CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or na \ me C or name O or name CB )) or resid 375 through 442 or resid 452 or resid 454 \ or resid 462 through 463 or resid 492 through 496 or (resid 497 through 498 and \ (name N or name CA or name C or name O or name CB )) or resid 499 through 508 or \ (resid 509 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 0 through 527 or (resid 528 through 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 543 or (resid 544 and (name N or name CA o \ r name C or name O or name CB )) or resid 545 through 620 or resid 640 through 8 \ 11 or resid 815 through 1207)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 81 or re \ sid 83 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 or (resid 99 through 100 and (name N or name CA o \ r name C or name O or name CB )) or resid 101 through 104 or (resid 105 and (nam \ e N or name CA or name C or name O or name CB )) or resid 106 through 139 or (re \ sid 140 through 141 and (name N or name CA or name C or name O or name CB )) or \ resid 142 through 155 or (resid 156 and (name N or name CA or name C or name O o \ r name CB )) or resid 157 through 158 or (resid 159 and (name N or name CA or na \ me C or name O or name CB )) or resid 165 through 199 or (resid 200 and (name N \ or name CA or name C or name O or name CB )) or resid 201 through 243 or resid 2 \ 64 through 331 or (resid 332 through 333 and (name N or name CA or name C or nam \ e O or name CB )) or resid 334 or (resid 335 and (name N or name CA or name C or \ name O or name CB )) or resid 336 through 343 or resid 355 through 402 or (resi \ d 403 and (name N or name CA or name C or name O or name CB )) or resid 404 thro \ ugh 440 or (resid 441 and (name N or name CA or name C or name O or name CB )) o \ r resid 442 or resid 455 or (resid 457 and (name N or name CA or name C or name \ O or name CB )) or resid 458 or resid 491 through 500 or resid 503 through 504 o \ r (resid 505 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 06 through 543 or (resid 544 and (name N or name CA or name C or name O or name \ CB )) or resid 545 through 620 or resid 640 through 672 or resid 687 through 811 \ or resid 815 through 1207)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'N' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'f' } ncs_group { reference = chain 'Q' selection = chain 'h' } ncs_group { reference = (chain 'V' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.800 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 : 0.011 0.233 24661 Z= 0.578 Angle : 1.343 50.098 33721 Z= 0.713 Chirality : 0.067 0.993 4035 Planarity : 0.010 0.288 4250 Dihedral : 16.720 112.925 9456 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 47.43 Ramachandran Plot: Outliers : 1.13 % Allowed : 21.36 % Favored : 77.51 % Rotamer: Outliers : 2.39 % Allowed : 16.18 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.89 (0.11), residues: 3006 helix: -3.38 (0.14), residues: 625 sheet: -3.19 (0.22), residues: 384 loop : -4.58 (0.10), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1107 TYR 0.036 0.004 TYR B 313 PHE 0.041 0.003 PHE B 515 TRP 0.017 0.003 TRP C 64 HIS 0.013 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.01067 (24570) covalent geometry : angle 1.18524 (33483) SS BOND : bond 0.05006 ( 35) SS BOND : angle 5.73334 ( 70) hydrogen bonds : bond 0.18950 ( 696) hydrogen bonds : angle 8.90946 ( 1932) link_ALPHA1-3 : bond 0.00239 ( 1) link_ALPHA1-3 : angle 3.87760 ( 3) link_ALPHA1-6 : bond 0.00233 ( 1) link_ALPHA1-6 : angle 1.96316 ( 3) link_BETA1-4 : bond 0.00816 ( 17) link_BETA1-4 : angle 3.99574 ( 51) link_BETA1-6 : bond 0.01104 ( 1) link_BETA1-6 : angle 2.78536 ( 3) link_NAG-ASN : bond 0.04695 ( 36) link_NAG-ASN : angle 9.90640 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 612 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8693 (tp) cc_final: 0.8332 (tp) REVERT: A 145 TYR cc_start: 0.6939 (m-10) cc_final: 0.6726 (m-10) REVERT: A 153 MET cc_start: 0.4748 (OUTLIER) cc_final: 0.4000 (tmm) REVERT: A 369 TYR cc_start: 0.6319 (t80) cc_final: 0.5253 (m-80) REVERT: A 391 CYS cc_start: 0.1014 (OUTLIER) cc_final: 0.0689 (p) REVERT: A 595 VAL cc_start: 0.8962 (t) cc_final: 0.8714 (p) REVERT: A 726 ILE cc_start: 0.9132 (pt) cc_final: 0.8904 (pt) REVERT: A 733 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8694 (mppt) REVERT: A 779 GLN cc_start: 0.9359 (tm-30) cc_final: 0.9038 (tm-30) REVERT: A 790 LYS cc_start: 0.7729 (pttm) cc_final: 0.6819 (mmtm) REVERT: A 868 GLU cc_start: 0.8303 (pm20) cc_final: 0.7336 (tm-30) REVERT: A 873 TYR cc_start: 0.9210 (m-80) cc_final: 0.8888 (m-80) REVERT: A 1010 GLN cc_start: 0.8889 (mp10) cc_final: 0.8559 (mp10) REVERT: A 1036 GLN cc_start: 0.8763 (tt0) cc_final: 0.7439 (pt0) REVERT: A 1047 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: A 1113 GLN cc_start: 0.8676 (mt0) cc_final: 0.8444 (mt0) REVERT: B 32 PHE cc_start: 0.3453 (OUTLIER) cc_final: 0.2501 (m-10) REVERT: B 69 HIS cc_start: 0.6645 (m90) cc_final: 0.6404 (m170) REVERT: B 131 CYS cc_start: 0.6847 (OUTLIER) cc_final: 0.4974 (t) REVERT: B 153 MET cc_start: 0.7729 (mtm) cc_final: 0.6767 (tpt) REVERT: B 280 ASN cc_start: 0.8350 (t0) cc_final: 0.7964 (p0) REVERT: B 318 PHE cc_start: 0.8205 (p90) cc_final: 0.7810 (p90) REVERT: B 378 LYS cc_start: 0.6113 (mmtt) cc_final: 0.5701 (mmmt) REVERT: B 395 VAL cc_start: 0.8856 (t) cc_final: 0.8536 (t) REVERT: B 731 MET cc_start: 0.8064 (ttt) cc_final: 0.7726 (ttt) REVERT: B 780 GLU cc_start: 0.8490 (pt0) cc_final: 0.8257 (pt0) REVERT: B 821 LEU cc_start: 0.9302 (tp) cc_final: 0.8423 (tp) REVERT: B 825 LYS cc_start: 0.9143 (mtpp) cc_final: 0.8737 (mtpt) REVERT: B 864 LEU cc_start: 0.9393 (tp) cc_final: 0.9176 (tp) REVERT: B 869 MET cc_start: 0.9076 (tpt) cc_final: 0.8656 (tpp) REVERT: B 902 MET cc_start: 0.8798 (mmp) cc_final: 0.8213 (mmp) REVERT: B 977 LEU cc_start: 0.8881 (pt) cc_final: 0.8593 (pp) REVERT: B 1010 GLN cc_start: 0.9308 (mt0) cc_final: 0.9010 (mt0) REVERT: B 1038 LYS cc_start: 0.8845 (mmtp) cc_final: 0.8524 (mmtp) REVERT: B 1039 ARG cc_start: 0.8511 (ptm160) cc_final: 0.8265 (ptm160) REVERT: B 1095 PHE cc_start: 0.8958 (m-10) cc_final: 0.8629 (m-10) REVERT: B 1125 ASN cc_start: 0.8339 (p0) cc_final: 0.7936 (p0) REVERT: C 157 PHE cc_start: 0.5821 (m-80) cc_final: 0.4826 (t80) REVERT: C 200 TYR cc_start: 0.8112 (m-10) cc_final: 0.7885 (m-80) REVERT: C 298 GLU cc_start: 0.9006 (mp0) cc_final: 0.8709 (mp0) REVERT: C 314 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8909 (tm-30) REVERT: C 324 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8145 (tm-30) REVERT: C 357 ARG cc_start: 0.8267 (ttp-170) cc_final: 0.7951 (ttp-170) REVERT: C 396 TYR cc_start: 0.7107 (m-80) cc_final: 0.5775 (m-80) REVERT: C 741 TYR cc_start: 0.9024 (t80) cc_final: 0.8778 (t80) REVERT: C 751 ASN cc_start: 0.8555 (t0) cc_final: 0.8138 (t0) REVERT: C 755 GLN cc_start: 0.7646 (mt0) cc_final: 0.7357 (mt0) REVERT: C 762 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8818 (tp-100) REVERT: C 764 ASN cc_start: 0.8580 (m-40) cc_final: 0.8280 (m-40) REVERT: C 919 ASN cc_start: 0.9220 (t0) cc_final: 0.8933 (t0) REVERT: C 923 ILE cc_start: 0.9451 (mm) cc_final: 0.9188 (mt) REVERT: C 1028 LYS cc_start: 0.9318 (mttm) cc_final: 0.8915 (mttm) REVERT: C 1039 ARG cc_start: 0.9159 (mtp180) cc_final: 0.8599 (mtp85) REVERT: C 1111 GLU cc_start: 0.8546 (tp30) cc_final: 0.8299 (tp30) REVERT: C 1113 GLN cc_start: 0.8992 (mp10) cc_final: 0.8534 (mp10) outliers start: 60 outliers final: 32 residues processed: 656 average time/residue: 0.1768 time to fit residues: 181.2892 Evaluate side-chains 549 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 512 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN A 125 ASN A 134 GLN A 148 ASN A 207 HIS A 613 GLN A 655 HIS ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1058 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS A1108 ASN B 49 HIS B 121 ASN B 317 ASN B 542 ASN B 564 GLN B 607 GLN B 613 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 953 ASN B 954 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 506 GLN C 644 GLN C 978 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.169436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139317 restraints weight = 55575.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143438 restraints weight = 32368.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.146200 restraints weight = 21381.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.148150 restraints weight = 15567.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149482 restraints weight = 12134.220| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24661 Z= 0.225 Angle : 0.960 21.119 33721 Z= 0.464 Chirality : 0.055 0.572 4035 Planarity : 0.006 0.074 4250 Dihedral : 11.700 104.600 4401 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.67 % Favored : 86.16 % Rotamer: Outliers : 0.24 % Allowed : 7.91 % Favored : 91.85 % 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: -4.73 (0.12), residues: 3006 helix: -1.92 (0.17), residues: 620 sheet: -2.73 (0.24), residues: 384 loop : -3.92 (0.11), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 457 TYR 0.036 0.002 TYR B 269 PHE 0.043 0.003 PHE C 140 TRP 0.027 0.002 TRP A 886 HIS 0.009 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00479 (24570) covalent geometry : angle 0.89956 (33483) SS BOND : bond 0.00947 ( 35) SS BOND : angle 1.80491 ( 70) hydrogen bonds : bond 0.05735 ( 696) hydrogen bonds : angle 6.97542 ( 1932) link_ALPHA1-3 : bond 0.00360 ( 1) link_ALPHA1-3 : angle 1.39225 ( 3) link_ALPHA1-6 : bond 0.01212 ( 1) link_ALPHA1-6 : angle 1.87922 ( 3) link_BETA1-4 : bond 0.00454 ( 17) link_BETA1-4 : angle 3.34568 ( 51) link_BETA1-6 : bond 0.01570 ( 1) link_BETA1-6 : angle 3.17048 ( 3) link_NAG-ASN : bond 0.00784 ( 36) link_NAG-ASN : angle 5.39370 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 649 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8276 (tp) cc_final: 0.7710 (tp) REVERT: A 49 HIS cc_start: 0.7502 (t70) cc_final: 0.6731 (t-90) REVERT: A 153 MET cc_start: 0.5885 (ptt) cc_final: 0.5320 (tmm) REVERT: A 170 TYR cc_start: 0.8239 (t80) cc_final: 0.8017 (t80) REVERT: A 195 LYS cc_start: 0.8355 (ptmt) cc_final: 0.8068 (ptmt) REVERT: A 297 SER cc_start: 0.9463 (m) cc_final: 0.8955 (p) REVERT: A 369 TYR cc_start: 0.5968 (t80) cc_final: 0.5058 (m-80) REVERT: A 391 CYS cc_start: 0.1661 (OUTLIER) cc_final: 0.1330 (p) REVERT: A 595 VAL cc_start: 0.8905 (t) cc_final: 0.8526 (p) REVERT: A 598 ILE cc_start: 0.8989 (mt) cc_final: 0.8686 (tt) REVERT: A 699 LEU cc_start: 0.9105 (pt) cc_final: 0.8607 (mp) REVERT: A 726 ILE cc_start: 0.9143 (pt) cc_final: 0.8645 (pt) REVERT: A 733 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7792 (mptt) REVERT: A 742 ILE cc_start: 0.9326 (tp) cc_final: 0.9080 (tp) REVERT: A 779 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8895 (tm-30) REVERT: A 790 LYS cc_start: 0.7308 (pttm) cc_final: 0.6653 (mmtm) REVERT: A 868 GLU cc_start: 0.7978 (pm20) cc_final: 0.7133 (tm-30) REVERT: A 920 GLN cc_start: 0.8678 (pt0) cc_final: 0.8213 (tp40) REVERT: A 948 LEU cc_start: 0.9314 (mt) cc_final: 0.9003 (mt) REVERT: A 979 ASP cc_start: 0.9275 (t0) cc_final: 0.9072 (t70) REVERT: A 983 ARG cc_start: 0.8768 (ptt90) cc_final: 0.8107 (ptt90) REVERT: A 1018 ILE cc_start: 0.9581 (tp) cc_final: 0.9300 (tt) REVERT: A 1036 GLN cc_start: 0.8717 (tt0) cc_final: 0.8235 (tt0) REVERT: A 1113 GLN cc_start: 0.8706 (mt0) cc_final: 0.8460 (mt0) REVERT: B 58 PHE cc_start: 0.7895 (m-10) cc_final: 0.7125 (m-10) REVERT: B 153 MET cc_start: 0.7887 (mtm) cc_final: 0.7063 (tpt) REVERT: B 280 ASN cc_start: 0.8053 (t0) cc_final: 0.7663 (t0) REVERT: B 378 LYS cc_start: 0.6219 (mmtt) cc_final: 0.5873 (mmmt) REVERT: B 764 ASN cc_start: 0.8878 (m110) cc_final: 0.8641 (m110) REVERT: B 773 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8512 (tp30) REVERT: B 776 LYS cc_start: 0.9279 (ttpp) cc_final: 0.8572 (tmmt) REVERT: B 780 GLU cc_start: 0.8600 (pt0) cc_final: 0.7759 (pt0) REVERT: B 802 PHE cc_start: 0.7882 (m-80) cc_final: 0.7193 (m-80) REVERT: B 805 ILE cc_start: 0.9491 (mp) cc_final: 0.9193 (mp) REVERT: B 825 LYS cc_start: 0.8980 (mtpp) cc_final: 0.8694 (tptt) REVERT: B 902 MET cc_start: 0.7768 (mmp) cc_final: 0.7080 (mmp) REVERT: B 945 LEU cc_start: 0.8473 (mt) cc_final: 0.8247 (mt) REVERT: B 957 GLN cc_start: 0.9276 (pp30) cc_final: 0.9073 (pp30) REVERT: B 1010 GLN cc_start: 0.9159 (mt0) cc_final: 0.8576 (mt0) REVERT: B 1028 LYS cc_start: 0.9110 (mttm) cc_final: 0.8775 (mtmt) REVERT: B 1036 GLN cc_start: 0.8043 (tt0) cc_final: 0.7549 (mt0) REVERT: B 1038 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8400 (mmtp) REVERT: B 1039 ARG cc_start: 0.8394 (ptm160) cc_final: 0.7699 (ptp90) REVERT: B 1095 PHE cc_start: 0.8795 (m-10) cc_final: 0.7852 (m-10) REVERT: B 1109 PHE cc_start: 0.8972 (t80) cc_final: 0.8649 (t80) REVERT: B 1111 GLU cc_start: 0.8941 (tp30) cc_final: 0.8620 (tp30) REVERT: B 1125 ASN cc_start: 0.7877 (p0) cc_final: 0.7588 (p0) REVERT: C 105 ILE cc_start: 0.8559 (mt) cc_final: 0.8332 (mp) REVERT: C 200 TYR cc_start: 0.7844 (m-10) cc_final: 0.7539 (m-80) REVERT: C 314 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8929 (tm-30) REVERT: C 646 ARG cc_start: 0.8020 (tpt170) cc_final: 0.7685 (tpt170) REVERT: C 741 TYR cc_start: 0.8875 (t80) cc_final: 0.8617 (t80) REVERT: C 755 GLN cc_start: 0.7449 (mt0) cc_final: 0.7198 (mt0) REVERT: C 762 GLN cc_start: 0.8925 (tp-100) cc_final: 0.8645 (tp-100) REVERT: C 764 ASN cc_start: 0.8302 (m-40) cc_final: 0.7869 (m-40) REVERT: C 913 GLN cc_start: 0.8304 (mt0) cc_final: 0.7965 (mt0) REVERT: C 919 ASN cc_start: 0.9326 (t0) cc_final: 0.8859 (t0) REVERT: C 923 ILE cc_start: 0.9382 (mm) cc_final: 0.8705 (mm) REVERT: C 925 ASN cc_start: 0.9436 (t0) cc_final: 0.9154 (t0) REVERT: C 955 ASN cc_start: 0.8267 (m-40) cc_final: 0.7369 (m-40) REVERT: C 1005 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8683 (tm-30) REVERT: C 1009 THR cc_start: 0.9549 (p) cc_final: 0.9327 (p) REVERT: C 1010 GLN cc_start: 0.8992 (pm20) cc_final: 0.8546 (pm20) REVERT: C 1109 PHE cc_start: 0.8873 (t80) cc_final: 0.8546 (t80) REVERT: C 1111 GLU cc_start: 0.8346 (tp30) cc_final: 0.7793 (tp30) REVERT: C 1113 GLN cc_start: 0.8970 (mp10) cc_final: 0.7887 (mp10) outliers start: 6 outliers final: 0 residues processed: 655 average time/residue: 0.1662 time to fit residues: 173.1030 Evaluate side-chains 555 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 554 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 202 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 283 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 overall best weight: 5.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.166592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.136486 restraints weight = 56727.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140521 restraints weight = 33314.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143220 restraints weight = 22111.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145073 restraints weight = 16138.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146357 restraints weight = 12701.130| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 24661 Z= 0.298 Angle : 0.980 19.887 33721 Z= 0.478 Chirality : 0.054 0.490 4035 Planarity : 0.006 0.075 4250 Dihedral : 11.038 101.088 4401 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.70 % Favored : 84.13 % Rotamer: Outliers : 0.16 % Allowed : 6.40 % Favored : 93.44 % 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: -4.41 (0.13), residues: 3006 helix: -1.51 (0.18), residues: 623 sheet: -2.59 (0.24), residues: 409 loop : -3.75 (0.11), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 815 TYR 0.050 0.003 TYR B 313 PHE 0.036 0.003 PHE C 823 TRP 0.025 0.003 TRP A 886 HIS 0.009 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00626 (24570) covalent geometry : angle 0.92997 (33483) SS BOND : bond 0.00571 ( 35) SS BOND : angle 1.76620 ( 70) hydrogen bonds : bond 0.06002 ( 696) hydrogen bonds : angle 6.95403 ( 1932) link_ALPHA1-3 : bond 0.00780 ( 1) link_ALPHA1-3 : angle 1.63722 ( 3) link_ALPHA1-6 : bond 0.00041 ( 1) link_ALPHA1-6 : angle 1.95271 ( 3) link_BETA1-4 : bond 0.00430 ( 17) link_BETA1-4 : angle 3.44717 ( 51) link_BETA1-6 : bond 0.01234 ( 1) link_BETA1-6 : angle 1.81246 ( 3) link_NAG-ASN : bond 0.00793 ( 36) link_NAG-ASN : angle 4.87234 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 631 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8208 (tp) cc_final: 0.7735 (tp) REVERT: A 49 HIS cc_start: 0.7508 (t70) cc_final: 0.6757 (t-90) REVERT: A 117 LEU cc_start: 0.9010 (tp) cc_final: 0.8771 (tp) REVERT: A 153 MET cc_start: 0.5771 (ptt) cc_final: 0.5213 (tmm) REVERT: A 170 TYR cc_start: 0.8268 (t80) cc_final: 0.8059 (t80) REVERT: A 195 LYS cc_start: 0.8308 (ptmt) cc_final: 0.8047 (ptmt) REVERT: A 297 SER cc_start: 0.9481 (m) cc_final: 0.8992 (p) REVERT: A 369 TYR cc_start: 0.5947 (t80) cc_final: 0.5056 (m-80) REVERT: A 391 CYS cc_start: 0.1548 (OUTLIER) cc_final: 0.1272 (p) REVERT: A 595 VAL cc_start: 0.8996 (t) cc_final: 0.8660 (p) REVERT: A 598 ILE cc_start: 0.8987 (mt) cc_final: 0.8761 (tt) REVERT: A 726 ILE cc_start: 0.9062 (pt) cc_final: 0.8599 (pt) REVERT: A 733 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8060 (mptt) REVERT: A 779 GLN cc_start: 0.9200 (tm-30) cc_final: 0.8842 (tm-30) REVERT: A 790 LYS cc_start: 0.7404 (pttm) cc_final: 0.6686 (mmtm) REVERT: A 867 ASP cc_start: 0.9213 (p0) cc_final: 0.8862 (p0) REVERT: A 868 GLU cc_start: 0.8046 (pm20) cc_final: 0.7099 (tm-30) REVERT: A 948 LEU cc_start: 0.9353 (mt) cc_final: 0.8986 (mt) REVERT: A 969 ASN cc_start: 0.9302 (m-40) cc_final: 0.8912 (m-40) REVERT: A 983 ARG cc_start: 0.8777 (ptt90) cc_final: 0.8307 (ptt90) REVERT: A 1039 ARG cc_start: 0.8292 (ptp-170) cc_final: 0.7995 (ptp-170) REVERT: A 1111 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8581 (mt-10) REVERT: A 1113 GLN cc_start: 0.8744 (mt0) cc_final: 0.8440 (mt0) REVERT: B 152 TRP cc_start: 0.7939 (t60) cc_final: 0.7361 (t60) REVERT: B 153 MET cc_start: 0.8018 (mtm) cc_final: 0.7068 (tpt) REVERT: B 378 LYS cc_start: 0.6295 (mmtt) cc_final: 0.5910 (mmmt) REVERT: B 745 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: B 764 ASN cc_start: 0.8858 (m110) cc_final: 0.8636 (m110) REVERT: B 776 LYS cc_start: 0.9273 (ttpp) cc_final: 0.8560 (tmmt) REVERT: B 780 GLU cc_start: 0.8728 (pt0) cc_final: 0.7713 (pt0) REVERT: B 902 MET cc_start: 0.7943 (mmp) cc_final: 0.7027 (mmp) REVERT: B 949 GLN cc_start: 0.8742 (tp40) cc_final: 0.7720 (tp-100) REVERT: B 955 ASN cc_start: 0.7954 (t0) cc_final: 0.7737 (t0) REVERT: B 1010 GLN cc_start: 0.9102 (mt0) cc_final: 0.8583 (mt0) REVERT: B 1028 LYS cc_start: 0.9067 (mttm) cc_final: 0.8792 (mtmt) REVERT: B 1036 GLN cc_start: 0.8158 (tt0) cc_final: 0.7225 (mt0) REVERT: B 1038 LYS cc_start: 0.8789 (mppt) cc_final: 0.8539 (mmtt) REVERT: B 1039 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7555 (ptm160) REVERT: B 1109 PHE cc_start: 0.9448 (t80) cc_final: 0.8535 (t80) REVERT: B 1111 GLU cc_start: 0.8809 (tp30) cc_final: 0.8323 (tp30) REVERT: C 314 GLN cc_start: 0.9235 (tm-30) cc_final: 0.9025 (tm-30) REVERT: C 646 ARG cc_start: 0.8124 (tpt170) cc_final: 0.7758 (tpt170) REVERT: C 741 TYR cc_start: 0.8934 (t80) cc_final: 0.8679 (t80) REVERT: C 755 GLN cc_start: 0.7630 (mt0) cc_final: 0.7354 (mt0) REVERT: C 762 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8711 (tp-100) REVERT: C 764 ASN cc_start: 0.8344 (m-40) cc_final: 0.7901 (m-40) REVERT: C 919 ASN cc_start: 0.9384 (t0) cc_final: 0.9014 (t0) REVERT: C 923 ILE cc_start: 0.9403 (mm) cc_final: 0.8997 (mt) REVERT: C 925 ASN cc_start: 0.9462 (t0) cc_final: 0.9197 (t0) REVERT: C 950 ASP cc_start: 0.8819 (m-30) cc_final: 0.8329 (m-30) REVERT: C 961 THR cc_start: 0.9533 (p) cc_final: 0.9128 (p) REVERT: C 965 GLN cc_start: 0.9554 (mm-40) cc_final: 0.9320 (mm-40) REVERT: C 1004 LEU cc_start: 0.9442 (tp) cc_final: 0.9164 (tp) REVERT: C 1005 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8723 (tm-30) REVERT: C 1006 THR cc_start: 0.9249 (p) cc_final: 0.8562 (p) REVERT: C 1010 GLN cc_start: 0.9147 (pm20) cc_final: 0.8703 (pm20) REVERT: C 1081 ILE cc_start: 0.8235 (mm) cc_final: 0.8032 (mm) REVERT: C 1111 GLU cc_start: 0.8652 (tp30) cc_final: 0.8211 (tp30) REVERT: C 1113 GLN cc_start: 0.8871 (mp10) cc_final: 0.7854 (mp10) outliers start: 4 outliers final: 0 residues processed: 635 average time/residue: 0.1662 time to fit residues: 168.8142 Evaluate side-chains 531 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 529 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 263 optimal weight: 0.4980 chunk 22 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 288 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 240 optimal weight: 0.6980 chunk 265 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 87 ASN B 542 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B 957 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C 992 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.173043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142409 restraints weight = 54709.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146477 restraints weight = 32516.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149285 restraints weight = 21783.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151231 restraints weight = 15912.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152524 restraints weight = 12495.132| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24661 Z= 0.162 Angle : 0.841 20.067 33721 Z= 0.407 Chirality : 0.051 0.487 4035 Planarity : 0.005 0.074 4250 Dihedral : 9.936 102.609 4401 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.21 % Favored : 87.69 % Rotamer: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.90 % 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: -3.86 (0.13), residues: 3006 helix: -0.74 (0.20), residues: 620 sheet: -2.34 (0.24), residues: 405 loop : -3.47 (0.12), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1039 TYR 0.027 0.002 TYR C 505 PHE 0.033 0.002 PHE B 823 TRP 0.032 0.002 TRP C 64 HIS 0.019 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00347 (24570) covalent geometry : angle 0.79288 (33483) SS BOND : bond 0.00491 ( 35) SS BOND : angle 1.84490 ( 70) hydrogen bonds : bond 0.04972 ( 696) hydrogen bonds : angle 6.39918 ( 1932) link_ALPHA1-3 : bond 0.00847 ( 1) link_ALPHA1-3 : angle 1.36035 ( 3) link_ALPHA1-6 : bond 0.00505 ( 1) link_ALPHA1-6 : angle 1.51350 ( 3) link_BETA1-4 : bond 0.00450 ( 17) link_BETA1-4 : angle 3.15278 ( 51) link_BETA1-6 : bond 0.00973 ( 1) link_BETA1-6 : angle 2.15676 ( 3) link_NAG-ASN : bond 0.00703 ( 36) link_NAG-ASN : angle 4.36323 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 636 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8238 (tp) cc_final: 0.7630 (tp) REVERT: A 49 HIS cc_start: 0.7394 (t70) cc_final: 0.6625 (t70) REVERT: A 145 TYR cc_start: 0.7200 (m-10) cc_final: 0.6800 (m-80) REVERT: A 153 MET cc_start: 0.5513 (ptt) cc_final: 0.5082 (tmm) REVERT: A 170 TYR cc_start: 0.8161 (t80) cc_final: 0.7951 (t80) REVERT: A 195 LYS cc_start: 0.8058 (ptmt) cc_final: 0.7824 (ptmt) REVERT: A 297 SER cc_start: 0.9501 (m) cc_final: 0.9031 (p) REVERT: A 369 TYR cc_start: 0.6050 (t80) cc_final: 0.5167 (m-80) REVERT: A 598 ILE cc_start: 0.8901 (mt) cc_final: 0.8682 (tt) REVERT: A 726 ILE cc_start: 0.9092 (pt) cc_final: 0.8548 (pt) REVERT: A 742 ILE cc_start: 0.9388 (tp) cc_final: 0.9184 (tp) REVERT: A 790 LYS cc_start: 0.7202 (pttm) cc_final: 0.6759 (mmtm) REVERT: A 867 ASP cc_start: 0.9160 (p0) cc_final: 0.8856 (p0) REVERT: A 868 GLU cc_start: 0.7970 (pm20) cc_final: 0.7127 (tm-30) REVERT: A 901 GLN cc_start: 0.8827 (tt0) cc_final: 0.8608 (tt0) REVERT: A 902 MET cc_start: 0.8510 (mmp) cc_final: 0.7955 (mmt) REVERT: A 948 LEU cc_start: 0.9284 (mt) cc_final: 0.8934 (mt) REVERT: A 983 ARG cc_start: 0.8766 (ptt90) cc_final: 0.8062 (ptt90) REVERT: A 1018 ILE cc_start: 0.9484 (tp) cc_final: 0.9273 (tt) REVERT: A 1113 GLN cc_start: 0.8726 (mt0) cc_final: 0.8428 (mt0) REVERT: B 58 PHE cc_start: 0.7866 (m-10) cc_final: 0.7621 (m-80) REVERT: B 152 TRP cc_start: 0.7917 (t60) cc_final: 0.7402 (t60) REVERT: B 153 MET cc_start: 0.7898 (mtm) cc_final: 0.7104 (tpt) REVERT: B 378 LYS cc_start: 0.6291 (mmtt) cc_final: 0.5911 (mmmt) REVERT: B 764 ASN cc_start: 0.8805 (m110) cc_final: 0.8605 (m110) REVERT: B 776 LYS cc_start: 0.9231 (ttpp) cc_final: 0.8572 (tmmt) REVERT: B 780 GLU cc_start: 0.8482 (pt0) cc_final: 0.7548 (pt0) REVERT: B 825 LYS cc_start: 0.8893 (tttt) cc_final: 0.8295 (tttt) REVERT: B 902 MET cc_start: 0.7618 (mmp) cc_final: 0.7064 (mmp) REVERT: B 945 LEU cc_start: 0.8471 (mt) cc_final: 0.8146 (mt) REVERT: B 949 GLN cc_start: 0.8667 (tp40) cc_final: 0.8128 (tp-100) REVERT: B 969 ASN cc_start: 0.8983 (p0) cc_final: 0.8738 (p0) REVERT: B 1010 GLN cc_start: 0.8931 (mt0) cc_final: 0.8679 (mt0) REVERT: B 1028 LYS cc_start: 0.9037 (mttm) cc_final: 0.8656 (mtmm) REVERT: B 1038 LYS cc_start: 0.8867 (mppt) cc_final: 0.8647 (mmtt) REVERT: B 1095 PHE cc_start: 0.8593 (m-10) cc_final: 0.7676 (m-10) REVERT: B 1106 GLN cc_start: 0.8503 (pm20) cc_final: 0.8265 (pm20) REVERT: B 1109 PHE cc_start: 0.9304 (t80) cc_final: 0.8412 (t80) REVERT: B 1111 GLU cc_start: 0.8795 (tp30) cc_final: 0.8124 (tp30) REVERT: C 314 GLN cc_start: 0.9313 (tm-30) cc_final: 0.8998 (tm-30) REVERT: C 646 ARG cc_start: 0.7984 (tpt170) cc_final: 0.7668 (tpt170) REVERT: C 725 GLU cc_start: 0.7902 (pm20) cc_final: 0.7436 (pm20) REVERT: C 741 TYR cc_start: 0.8868 (t80) cc_final: 0.8539 (t80) REVERT: C 755 GLN cc_start: 0.7450 (mt0) cc_final: 0.7175 (mt0) REVERT: C 764 ASN cc_start: 0.8275 (m-40) cc_final: 0.7871 (m-40) REVERT: C 919 ASN cc_start: 0.9383 (t0) cc_final: 0.9121 (t0) REVERT: C 925 ASN cc_start: 0.9375 (t0) cc_final: 0.9053 (t0) REVERT: C 964 LYS cc_start: 0.9299 (mtmm) cc_final: 0.8851 (mttm) REVERT: C 1004 LEU cc_start: 0.9319 (tp) cc_final: 0.9082 (tp) REVERT: C 1005 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8444 (tm-30) REVERT: C 1006 THR cc_start: 0.9056 (p) cc_final: 0.8292 (p) REVERT: C 1010 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8729 (pm20) REVERT: C 1081 ILE cc_start: 0.8291 (mm) cc_final: 0.8080 (mm) REVERT: C 1109 PHE cc_start: 0.8634 (t80) cc_final: 0.8403 (t80) REVERT: C 1111 GLU cc_start: 0.8648 (tp30) cc_final: 0.8107 (tp30) REVERT: C 1113 GLN cc_start: 0.8891 (mp10) cc_final: 0.7825 (mp10) REVERT: C 1135 ASN cc_start: 0.5737 (t0) cc_final: 0.5431 (t0) outliers start: 3 outliers final: 1 residues processed: 637 average time/residue: 0.1673 time to fit residues: 169.6166 Evaluate side-chains 540 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 538 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 130 optimal weight: 8.9990 chunk 193 optimal weight: 0.0370 chunk 123 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 293 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 301 optimal weight: 0.0670 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 920 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 542 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN C 49 HIS C 66 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.176715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145984 restraints weight = 55590.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.150339 restraints weight = 33977.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154869 restraints weight = 21306.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.155559 restraints weight = 13508.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155936 restraints weight = 11453.499| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24661 Z= 0.143 Angle : 0.812 20.234 33721 Z= 0.389 Chirality : 0.050 0.443 4035 Planarity : 0.005 0.098 4250 Dihedral : 9.243 103.839 4401 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.78 % Favored : 88.12 % Rotamer: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.43 (0.14), residues: 3006 helix: -0.26 (0.20), residues: 615 sheet: -2.05 (0.26), residues: 380 loop : -3.23 (0.12), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 44 TYR 0.025 0.002 TYR C 505 PHE 0.026 0.002 PHE B 559 TRP 0.023 0.002 TRP C 64 HIS 0.012 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00305 (24570) covalent geometry : angle 0.76533 (33483) SS BOND : bond 0.00462 ( 35) SS BOND : angle 1.59052 ( 70) hydrogen bonds : bond 0.04603 ( 696) hydrogen bonds : angle 6.09702 ( 1932) link_ALPHA1-3 : bond 0.01060 ( 1) link_ALPHA1-3 : angle 1.13055 ( 3) link_ALPHA1-6 : bond 0.00292 ( 1) link_ALPHA1-6 : angle 1.66028 ( 3) link_BETA1-4 : bond 0.00589 ( 17) link_BETA1-4 : angle 2.99145 ( 51) link_BETA1-6 : bond 0.01467 ( 1) link_BETA1-6 : angle 2.03467 ( 3) link_NAG-ASN : bond 0.01119 ( 36) link_NAG-ASN : angle 4.28738 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 646 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.8982 (t0) cc_final: 0.8766 (t0) REVERT: A 34 ARG cc_start: 0.7933 (mmp80) cc_final: 0.7689 (mmp80) REVERT: A 48 LEU cc_start: 0.8159 (tp) cc_final: 0.7882 (tp) REVERT: A 49 HIS cc_start: 0.7118 (t70) cc_final: 0.6567 (t70) REVERT: A 153 MET cc_start: 0.5440 (ptt) cc_final: 0.4982 (tmm) REVERT: A 170 TYR cc_start: 0.8109 (t80) cc_final: 0.7891 (t80) REVERT: A 250 THR cc_start: 0.7846 (p) cc_final: 0.7598 (t) REVERT: A 297 SER cc_start: 0.9417 (m) cc_final: 0.8996 (p) REVERT: A 302 THR cc_start: 0.8348 (t) cc_final: 0.7987 (t) REVERT: A 369 TYR cc_start: 0.6036 (t80) cc_final: 0.5168 (m-80) REVERT: A 726 ILE cc_start: 0.9117 (pt) cc_final: 0.8568 (pt) REVERT: A 752 LEU cc_start: 0.8339 (mm) cc_final: 0.7078 (mm) REVERT: A 770 ILE cc_start: 0.9162 (tt) cc_final: 0.8953 (tp) REVERT: A 867 ASP cc_start: 0.9122 (p0) cc_final: 0.8686 (p0) REVERT: A 868 GLU cc_start: 0.8053 (pm20) cc_final: 0.6873 (tm-30) REVERT: A 869 MET cc_start: 0.8785 (ptt) cc_final: 0.8548 (ppp) REVERT: A 902 MET cc_start: 0.8707 (mmp) cc_final: 0.8503 (mmp) REVERT: A 948 LEU cc_start: 0.9281 (mt) cc_final: 0.8948 (mt) REVERT: A 969 ASN cc_start: 0.9174 (m-40) cc_final: 0.8660 (m-40) REVERT: A 983 ARG cc_start: 0.8687 (ptt90) cc_final: 0.8267 (ptt180) REVERT: A 1018 ILE cc_start: 0.9467 (tp) cc_final: 0.9202 (tt) REVERT: B 104 TRP cc_start: 0.6954 (m-90) cc_final: 0.6564 (m-90) REVERT: B 152 TRP cc_start: 0.7954 (t60) cc_final: 0.7518 (t60) REVERT: B 153 MET cc_start: 0.7826 (mtm) cc_final: 0.7162 (tpt) REVERT: B 378 LYS cc_start: 0.6472 (mmtt) cc_final: 0.6066 (mmmt) REVERT: B 542 ASN cc_start: 0.7675 (m-40) cc_final: 0.6666 (t0) REVERT: B 727 LEU cc_start: 0.8898 (mt) cc_final: 0.8052 (mt) REVERT: B 731 MET cc_start: 0.6890 (ttt) cc_final: 0.5495 (ttt) REVERT: B 773 GLU cc_start: 0.9104 (tp30) cc_final: 0.8572 (tp30) REVERT: B 774 GLN cc_start: 0.8678 (tt0) cc_final: 0.8130 (tp-100) REVERT: B 776 LYS cc_start: 0.9330 (ttpp) cc_final: 0.8657 (tmmt) REVERT: B 780 GLU cc_start: 0.8530 (pt0) cc_final: 0.7838 (pt0) REVERT: B 825 LYS cc_start: 0.8771 (tttt) cc_final: 0.8015 (tptt) REVERT: B 861 LEU cc_start: 0.9633 (tt) cc_final: 0.9392 (tt) REVERT: B 949 GLN cc_start: 0.8592 (tp40) cc_final: 0.7860 (tp-100) REVERT: B 969 ASN cc_start: 0.8855 (p0) cc_final: 0.8652 (p0) REVERT: B 1010 GLN cc_start: 0.9058 (mt0) cc_final: 0.8802 (mt0) REVERT: B 1028 LYS cc_start: 0.8979 (mttm) cc_final: 0.8536 (mtpp) REVERT: B 1038 LYS cc_start: 0.8854 (mppt) cc_final: 0.8629 (mmtt) REVERT: B 1052 PHE cc_start: 0.8182 (m-10) cc_final: 0.7893 (m-10) REVERT: B 1095 PHE cc_start: 0.8308 (m-10) cc_final: 0.7261 (m-10) REVERT: B 1109 PHE cc_start: 0.9193 (t80) cc_final: 0.8325 (t80) REVERT: B 1111 GLU cc_start: 0.8627 (tp30) cc_final: 0.8021 (tp30) REVERT: C 307 THR cc_start: 0.7816 (t) cc_final: 0.7532 (t) REVERT: C 314 GLN cc_start: 0.9414 (tm-30) cc_final: 0.9088 (tm-30) REVERT: C 741 TYR cc_start: 0.8759 (t80) cc_final: 0.8340 (t80) REVERT: C 755 GLN cc_start: 0.7477 (mt0) cc_final: 0.7189 (mt0) REVERT: C 764 ASN cc_start: 0.8255 (m-40) cc_final: 0.7827 (m-40) REVERT: C 776 LYS cc_start: 0.9172 (tmmt) cc_final: 0.8498 (tmmt) REVERT: C 780 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8472 (mt-10) REVERT: C 815 ARG cc_start: 0.8301 (tpm170) cc_final: 0.7962 (tpm170) REVERT: C 895 GLN cc_start: 0.8043 (pm20) cc_final: 0.7689 (pm20) REVERT: C 917 TYR cc_start: 0.7042 (m-10) cc_final: 0.5747 (m-10) REVERT: C 919 ASN cc_start: 0.9418 (t0) cc_final: 0.9171 (t0) REVERT: C 925 ASN cc_start: 0.9347 (t0) cc_final: 0.8998 (t0) REVERT: C 953 ASN cc_start: 0.8512 (m110) cc_final: 0.8295 (m-40) REVERT: C 963 VAL cc_start: 0.8815 (p) cc_final: 0.8582 (p) REVERT: C 964 LYS cc_start: 0.9215 (mtmm) cc_final: 0.8773 (mttm) REVERT: C 965 GLN cc_start: 0.9369 (mm-40) cc_final: 0.9144 (mm-40) REVERT: C 1004 LEU cc_start: 0.9303 (tp) cc_final: 0.9057 (tp) REVERT: C 1005 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8528 (tm-30) REVERT: C 1006 THR cc_start: 0.9036 (p) cc_final: 0.8430 (p) REVERT: C 1010 GLN cc_start: 0.8892 (pm20) cc_final: 0.8607 (pm20) REVERT: C 1064 HIS cc_start: 0.7797 (m-70) cc_final: 0.7343 (m-70) REVERT: C 1109 PHE cc_start: 0.8606 (t80) cc_final: 0.8341 (t80) REVERT: C 1110 TYR cc_start: 0.9151 (t80) cc_final: 0.8892 (t80) REVERT: C 1111 GLU cc_start: 0.8520 (tp30) cc_final: 0.7888 (tp30) REVERT: C 1113 GLN cc_start: 0.8803 (mp10) cc_final: 0.7728 (mp10) REVERT: C 1135 ASN cc_start: 0.5848 (t0) cc_final: 0.5602 (t0) outliers start: 2 outliers final: 1 residues processed: 648 average time/residue: 0.1633 time to fit residues: 169.0891 Evaluate side-chains 558 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 557 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 229 optimal weight: 7.9990 chunk 192 optimal weight: 0.0170 chunk 11 optimal weight: 0.0170 chunk 264 optimal weight: 1.9990 chunk 260 optimal weight: 0.1980 chunk 280 optimal weight: 7.9990 chunk 276 optimal weight: 0.7980 chunk 241 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 774 GLN A 804 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 953 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 66 HIS C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.179287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148057 restraints weight = 54266.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152200 restraints weight = 32838.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155080 restraints weight = 22208.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.157089 restraints weight = 16297.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.158548 restraints weight = 12831.264| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24661 Z= 0.135 Angle : 0.793 20.212 33721 Z= 0.380 Chirality : 0.050 0.633 4035 Planarity : 0.005 0.070 4250 Dihedral : 8.877 110.113 4401 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.35 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -3.21 (0.14), residues: 3006 helix: -0.10 (0.20), residues: 622 sheet: -1.87 (0.26), residues: 365 loop : -3.08 (0.12), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 905 TYR 0.030 0.002 TYR C 505 PHE 0.032 0.002 PHE C 823 TRP 0.019 0.002 TRP B 886 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00290 (24570) covalent geometry : angle 0.74542 (33483) SS BOND : bond 0.00457 ( 35) SS BOND : angle 1.70741 ( 70) hydrogen bonds : bond 0.04424 ( 696) hydrogen bonds : angle 5.99392 ( 1932) link_ALPHA1-3 : bond 0.01107 ( 1) link_ALPHA1-3 : angle 1.10131 ( 3) link_ALPHA1-6 : bond 0.00503 ( 1) link_ALPHA1-6 : angle 1.52364 ( 3) link_BETA1-4 : bond 0.00554 ( 17) link_BETA1-4 : angle 2.84094 ( 51) link_BETA1-6 : bond 0.01134 ( 1) link_BETA1-6 : angle 1.61179 ( 3) link_NAG-ASN : bond 0.00852 ( 36) link_NAG-ASN : angle 4.29396 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.9021 (t0) cc_final: 0.8801 (t0) REVERT: A 49 HIS cc_start: 0.7333 (t70) cc_final: 0.6745 (t70) REVERT: A 117 LEU cc_start: 0.8836 (tp) cc_final: 0.8619 (tp) REVERT: A 153 MET cc_start: 0.5251 (ptt) cc_final: 0.4918 (tmm) REVERT: A 170 TYR cc_start: 0.8189 (t80) cc_final: 0.7980 (t80) REVERT: A 250 THR cc_start: 0.7777 (p) cc_final: 0.7537 (t) REVERT: A 297 SER cc_start: 0.9509 (m) cc_final: 0.9076 (p) REVERT: A 369 TYR cc_start: 0.6042 (t80) cc_final: 0.5170 (m-80) REVERT: A 726 ILE cc_start: 0.9186 (pt) cc_final: 0.8627 (pt) REVERT: A 764 ASN cc_start: 0.9087 (m-40) cc_final: 0.8860 (m-40) REVERT: A 765 ARG cc_start: 0.8972 (mtm180) cc_final: 0.8550 (ptp-170) REVERT: A 867 ASP cc_start: 0.9093 (p0) cc_final: 0.8661 (p0) REVERT: A 868 GLU cc_start: 0.8031 (pm20) cc_final: 0.6884 (tm-30) REVERT: A 869 MET cc_start: 0.8793 (ptt) cc_final: 0.8312 (ppp) REVERT: A 902 MET cc_start: 0.8552 (mmp) cc_final: 0.8329 (mmp) REVERT: A 947 LYS cc_start: 0.9143 (mttt) cc_final: 0.8940 (mttt) REVERT: A 948 LEU cc_start: 0.9294 (mt) cc_final: 0.8998 (mt) REVERT: A 969 ASN cc_start: 0.9066 (m-40) cc_final: 0.8499 (m-40) REVERT: A 983 ARG cc_start: 0.8960 (ptt90) cc_final: 0.8325 (ptt90) REVERT: A 990 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8824 (tp30) REVERT: A 1018 ILE cc_start: 0.9460 (tp) cc_final: 0.9200 (tt) REVERT: A 1110 TYR cc_start: 0.8567 (t80) cc_final: 0.8323 (t80) REVERT: B 104 TRP cc_start: 0.6908 (m-90) cc_final: 0.6474 (m-90) REVERT: B 144 TYR cc_start: 0.5317 (t80) cc_final: 0.4963 (p90) REVERT: B 152 TRP cc_start: 0.7951 (t60) cc_final: 0.7476 (t60) REVERT: B 153 MET cc_start: 0.7696 (mtm) cc_final: 0.7229 (tpt) REVERT: B 275 PHE cc_start: 0.7380 (m-80) cc_final: 0.6144 (m-10) REVERT: B 318 PHE cc_start: 0.7635 (p90) cc_final: 0.7330 (p90) REVERT: B 378 LYS cc_start: 0.6492 (mmtt) cc_final: 0.6074 (mmmt) REVERT: B 542 ASN cc_start: 0.7607 (m-40) cc_final: 0.6635 (t0) REVERT: B 661 GLU cc_start: 0.8877 (pp20) cc_final: 0.8368 (pp20) REVERT: B 727 LEU cc_start: 0.8883 (mt) cc_final: 0.7962 (mt) REVERT: B 731 MET cc_start: 0.7008 (ttt) cc_final: 0.6633 (ptm) REVERT: B 773 GLU cc_start: 0.9128 (tp30) cc_final: 0.8758 (tp30) REVERT: B 774 GLN cc_start: 0.8789 (tt0) cc_final: 0.8433 (tp-100) REVERT: B 776 LYS cc_start: 0.9285 (ttpp) cc_final: 0.8634 (tmmt) REVERT: B 780 GLU cc_start: 0.8509 (pt0) cc_final: 0.7730 (pt0) REVERT: B 811 LYS cc_start: 0.8525 (mmmm) cc_final: 0.8109 (mmmt) REVERT: B 825 LYS cc_start: 0.8779 (tttt) cc_final: 0.8054 (tptt) REVERT: B 861 LEU cc_start: 0.9636 (tt) cc_final: 0.9419 (tt) REVERT: B 901 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8136 (mm-40) REVERT: B 949 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8080 (tp-100) REVERT: B 969 ASN cc_start: 0.8771 (p0) cc_final: 0.8375 (p0) REVERT: B 1010 GLN cc_start: 0.8975 (mt0) cc_final: 0.8772 (mt0) REVERT: B 1028 LYS cc_start: 0.8829 (mttm) cc_final: 0.8506 (mtmm) REVERT: B 1064 HIS cc_start: 0.8216 (m-70) cc_final: 0.7919 (m-70) REVERT: B 1106 GLN cc_start: 0.8538 (pm20) cc_final: 0.8290 (pm20) REVERT: B 1109 PHE cc_start: 0.9190 (t80) cc_final: 0.8262 (t80) REVERT: B 1111 GLU cc_start: 0.8616 (tp30) cc_final: 0.7906 (tp30) REVERT: C 58 PHE cc_start: 0.6762 (m-80) cc_final: 0.6463 (m-80) REVERT: C 269 TYR cc_start: 0.7914 (m-10) cc_final: 0.7234 (m-10) REVERT: C 307 THR cc_start: 0.7830 (t) cc_final: 0.7122 (t) REVERT: C 314 GLN cc_start: 0.9427 (tm-30) cc_final: 0.9082 (tm-30) REVERT: C 699 LEU cc_start: 0.8247 (mp) cc_final: 0.6574 (tp) REVERT: C 764 ASN cc_start: 0.8266 (m-40) cc_final: 0.7880 (m-40) REVERT: C 773 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8361 (mt-10) REVERT: C 776 LYS cc_start: 0.9134 (tmmt) cc_final: 0.8612 (tmmt) REVERT: C 780 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8488 (mt-10) REVERT: C 815 ARG cc_start: 0.8363 (tpm170) cc_final: 0.7983 (tpm170) REVERT: C 895 GLN cc_start: 0.7999 (pm20) cc_final: 0.7489 (pm20) REVERT: C 917 TYR cc_start: 0.7083 (m-10) cc_final: 0.5379 (m-10) REVERT: C 919 ASN cc_start: 0.9433 (t0) cc_final: 0.9217 (t0) REVERT: C 925 ASN cc_start: 0.9302 (t0) cc_final: 0.8917 (t0) REVERT: C 953 ASN cc_start: 0.8467 (m110) cc_final: 0.8209 (m-40) REVERT: C 961 THR cc_start: 0.9309 (p) cc_final: 0.8903 (p) REVERT: C 964 LYS cc_start: 0.9254 (mtmm) cc_final: 0.8717 (mttm) REVERT: C 965 GLN cc_start: 0.9425 (mm-40) cc_final: 0.9203 (mm-40) REVERT: C 1005 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 1006 THR cc_start: 0.8970 (p) cc_final: 0.8240 (p) REVERT: C 1010 GLN cc_start: 0.8783 (pm20) cc_final: 0.8557 (pm20) REVERT: C 1109 PHE cc_start: 0.8587 (t80) cc_final: 0.8279 (t80) REVERT: C 1110 TYR cc_start: 0.9130 (t80) cc_final: 0.8868 (t80) REVERT: C 1111 GLU cc_start: 0.8468 (tp30) cc_final: 0.7867 (tp30) REVERT: C 1113 GLN cc_start: 0.8670 (mp10) cc_final: 0.7632 (mp10) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.1631 time to fit residues: 167.0188 Evaluate side-chains 555 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 555 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 242 optimal weight: 8.9990 chunk 267 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 954 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 928 ASN B1011 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.176842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145615 restraints weight = 54510.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149716 restraints weight = 33060.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152563 restraints weight = 22356.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.154459 restraints weight = 16435.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.155921 restraints weight = 13025.012| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24661 Z= 0.152 Angle : 0.785 20.048 33721 Z= 0.377 Chirality : 0.049 0.535 4035 Planarity : 0.005 0.073 4250 Dihedral : 8.821 108.817 4401 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.08 % Favored : 88.82 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: -3.11 (0.14), residues: 3006 helix: -0.05 (0.20), residues: 628 sheet: -1.80 (0.27), residues: 363 loop : -3.01 (0.12), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 765 TYR 0.031 0.002 TYR C 505 PHE 0.027 0.002 PHE C 823 TRP 0.020 0.001 TRP C 64 HIS 0.010 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00334 (24570) covalent geometry : angle 0.73753 (33483) SS BOND : bond 0.00441 ( 35) SS BOND : angle 1.78299 ( 70) hydrogen bonds : bond 0.04434 ( 696) hydrogen bonds : angle 5.93134 ( 1932) link_ALPHA1-3 : bond 0.01034 ( 1) link_ALPHA1-3 : angle 1.09458 ( 3) link_ALPHA1-6 : bond 0.00289 ( 1) link_ALPHA1-6 : angle 1.62275 ( 3) link_BETA1-4 : bond 0.00491 ( 17) link_BETA1-4 : angle 2.78368 ( 51) link_BETA1-6 : bond 0.01185 ( 1) link_BETA1-6 : angle 1.67910 ( 3) link_NAG-ASN : bond 0.00762 ( 36) link_NAG-ASN : angle 4.22816 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 630 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.9035 (t0) cc_final: 0.8814 (t0) REVERT: A 51 THR cc_start: 0.9202 (p) cc_final: 0.9000 (p) REVERT: A 117 LEU cc_start: 0.8843 (tp) cc_final: 0.8620 (tp) REVERT: A 145 TYR cc_start: 0.7154 (m-80) cc_final: 0.6876 (m-80) REVERT: A 153 MET cc_start: 0.5152 (ptt) cc_final: 0.4867 (tmm) REVERT: A 250 THR cc_start: 0.7820 (p) cc_final: 0.7585 (t) REVERT: A 297 SER cc_start: 0.9589 (m) cc_final: 0.9197 (p) REVERT: A 369 TYR cc_start: 0.6055 (t80) cc_final: 0.5206 (m-80) REVERT: A 782 PHE cc_start: 0.8894 (m-80) cc_final: 0.8657 (m-10) REVERT: A 867 ASP cc_start: 0.9148 (p0) cc_final: 0.8685 (p0) REVERT: A 868 GLU cc_start: 0.8048 (pm20) cc_final: 0.6771 (tm-30) REVERT: A 869 MET cc_start: 0.8845 (ptt) cc_final: 0.8478 (ppp) REVERT: A 901 GLN cc_start: 0.8725 (tt0) cc_final: 0.8413 (tt0) REVERT: A 902 MET cc_start: 0.8635 (mmp) cc_final: 0.8376 (mmp) REVERT: A 969 ASN cc_start: 0.9129 (m-40) cc_final: 0.8599 (m-40) REVERT: A 983 ARG cc_start: 0.8990 (ptt90) cc_final: 0.8510 (ptt90) REVERT: A 990 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8705 (tp30) REVERT: A 1107 ARG cc_start: 0.8570 (mmt-90) cc_final: 0.8251 (tpp80) REVERT: B 104 TRP cc_start: 0.6914 (m-90) cc_final: 0.6449 (m-90) REVERT: B 144 TYR cc_start: 0.5383 (t80) cc_final: 0.4869 (p90) REVERT: B 152 TRP cc_start: 0.8026 (t60) cc_final: 0.7564 (t60) REVERT: B 153 MET cc_start: 0.7775 (mtm) cc_final: 0.7253 (tpt) REVERT: B 275 PHE cc_start: 0.7245 (m-80) cc_final: 0.6322 (m-10) REVERT: B 318 PHE cc_start: 0.7775 (p90) cc_final: 0.7304 (p90) REVERT: B 378 LYS cc_start: 0.6506 (mmtt) cc_final: 0.6107 (mmmt) REVERT: B 542 ASN cc_start: 0.7668 (m-40) cc_final: 0.6703 (t0) REVERT: B 646 ARG cc_start: 0.7924 (ptm160) cc_final: 0.7103 (tpt170) REVERT: B 661 GLU cc_start: 0.8870 (pp20) cc_final: 0.8357 (pp20) REVERT: B 726 ILE cc_start: 0.7788 (pt) cc_final: 0.7423 (pt) REVERT: B 727 LEU cc_start: 0.8952 (mt) cc_final: 0.8109 (mt) REVERT: B 731 MET cc_start: 0.6955 (ttt) cc_final: 0.6701 (ttt) REVERT: B 773 GLU cc_start: 0.9135 (tp30) cc_final: 0.8723 (tp30) REVERT: B 774 GLN cc_start: 0.8815 (tt0) cc_final: 0.8319 (tp-100) REVERT: B 776 LYS cc_start: 0.9324 (ttpp) cc_final: 0.8644 (tmmt) REVERT: B 780 GLU cc_start: 0.8483 (pt0) cc_final: 0.7786 (pt0) REVERT: B 825 LYS cc_start: 0.8795 (tttt) cc_final: 0.8105 (tptt) REVERT: B 861 LEU cc_start: 0.9618 (tt) cc_final: 0.9345 (tt) REVERT: B 949 GLN cc_start: 0.8430 (tp-100) cc_final: 0.7953 (tp-100) REVERT: B 969 ASN cc_start: 0.8888 (p0) cc_final: 0.8521 (p0) REVERT: B 1028 LYS cc_start: 0.8847 (mttm) cc_final: 0.8582 (mtpp) REVERT: B 1064 HIS cc_start: 0.8294 (m-70) cc_final: 0.7870 (m-70) REVERT: B 1106 GLN cc_start: 0.8486 (pm20) cc_final: 0.8282 (pm20) REVERT: C 58 PHE cc_start: 0.7264 (m-80) cc_final: 0.6809 (m-80) REVERT: C 152 TRP cc_start: 0.6803 (p-90) cc_final: 0.6107 (p-90) REVERT: C 269 TYR cc_start: 0.7961 (m-10) cc_final: 0.7231 (m-80) REVERT: C 314 GLN cc_start: 0.9448 (tm-30) cc_final: 0.9101 (tm-30) REVERT: C 324 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7864 (tm-30) REVERT: C 764 ASN cc_start: 0.8307 (m-40) cc_final: 0.7950 (m-40) REVERT: C 781 VAL cc_start: 0.9771 (t) cc_final: 0.9560 (t) REVERT: C 815 ARG cc_start: 0.8508 (tpm170) cc_final: 0.8015 (tpm170) REVERT: C 895 GLN cc_start: 0.8032 (pm20) cc_final: 0.7397 (pm20) REVERT: C 917 TYR cc_start: 0.7149 (m-10) cc_final: 0.5493 (m-10) REVERT: C 919 ASN cc_start: 0.9453 (t0) cc_final: 0.9237 (t0) REVERT: C 925 ASN cc_start: 0.9286 (t0) cc_final: 0.8924 (t0) REVERT: C 953 ASN cc_start: 0.8508 (m110) cc_final: 0.8263 (m-40) REVERT: C 961 THR cc_start: 0.9326 (p) cc_final: 0.8956 (p) REVERT: C 964 LYS cc_start: 0.9215 (mtmm) cc_final: 0.8745 (mttm) REVERT: C 1004 LEU cc_start: 0.9350 (tp) cc_final: 0.9138 (tp) REVERT: C 1005 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8492 (tm-30) REVERT: C 1006 THR cc_start: 0.9021 (p) cc_final: 0.8414 (p) REVERT: C 1010 GLN cc_start: 0.8746 (pm20) cc_final: 0.8461 (pm20) REVERT: C 1064 HIS cc_start: 0.7764 (m-70) cc_final: 0.7471 (m-70) REVERT: C 1109 PHE cc_start: 0.8635 (t80) cc_final: 0.8389 (t80) REVERT: C 1110 TYR cc_start: 0.9119 (t80) cc_final: 0.8844 (t80) REVERT: C 1111 GLU cc_start: 0.8469 (tp30) cc_final: 0.7870 (tp30) REVERT: C 1113 GLN cc_start: 0.8706 (mp10) cc_final: 0.7647 (mp10) outliers start: 0 outliers final: 0 residues processed: 630 average time/residue: 0.1653 time to fit residues: 165.8030 Evaluate side-chains 536 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 1.9990 chunk 50 optimal weight: 0.0970 chunk 71 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 226 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 141 optimal weight: 0.0470 chunk 128 optimal weight: 7.9990 chunk 290 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN A1064 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 957 GLN C 965 GLN C 978 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.180451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148930 restraints weight = 54257.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153174 restraints weight = 32738.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156081 restraints weight = 22085.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158103 restraints weight = 16228.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.159423 restraints weight = 12759.941| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24661 Z= 0.130 Angle : 0.772 20.199 33721 Z= 0.369 Chirality : 0.049 0.488 4035 Planarity : 0.005 0.081 4250 Dihedral : 8.421 108.786 4401 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.45 % Favored : 90.45 % Rotamer: Outliers : 0.04 % Allowed : 1.15 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.92 (0.14), residues: 3006 helix: 0.09 (0.21), residues: 622 sheet: -1.63 (0.27), residues: 357 loop : -2.88 (0.12), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1014 TYR 0.023 0.001 TYR C 505 PHE 0.031 0.002 PHE B 823 TRP 0.016 0.001 TRP C 64 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00280 (24570) covalent geometry : angle 0.72815 (33483) SS BOND : bond 0.00404 ( 35) SS BOND : angle 1.50151 ( 70) hydrogen bonds : bond 0.04263 ( 696) hydrogen bonds : angle 5.78938 ( 1932) link_ALPHA1-3 : bond 0.01050 ( 1) link_ALPHA1-3 : angle 1.21996 ( 3) link_ALPHA1-6 : bond 0.00465 ( 1) link_ALPHA1-6 : angle 1.47019 ( 3) link_BETA1-4 : bond 0.00583 ( 17) link_BETA1-4 : angle 2.66687 ( 51) link_BETA1-6 : bond 0.01146 ( 1) link_BETA1-6 : angle 1.98094 ( 3) link_NAG-ASN : bond 0.00781 ( 36) link_NAG-ASN : angle 4.09422 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 627 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.9082 (t0) cc_final: 0.8860 (t0) REVERT: A 51 THR cc_start: 0.9190 (p) cc_final: 0.8974 (p) REVERT: A 117 LEU cc_start: 0.8832 (tp) cc_final: 0.8623 (tp) REVERT: A 145 TYR cc_start: 0.7220 (m-80) cc_final: 0.6966 (m-80) REVERT: A 297 SER cc_start: 0.9560 (m) cc_final: 0.9229 (p) REVERT: A 369 TYR cc_start: 0.6109 (t80) cc_final: 0.5209 (m-80) REVERT: A 765 ARG cc_start: 0.8414 (mtp180) cc_final: 0.8124 (ptp-170) REVERT: A 867 ASP cc_start: 0.9043 (p0) cc_final: 0.8582 (p0) REVERT: A 868 GLU cc_start: 0.7983 (pm20) cc_final: 0.6734 (tm-30) REVERT: A 869 MET cc_start: 0.8677 (ptt) cc_final: 0.8387 (ppp) REVERT: A 901 GLN cc_start: 0.8655 (tt0) cc_final: 0.8319 (tt0) REVERT: A 902 MET cc_start: 0.8600 (mmp) cc_final: 0.8326 (mmp) REVERT: A 969 ASN cc_start: 0.9030 (m-40) cc_final: 0.8499 (m-40) REVERT: A 983 ARG cc_start: 0.8909 (ptt90) cc_final: 0.8382 (ptt90) REVERT: A 990 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8608 (tp30) REVERT: B 104 TRP cc_start: 0.6857 (m-90) cc_final: 0.6428 (m-90) REVERT: B 144 TYR cc_start: 0.5286 (t80) cc_final: 0.4791 (p90) REVERT: B 153 MET cc_start: 0.7603 (mtm) cc_final: 0.7174 (tpt) REVERT: B 202 LYS cc_start: 0.8069 (pttt) cc_final: 0.7817 (pttt) REVERT: B 318 PHE cc_start: 0.7547 (p90) cc_final: 0.7129 (p90) REVERT: B 378 LYS cc_start: 0.6455 (mmtt) cc_final: 0.6030 (mmmt) REVERT: B 542 ASN cc_start: 0.7547 (m-40) cc_final: 0.6634 (t0) REVERT: B 563 GLN cc_start: 0.7773 (mt0) cc_final: 0.6896 (mp10) REVERT: B 661 GLU cc_start: 0.8775 (pp20) cc_final: 0.8366 (pp20) REVERT: B 727 LEU cc_start: 0.8896 (mt) cc_final: 0.8052 (mt) REVERT: B 764 ASN cc_start: 0.8813 (m-40) cc_final: 0.8465 (m-40) REVERT: B 773 GLU cc_start: 0.9118 (tp30) cc_final: 0.8750 (tp30) REVERT: B 774 GLN cc_start: 0.8750 (tt0) cc_final: 0.8273 (tp40) REVERT: B 776 LYS cc_start: 0.9298 (ttpp) cc_final: 0.8601 (tmmt) REVERT: B 780 GLU cc_start: 0.8514 (pt0) cc_final: 0.7684 (pt0) REVERT: B 811 LYS cc_start: 0.8572 (mmmm) cc_final: 0.8118 (mmmt) REVERT: B 823 PHE cc_start: 0.7182 (m-80) cc_final: 0.6930 (m-80) REVERT: B 825 LYS cc_start: 0.8641 (tttt) cc_final: 0.7925 (tptt) REVERT: B 861 LEU cc_start: 0.9582 (tt) cc_final: 0.9331 (tt) REVERT: B 949 GLN cc_start: 0.8260 (tp-100) cc_final: 0.7412 (tp-100) REVERT: B 1028 LYS cc_start: 0.8744 (mttm) cc_final: 0.8464 (mtpp) REVERT: B 1106 GLN cc_start: 0.8418 (pm20) cc_final: 0.8176 (pm20) REVERT: B 1110 TYR cc_start: 0.7990 (t80) cc_final: 0.7748 (t80) REVERT: C 58 PHE cc_start: 0.6867 (m-80) cc_final: 0.6608 (m-80) REVERT: C 314 GLN cc_start: 0.9472 (tm-30) cc_final: 0.9141 (tm-30) REVERT: C 453 TYR cc_start: 0.8162 (p90) cc_final: 0.7219 (p90) REVERT: C 761 THR cc_start: 0.8380 (p) cc_final: 0.8164 (p) REVERT: C 764 ASN cc_start: 0.8205 (m-40) cc_final: 0.7936 (m-40) REVERT: C 773 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8171 (mt-10) REVERT: C 776 LYS cc_start: 0.9202 (tmmt) cc_final: 0.8710 (tmmt) REVERT: C 780 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8472 (mt-10) REVERT: C 815 ARG cc_start: 0.8338 (tpm170) cc_final: 0.8001 (tpm170) REVERT: C 909 ILE cc_start: 0.8521 (mm) cc_final: 0.8065 (mm) REVERT: C 917 TYR cc_start: 0.7091 (m-10) cc_final: 0.6060 (m-10) REVERT: C 925 ASN cc_start: 0.9267 (t0) cc_final: 0.9010 (t0) REVERT: C 964 LYS cc_start: 0.9232 (mtmm) cc_final: 0.8658 (mttm) REVERT: C 966 LEU cc_start: 0.9350 (mm) cc_final: 0.9148 (mm) REVERT: C 1000 ARG cc_start: 0.8950 (mtt180) cc_final: 0.8674 (mtt180) REVERT: C 1004 LEU cc_start: 0.9179 (tp) cc_final: 0.8889 (tp) REVERT: C 1005 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8480 (tm-30) REVERT: C 1006 THR cc_start: 0.9057 (p) cc_final: 0.8115 (p) REVERT: C 1010 GLN cc_start: 0.8834 (pm20) cc_final: 0.8617 (pm20) REVERT: C 1064 HIS cc_start: 0.7576 (m-70) cc_final: 0.7187 (m-70) REVERT: C 1109 PHE cc_start: 0.8504 (t80) cc_final: 0.8226 (t80) REVERT: C 1110 TYR cc_start: 0.9033 (t80) cc_final: 0.8813 (t80) REVERT: C 1111 GLU cc_start: 0.8386 (tp30) cc_final: 0.7790 (tp30) REVERT: C 1113 GLN cc_start: 0.8580 (mp10) cc_final: 0.7550 (mp10) outliers start: 1 outliers final: 0 residues processed: 627 average time/residue: 0.1656 time to fit residues: 164.9853 Evaluate side-chains 550 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 550 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 219 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 264 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 210 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 370 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN B 949 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.173200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142613 restraints weight = 55266.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.146636 restraints weight = 33177.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149409 restraints weight = 22359.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.151392 restraints weight = 16467.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152568 restraints weight = 12955.265| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24661 Z= 0.219 Angle : 0.836 19.833 33721 Z= 0.408 Chirality : 0.050 0.455 4035 Planarity : 0.006 0.079 4250 Dihedral : 8.904 106.726 4401 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.34 % Favored : 87.59 % Rotamer: Outliers : 0.04 % Allowed : 0.95 % Favored : 99.01 % 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: -3.07 (0.14), residues: 3006 helix: -0.12 (0.20), residues: 620 sheet: -1.85 (0.26), residues: 375 loop : -2.93 (0.12), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 765 TYR 0.030 0.002 TYR B1007 PHE 0.033 0.002 PHE B 823 TRP 0.031 0.002 TRP C 258 HIS 0.009 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00475 (24570) covalent geometry : angle 0.79364 (33483) SS BOND : bond 0.00446 ( 35) SS BOND : angle 1.68386 ( 70) hydrogen bonds : bond 0.04702 ( 696) hydrogen bonds : angle 6.06888 ( 1932) link_ALPHA1-3 : bond 0.00785 ( 1) link_ALPHA1-3 : angle 1.17464 ( 3) link_ALPHA1-6 : bond 0.00148 ( 1) link_ALPHA1-6 : angle 1.70903 ( 3) link_BETA1-4 : bond 0.00423 ( 17) link_BETA1-4 : angle 2.79437 ( 51) link_BETA1-6 : bond 0.01479 ( 1) link_BETA1-6 : angle 1.58990 ( 3) link_NAG-ASN : bond 0.00722 ( 36) link_NAG-ASN : angle 4.16973 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 613 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.7415 (m-80) cc_final: 0.7021 (m-80) REVERT: A 153 MET cc_start: 0.7229 (tmm) cc_final: 0.7027 (tmm) REVERT: A 170 TYR cc_start: 0.8177 (t80) cc_final: 0.7977 (t80) REVERT: A 200 TYR cc_start: 0.6115 (m-80) cc_final: 0.5471 (m-80) REVERT: A 271 GLN cc_start: 0.8685 (pm20) cc_final: 0.8445 (pm20) REVERT: A 297 SER cc_start: 0.9558 (m) cc_final: 0.9223 (p) REVERT: A 369 TYR cc_start: 0.6106 (t80) cc_final: 0.5178 (m-80) REVERT: A 541 PHE cc_start: 0.6835 (p90) cc_final: 0.5964 (p90) REVERT: A 696 THR cc_start: 0.8205 (m) cc_final: 0.7932 (m) REVERT: A 737 ASP cc_start: 0.8438 (p0) cc_final: 0.8116 (p0) REVERT: A 742 ILE cc_start: 0.9426 (tp) cc_final: 0.9183 (tp) REVERT: A 752 LEU cc_start: 0.8324 (mm) cc_final: 0.7758 (mm) REVERT: A 782 PHE cc_start: 0.8939 (m-80) cc_final: 0.8631 (m-10) REVERT: A 901 GLN cc_start: 0.8808 (tt0) cc_final: 0.8539 (tt0) REVERT: A 969 ASN cc_start: 0.9207 (m-40) cc_final: 0.8755 (m-40) REVERT: A 983 ARG cc_start: 0.8943 (ptt90) cc_final: 0.8392 (ptt90) REVERT: A 990 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8429 (mm-30) REVERT: A 1050 MET cc_start: 0.7805 (ptm) cc_final: 0.7500 (ptt) REVERT: A 1113 GLN cc_start: 0.8694 (mt0) cc_final: 0.8421 (mt0) REVERT: B 104 TRP cc_start: 0.7084 (m-90) cc_final: 0.6581 (m-90) REVERT: B 144 TYR cc_start: 0.5228 (t80) cc_final: 0.4796 (p90) REVERT: B 153 MET cc_start: 0.7808 (mtm) cc_final: 0.7202 (tpt) REVERT: B 189 LEU cc_start: 0.6711 (pp) cc_final: 0.6500 (pp) REVERT: B 318 PHE cc_start: 0.7747 (p90) cc_final: 0.7400 (p90) REVERT: B 378 LYS cc_start: 0.6454 (mmtt) cc_final: 0.6040 (mmmt) REVERT: B 661 GLU cc_start: 0.8858 (pp20) cc_final: 0.8405 (pp20) REVERT: B 731 MET cc_start: 0.6787 (ttt) cc_final: 0.5893 (ttt) REVERT: B 764 ASN cc_start: 0.8881 (m-40) cc_final: 0.8673 (m110) REVERT: B 773 GLU cc_start: 0.9156 (tp30) cc_final: 0.8763 (tp30) REVERT: B 774 GLN cc_start: 0.8767 (tt0) cc_final: 0.8343 (tp40) REVERT: B 776 LYS cc_start: 0.9243 (ttpp) cc_final: 0.8424 (tmmt) REVERT: B 780 GLU cc_start: 0.8541 (pt0) cc_final: 0.7725 (pt0) REVERT: B 825 LYS cc_start: 0.8591 (tttt) cc_final: 0.7939 (tptt) REVERT: B 861 LEU cc_start: 0.9623 (tt) cc_final: 0.9320 (tt) REVERT: B 949 GLN cc_start: 0.8191 (tp40) cc_final: 0.7715 (tp-100) REVERT: B 1030 SER cc_start: 0.9692 (p) cc_final: 0.9472 (p) REVERT: B 1106 GLN cc_start: 0.8375 (pm20) cc_final: 0.8120 (pm20) REVERT: C 58 PHE cc_start: 0.7526 (m-80) cc_final: 0.6837 (m-80) REVERT: C 269 TYR cc_start: 0.7969 (m-10) cc_final: 0.7177 (m-80) REVERT: C 314 GLN cc_start: 0.9478 (tm-30) cc_final: 0.9125 (tm-30) REVERT: C 453 TYR cc_start: 0.8320 (p90) cc_final: 0.7389 (p90) REVERT: C 664 ILE cc_start: 0.8725 (mt) cc_final: 0.8160 (pt) REVERT: C 733 LYS cc_start: 0.9179 (pttm) cc_final: 0.8949 (pttm) REVERT: C 764 ASN cc_start: 0.8318 (m-40) cc_final: 0.8035 (m-40) REVERT: C 925 ASN cc_start: 0.9300 (t0) cc_final: 0.9045 (t0) REVERT: C 964 LYS cc_start: 0.9300 (mtmm) cc_final: 0.8883 (mttm) REVERT: C 1004 LEU cc_start: 0.9249 (tp) cc_final: 0.9025 (tp) REVERT: C 1005 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8531 (tm-30) REVERT: C 1006 THR cc_start: 0.9125 (p) cc_final: 0.8399 (p) REVERT: C 1010 GLN cc_start: 0.8980 (pm20) cc_final: 0.8720 (pm20) REVERT: C 1064 HIS cc_start: 0.8003 (m-70) cc_final: 0.7636 (m-70) REVERT: C 1103 PHE cc_start: 0.8593 (m-10) cc_final: 0.8386 (m-10) REVERT: C 1109 PHE cc_start: 0.8700 (t80) cc_final: 0.8473 (t80) REVERT: C 1110 TYR cc_start: 0.9051 (t80) cc_final: 0.8704 (t80) REVERT: C 1114 ILE cc_start: 0.7436 (mm) cc_final: 0.7212 (mm) outliers start: 1 outliers final: 0 residues processed: 614 average time/residue: 0.1648 time to fit residues: 161.2405 Evaluate side-chains 527 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 187 optimal weight: 1.9990 chunk 299 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 218 optimal weight: 30.0000 chunk 156 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 242 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN A1064 HIS B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN C 66 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.176295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145002 restraints weight = 54739.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.149112 restraints weight = 32988.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151928 restraints weight = 22320.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153944 restraints weight = 16429.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155347 restraints weight = 12970.969| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24661 Z= 0.158 Angle : 0.802 20.034 33721 Z= 0.387 Chirality : 0.050 0.467 4035 Planarity : 0.005 0.083 4250 Dihedral : 8.678 105.584 4401 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.81 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -3.00 (0.14), residues: 3006 helix: -0.04 (0.20), residues: 620 sheet: -1.68 (0.26), residues: 400 loop : -2.92 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 815 TYR 0.027 0.002 TYR B1007 PHE 0.040 0.002 PHE B 823 TRP 0.028 0.002 TRP C 886 HIS 0.009 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00345 (24570) covalent geometry : angle 0.75845 (33483) SS BOND : bond 0.00415 ( 35) SS BOND : angle 1.58767 ( 70) hydrogen bonds : bond 0.04500 ( 696) hydrogen bonds : angle 5.95981 ( 1932) link_ALPHA1-3 : bond 0.00855 ( 1) link_ALPHA1-3 : angle 1.28998 ( 3) link_ALPHA1-6 : bond 0.00405 ( 1) link_ALPHA1-6 : angle 1.49111 ( 3) link_BETA1-4 : bond 0.00508 ( 17) link_BETA1-4 : angle 2.71288 ( 51) link_BETA1-6 : bond 0.01626 ( 1) link_BETA1-6 : angle 1.84254 ( 3) link_NAG-ASN : bond 0.00743 ( 36) link_NAG-ASN : angle 4.13641 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7861 (t70) cc_final: 0.7130 (t-90) REVERT: A 117 LEU cc_start: 0.8908 (tp) cc_final: 0.8707 (tp) REVERT: A 145 TYR cc_start: 0.7505 (m-80) cc_final: 0.7176 (m-80) REVERT: A 153 MET cc_start: 0.7243 (tmm) cc_final: 0.7017 (tmm) REVERT: A 170 TYR cc_start: 0.8198 (t80) cc_final: 0.7978 (t80) REVERT: A 271 GLN cc_start: 0.8645 (pm20) cc_final: 0.8441 (pm20) REVERT: A 297 SER cc_start: 0.9516 (m) cc_final: 0.9117 (p) REVERT: A 369 TYR cc_start: 0.6140 (t80) cc_final: 0.5230 (m-80) REVERT: A 541 PHE cc_start: 0.6804 (p90) cc_final: 0.6067 (p90) REVERT: A 699 LEU cc_start: 0.9072 (mt) cc_final: 0.8805 (pt) REVERT: A 737 ASP cc_start: 0.8306 (p0) cc_final: 0.7890 (p0) REVERT: A 740 MET cc_start: 0.7900 (mtt) cc_final: 0.7582 (mtt) REVERT: A 742 ILE cc_start: 0.9386 (tp) cc_final: 0.9123 (tp) REVERT: A 752 LEU cc_start: 0.8367 (mm) cc_final: 0.7798 (mm) REVERT: A 764 ASN cc_start: 0.9234 (m-40) cc_final: 0.9004 (m-40) REVERT: A 869 MET cc_start: 0.8810 (ptt) cc_final: 0.8468 (ppp) REVERT: A 901 GLN cc_start: 0.8767 (tt0) cc_final: 0.8463 (tt0) REVERT: A 902 MET cc_start: 0.8703 (mmp) cc_final: 0.8302 (mmp) REVERT: A 969 ASN cc_start: 0.9160 (m-40) cc_final: 0.8649 (m-40) REVERT: A 983 ARG cc_start: 0.8973 (ptt90) cc_final: 0.8511 (ptt90) REVERT: A 990 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8255 (mm-30) REVERT: A 1113 GLN cc_start: 0.8704 (mt0) cc_final: 0.8445 (mt0) REVERT: B 104 TRP cc_start: 0.6932 (m-90) cc_final: 0.6424 (m-90) REVERT: B 144 TYR cc_start: 0.5177 (t80) cc_final: 0.4716 (p90) REVERT: B 153 MET cc_start: 0.7830 (mtm) cc_final: 0.7191 (tpt) REVERT: B 318 PHE cc_start: 0.7338 (p90) cc_final: 0.7050 (p90) REVERT: B 378 LYS cc_start: 0.6381 (mmtt) cc_final: 0.5986 (mmmt) REVERT: B 661 GLU cc_start: 0.8833 (pp20) cc_final: 0.8398 (pp20) REVERT: B 726 ILE cc_start: 0.7805 (pt) cc_final: 0.7469 (pt) REVERT: B 727 LEU cc_start: 0.8939 (mt) cc_final: 0.7987 (mt) REVERT: B 764 ASN cc_start: 0.8896 (m-40) cc_final: 0.8694 (m110) REVERT: B 773 GLU cc_start: 0.9173 (tp30) cc_final: 0.8781 (tp30) REVERT: B 776 LYS cc_start: 0.9278 (ttpp) cc_final: 0.8481 (tmmt) REVERT: B 780 GLU cc_start: 0.8596 (pt0) cc_final: 0.7794 (pt0) REVERT: B 811 LYS cc_start: 0.8553 (mmmm) cc_final: 0.8113 (mmmt) REVERT: B 825 LYS cc_start: 0.8423 (tttt) cc_final: 0.7772 (tptt) REVERT: B 861 LEU cc_start: 0.9615 (tt) cc_final: 0.9359 (tt) REVERT: B 949 GLN cc_start: 0.8211 (tp40) cc_final: 0.7793 (tp40) REVERT: B 1028 LYS cc_start: 0.8842 (mttm) cc_final: 0.8600 (mtmm) REVERT: B 1106 GLN cc_start: 0.8381 (pm20) cc_final: 0.8151 (pm20) REVERT: B 1110 TYR cc_start: 0.8086 (t80) cc_final: 0.7842 (t80) REVERT: C 58 PHE cc_start: 0.7404 (m-80) cc_final: 0.6834 (m-80) REVERT: C 314 GLN cc_start: 0.9480 (tm-30) cc_final: 0.8963 (tm-30) REVERT: C 453 TYR cc_start: 0.8340 (p90) cc_final: 0.7457 (p90) REVERT: C 664 ILE cc_start: 0.8740 (mt) cc_final: 0.8191 (pt) REVERT: C 761 THR cc_start: 0.8383 (p) cc_final: 0.8174 (p) REVERT: C 764 ASN cc_start: 0.8352 (m-40) cc_final: 0.8010 (m-40) REVERT: C 821 LEU cc_start: 0.8526 (mt) cc_final: 0.8239 (mt) REVERT: C 865 LEU cc_start: 0.9748 (mt) cc_final: 0.9538 (mt) REVERT: C 895 GLN cc_start: 0.7943 (pm20) cc_final: 0.7356 (pm20) REVERT: C 925 ASN cc_start: 0.9270 (t0) cc_final: 0.8893 (t0) REVERT: C 957 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8723 (tm-30) REVERT: C 964 LYS cc_start: 0.9326 (mtmm) cc_final: 0.8906 (mttm) REVERT: C 1005 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8504 (tm-30) REVERT: C 1006 THR cc_start: 0.9041 (p) cc_final: 0.8404 (p) REVERT: C 1010 GLN cc_start: 0.8964 (pm20) cc_final: 0.8712 (pm20) REVERT: C 1064 HIS cc_start: 0.7720 (m-70) cc_final: 0.7405 (m-70) REVERT: C 1103 PHE cc_start: 0.8595 (m-10) cc_final: 0.8337 (m-10) REVERT: C 1109 PHE cc_start: 0.8675 (t80) cc_final: 0.8436 (t80) REVERT: C 1110 TYR cc_start: 0.9110 (t80) cc_final: 0.8892 (t80) REVERT: C 1111 GLU cc_start: 0.8400 (tp30) cc_final: 0.7761 (tp30) REVERT: C 1113 GLN cc_start: 0.8637 (mp10) cc_final: 0.7526 (mp10) REVERT: C 1114 ILE cc_start: 0.7416 (mm) cc_final: 0.7126 (mm) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.1667 time to fit residues: 164.4072 Evaluate side-chains 524 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 38 optimal weight: 0.0770 chunk 206 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 253 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 901 GLN A 954 GLN A 955 ASN A1023 ASN A1064 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.179104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147476 restraints weight = 53822.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151701 restraints weight = 32467.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.154574 restraints weight = 21962.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.156608 restraints weight = 16213.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.158075 restraints weight = 12759.575| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24661 Z= 0.134 Angle : 0.783 20.229 33721 Z= 0.375 Chirality : 0.049 0.447 4035 Planarity : 0.005 0.079 4250 Dihedral : 8.320 105.927 4401 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.58 % Favored : 89.35 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -2.86 (0.14), residues: 3006 helix: 0.02 (0.20), residues: 624 sheet: -1.50 (0.26), residues: 385 loop : -2.83 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1091 TYR 0.033 0.002 TYR A1007 PHE 0.045 0.002 PHE C 823 TRP 0.027 0.002 TRP C 886 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00291 (24570) covalent geometry : angle 0.74027 (33483) SS BOND : bond 0.00378 ( 35) SS BOND : angle 1.47120 ( 70) hydrogen bonds : bond 0.04318 ( 696) hydrogen bonds : angle 5.82710 ( 1932) link_ALPHA1-3 : bond 0.00860 ( 1) link_ALPHA1-3 : angle 1.37367 ( 3) link_ALPHA1-6 : bond 0.00490 ( 1) link_ALPHA1-6 : angle 1.40872 ( 3) link_BETA1-4 : bond 0.00568 ( 17) link_BETA1-4 : angle 2.58930 ( 51) link_BETA1-6 : bond 0.01243 ( 1) link_BETA1-6 : angle 1.84866 ( 3) link_NAG-ASN : bond 0.00738 ( 36) link_NAG-ASN : angle 4.08754 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4816.13 seconds wall clock time: 84 minutes 29.76 seconds (5069.76 seconds total)