Starting phenix.real_space_refine on Sun Jul 5 00:38:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cn9_30419/07_2026/7cn9_30419.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cn9_30419/07_2026/7cn9_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 { model { file = "/net/cci-nas-00/data/ceres_data/7cn9_30419/07_2026/7cn9_30419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cn9_30419/07_2026/7cn9_30419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cn9_30419/07_2026/7cn9_30419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cn9_30419/07_2026/7cn9_30419.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cn9_30419/07_2026/7cn9_30419.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cn9_30419/07_2026/7cn9_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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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 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 chiralities: 7 Time building chain proxies: 5.58, per 1000 atoms: 0.23 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.81 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: 4.96 Time building geometry restraints manager: 2.76 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 - 17.93: 12400 17.93 - 35.86: 1422 35.86 - 53.78: 240 53.78 - 71.71: 38 71.71 - 89.64: 31 Dihedral angle restraints: 14131 sinusoidal: 5247 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 14128 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: 6.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.430 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 15.512 89.641 8296 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 are 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/Z covalent geometry : bond 0.01067 / 0.56 (24570) covalent geometry : angle 1.18524 / 0.68 (33483) SS BOND : bond 0.05006 / 2.39 ( 35) SS BOND : angle 5.73334 / 3.48 ( 70) hydrogen bonds : bond 0.18950 / 12.38 ( 696) hydrogen bonds : angle 8.90946 / 6.05 ( 1932) link_ALPHA1-3 : bond 0.00239 / 0.13 ( 1) link_ALPHA1-3 : angle 3.87760 / 1.39 ( 3) link_ALPHA1-6 : bond 0.00233 / 0.12 ( 1) link_ALPHA1-6 : angle 1.96316 / 0.95 ( 3) link_BETA1-4 : bond 0.00816 / 0.38 ( 17) link_BETA1-4 : angle 3.99574 / 2.53 ( 51) link_BETA1-6 : bond 0.01104 / 0.58 ( 1) link_BETA1-6 : angle 2.78536 / 1.44 ( 3) link_NAG-ASN : bond 0.04695 / 3.44 ( 36) link_NAG-ASN : angle 9.90640 / 6.98 ( 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 : 0.927 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: 0.3452 (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: 0.8206 (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: 0.8857 (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: 0.7647 (mt0) cc_final: 0.7357 (mt0) REVERT: C 762 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8819 (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: 0.1568 time to fit residues: 161.3734 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 : 0.696 ------------------------------------------------------------------------------- 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... 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** A 957 GLN 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: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.169459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139303 restraints weight = 55545.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143413 restraints weight = 32469.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146211 restraints weight = 21504.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.148148 restraints weight = 15587.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149464 restraints weight = 12203.365| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24661 Z= 0.229 Angle : 0.960 21.609 33721 Z= 0.464 Chirality : 0.054 0.537 4035 Planarity : 0.006 0.074 4250 Dihedral : 6.954 33.281 3241 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.64 % Favored : 86.19 % Rotamer: Outliers : 0.24 % Allowed : 7.95 % Favored : 91.81 % 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 are not related in a simple way. whole: -4.74 (0.12), residues: 3006 helix: -1.92 (0.17), residues: 619 sheet: -2.74 (0.24), residues: 384 loop : -3.93 (0.11), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 457 TYR 0.036 0.002 TYR B 269 PHE 0.040 0.003 PHE B 86 TRP 0.027 0.002 TRP A 886 HIS 0.009 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 (24570) covalent geometry : angle 0.90216 / 0.45 (33483) SS BOND : bond 0.00975 / 0.56 ( 35) SS BOND : angle 1.79951 / 1.16 ( 70) hydrogen bonds : bond 0.05770 / 3.86 ( 696) hydrogen bonds : angle 6.98785 / 4.74 ( 1932) link_ALPHA1-3 : bond 0.00204 / 0.11 ( 1) link_ALPHA1-3 : angle 1.70131 / 0.83 ( 3) link_ALPHA1-6 : bond 0.01102 / 0.58 ( 1) link_ALPHA1-6 : angle 1.87054 / 0.91 ( 3) link_BETA1-4 : bond 0.00708 / 0.38 ( 17) link_BETA1-4 : angle 3.12269 / 2.03 ( 51) link_BETA1-6 : bond 0.01425 / 0.75 ( 1) link_BETA1-6 : angle 2.58704 / 1.39 ( 3) link_NAG-ASN : bond 0.00882 / 0.53 ( 36) link_NAG-ASN : angle 5.33728 / 3.94 ( 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 657 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 651 time to evaluate : 0.884 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: 0.8275 (tp) cc_final: 0.7711 (tp) REVERT: A 49 HIS cc_start: 0.7495 (t70) cc_final: 0.6722 (t-90) REVERT: A 153 MET cc_start: 0.5870 (ptt) cc_final: 0.5308 (tmm) REVERT: A 170 TYR cc_start: 0.8237 (t80) cc_final: 0.8017 (t80) REVERT: A 195 LYS cc_start: 0.8359 (ptmt) cc_final: 0.8071 (ptmt) REVERT: A 297 SER cc_start: 0.9466 (m) cc_final: 0.8961 (p) REVERT: A 369 TYR cc_start: 0.5968 (t80) cc_final: 0.5058 (m-80) REVERT: A 391 CYS cc_start: 0.1656 (OUTLIER) cc_final: 0.1328 (p) REVERT: A 595 VAL cc_start: 0.8905 (t) cc_final: 0.8524 (p) REVERT: A 598 ILE cc_start: 0.8991 (mt) cc_final: 0.8687 (tt) REVERT: A 699 LEU cc_start: 0.9109 (pt) cc_final: 0.8614 (mp) REVERT: A 726 ILE cc_start: 0.9142 (pt) cc_final: 0.8640 (pt) REVERT: A 733 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7818 (mptt) REVERT: A 742 ILE cc_start: 0.9331 (tp) cc_final: 0.9085 (tp) REVERT: A 779 GLN cc_start: 0.9234 (tm-30) cc_final: 0.8899 (tm-30) REVERT: A 790 LYS cc_start: 0.7313 (pttm) cc_final: 0.6655 (mmtm) REVERT: A 868 GLU cc_start: 0.7979 (pm20) cc_final: 0.7130 (tm-30) REVERT: A 920 GLN cc_start: 0.8666 (pt0) cc_final: 0.8192 (tp40) REVERT: A 948 LEU cc_start: 0.9313 (mt) cc_final: 0.8999 (mt) REVERT: A 979 ASP cc_start: 0.9271 (t0) cc_final: 0.9070 (t70) REVERT: A 983 ARG cc_start: 0.8753 (ptt90) cc_final: 0.8095 (ptt90) REVERT: A 1018 ILE cc_start: 0.9585 (tp) cc_final: 0.9296 (tt) REVERT: A 1036 GLN cc_start: 0.8713 (tt0) cc_final: 0.8227 (tt0) REVERT: A 1113 GLN cc_start: 0.8699 (mt0) cc_final: 0.8462 (mt0) REVERT: B 58 PHE cc_start: 0.7887 (m-10) cc_final: 0.7125 (m-10) REVERT: B 153 MET cc_start: 0.7889 (mtm) cc_final: 0.7064 (tpt) REVERT: B 280 ASN cc_start: 0.8069 (t0) cc_final: 0.7694 (t0) REVERT: B 378 LYS cc_start: 0.6220 (mmtt) cc_final: 0.5874 (mmmt) REVERT: B 764 ASN cc_start: 0.8854 (m110) cc_final: 0.8615 (m110) REVERT: B 773 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8503 (tp30) REVERT: B 776 LYS cc_start: 0.9275 (ttpp) cc_final: 0.8566 (tmmt) REVERT: B 780 GLU cc_start: 0.8602 (pt0) cc_final: 0.7762 (pt0) REVERT: B 802 PHE cc_start: 0.7883 (m-80) cc_final: 0.7200 (m-80) REVERT: B 805 ILE cc_start: 0.9492 (mp) cc_final: 0.9193 (mp) REVERT: B 825 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8689 (tptt) REVERT: B 902 MET cc_start: 0.7763 (mmp) cc_final: 0.7087 (mmp) REVERT: B 945 LEU cc_start: 0.8470 (mt) cc_final: 0.8249 (mt) REVERT: B 957 GLN cc_start: 0.9278 (pp30) cc_final: 0.9076 (pp30) REVERT: B 1010 GLN cc_start: 0.9156 (mt0) cc_final: 0.8574 (mt0) REVERT: B 1028 LYS cc_start: 0.9107 (mttm) cc_final: 0.8780 (mtmt) REVERT: B 1036 GLN cc_start: 0.8040 (tt0) cc_final: 0.7613 (mt0) REVERT: B 1038 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8390 (mmtp) REVERT: B 1039 ARG cc_start: 0.8413 (ptm160) cc_final: 0.7606 (ptm160) REVERT: B 1095 PHE cc_start: 0.8798 (m-10) cc_final: 0.7848 (m-10) REVERT: B 1109 PHE cc_start: 0.8967 (t80) cc_final: 0.8649 (t80) REVERT: B 1111 GLU cc_start: 0.8942 (tp30) cc_final: 0.8617 (tp30) REVERT: B 1125 ASN cc_start: 0.7882 (p0) cc_final: 0.7596 (p0) REVERT: C 105 ILE cc_start: 0.8563 (mt) cc_final: 0.8337 (mp) REVERT: C 200 TYR cc_start: 0.7839 (m-10) cc_final: 0.7533 (m-80) REVERT: C 314 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8920 (tm-30) REVERT: C 646 ARG cc_start: 0.8024 (tpt170) cc_final: 0.7685 (tpt170) REVERT: C 741 TYR cc_start: 0.8880 (t80) cc_final: 0.8626 (t80) REVERT: C 755 GLN cc_start: 0.7445 (mt0) cc_final: 0.7195 (mt0) REVERT: C 762 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8638 (tp-100) REVERT: C 764 ASN cc_start: 0.8303 (m-40) cc_final: 0.7878 (m-40) REVERT: C 913 GLN cc_start: 0.8306 (mt0) cc_final: 0.7967 (mt0) REVERT: C 919 ASN cc_start: 0.9329 (t0) cc_final: 0.8862 (t0) REVERT: C 923 ILE cc_start: 0.9377 (mm) cc_final: 0.8699 (mm) REVERT: C 925 ASN cc_start: 0.9434 (t0) cc_final: 0.9152 (t0) REVERT: C 955 ASN cc_start: 0.8256 (m-40) cc_final: 0.7376 (m-40) REVERT: C 1005 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8682 (tm-30) REVERT: C 1009 THR cc_start: 0.9547 (p) cc_final: 0.9312 (p) REVERT: C 1010 GLN cc_start: 0.8995 (pm20) cc_final: 0.8545 (pm20) REVERT: C 1109 PHE cc_start: 0.8858 (t80) cc_final: 0.8536 (t80) REVERT: C 1111 GLU cc_start: 0.8350 (tp30) cc_final: 0.7799 (tp30) REVERT: C 1113 GLN cc_start: 0.8965 (mp10) cc_final: 0.7886 (mp10) outliers start: 6 outliers final: 0 residues processed: 657 average time/residue: 0.1427 time to fit residues: 149.8675 Evaluate side-chains 556 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 555 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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: 10.0000 chunk 298 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.167596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137275 restraints weight = 56827.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.141325 restraints weight = 33336.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144014 restraints weight = 22136.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145895 restraints weight = 16193.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.147158 restraints weight = 12723.642| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24661 Z= 0.273 Angle : 0.958 19.889 33721 Z= 0.466 Chirality : 0.054 0.450 4035 Planarity : 0.006 0.075 4250 Dihedral : 6.837 33.894 3241 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.34 % Favored : 84.50 % Rotamer: Outliers : 0.16 % Allowed : 6.56 % Favored : 93.28 % 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 are not related in a simple way. whole: -4.34 (0.13), residues: 3006 helix: -1.40 (0.18), residues: 618 sheet: -2.57 (0.24), residues: 409 loop : -3.72 (0.11), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1000 TYR 0.052 0.003 TYR B 313 PHE 0.035 0.003 PHE C 823 TRP 0.023 0.002 TRP A 886 HIS 0.009 0.002 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.27 (24570) covalent geometry : angle 0.91068 / 0.46 (33483) SS BOND : bond 0.00635 / 0.42 ( 35) SS BOND : angle 1.68205 / 1.10 ( 70) hydrogen bonds : bond 0.05824 / 3.86 ( 696) hydrogen bonds : angle 6.85812 / 4.64 ( 1932) link_ALPHA1-3 : bond 0.00135 / 0.07 ( 1) link_ALPHA1-3 : angle 2.19456 / 1.10 ( 3) link_ALPHA1-6 : bond 0.00308 / 0.16 ( 1) link_ALPHA1-6 : angle 1.91973 / 0.92 ( 3) link_BETA1-4 : bond 0.00429 / 0.27 ( 17) link_BETA1-4 : angle 3.20218 / 2.04 ( 51) link_BETA1-6 : bond 0.01249 / 0.66 ( 1) link_BETA1-6 : angle 1.53525 / 0.81 ( 3) link_NAG-ASN : bond 0.00760 / 0.47 ( 36) link_NAG-ASN : angle 4.74251 / 3.44 ( 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 639 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 635 time to evaluate : 0.565 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 48 LEU cc_start: 0.8241 (tp) cc_final: 0.7786 (tp) REVERT: A 49 HIS cc_start: 0.7516 (t70) cc_final: 0.6761 (t-90) REVERT: A 117 LEU cc_start: 0.9009 (tp) cc_final: 0.8766 (tp) REVERT: A 145 TYR cc_start: 0.7098 (m-10) cc_final: 0.6816 (m-80) REVERT: A 153 MET cc_start: 0.5664 (ptt) cc_final: 0.5152 (tmm) REVERT: A 170 TYR cc_start: 0.8226 (t80) cc_final: 0.8017 (t80) REVERT: A 195 LYS cc_start: 0.8211 (ptmt) cc_final: 0.7930 (ptmt) REVERT: A 297 SER cc_start: 0.9477 (m) cc_final: 0.8999 (p) REVERT: A 369 TYR cc_start: 0.5967 (t80) cc_final: 0.5068 (m-80) REVERT: A 391 CYS cc_start: 0.1471 (OUTLIER) cc_final: 0.1187 (p) REVERT: A 595 VAL cc_start: 0.8972 (t) cc_final: 0.8639 (p) REVERT: A 598 ILE cc_start: 0.8975 (mt) cc_final: 0.8751 (tt) REVERT: A 726 ILE cc_start: 0.9072 (pt) cc_final: 0.8599 (pt) REVERT: A 733 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8025 (mptt) REVERT: A 779 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8838 (tm-30) REVERT: A 790 LYS cc_start: 0.7337 (pttm) cc_final: 0.6651 (mmtm) REVERT: A 867 ASP cc_start: 0.9205 (p0) cc_final: 0.8861 (p0) REVERT: A 868 GLU cc_start: 0.8025 (pm20) cc_final: 0.7079 (tm-30) REVERT: A 948 LEU cc_start: 0.9349 (mt) cc_final: 0.8983 (mt) REVERT: A 969 ASN cc_start: 0.9287 (m-40) cc_final: 0.8891 (m-40) REVERT: A 981 LEU cc_start: 0.9250 (tp) cc_final: 0.8956 (tt) REVERT: A 983 ARG cc_start: 0.8778 (ptt90) cc_final: 0.8283 (ptt90) REVERT: A 1039 ARG cc_start: 0.8278 (ptp-170) cc_final: 0.7965 (ptp-170) REVERT: A 1113 GLN cc_start: 0.8761 (mt0) cc_final: 0.8473 (mt0) REVERT: B 152 TRP cc_start: 0.7939 (t60) cc_final: 0.7338 (t60) REVERT: B 153 MET cc_start: 0.8005 (mtm) cc_final: 0.7075 (tpt) REVERT: B 378 LYS cc_start: 0.6278 (mmtt) cc_final: 0.5907 (mmmt) REVERT: B 745 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: B 764 ASN cc_start: 0.8846 (m110) cc_final: 0.8632 (m110) REVERT: B 776 LYS cc_start: 0.9293 (ttpp) cc_final: 0.8596 (tmmt) REVERT: B 780 GLU cc_start: 0.8708 (pt0) cc_final: 0.7694 (pt0) REVERT: B 825 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8683 (tptt) REVERT: B 864 LEU cc_start: 0.9403 (tp) cc_final: 0.9168 (tp) REVERT: B 902 MET cc_start: 0.7891 (mmp) cc_final: 0.6947 (mmp) REVERT: B 945 LEU cc_start: 0.8467 (mt) cc_final: 0.8108 (mt) REVERT: B 949 GLN cc_start: 0.8720 (tp40) cc_final: 0.7738 (tp-100) REVERT: B 953 ASN cc_start: 0.9271 (m110) cc_final: 0.9002 (m110) REVERT: B 1010 GLN cc_start: 0.9090 (mt0) cc_final: 0.8574 (mt0) REVERT: B 1028 LYS cc_start: 0.9046 (mttm) cc_final: 0.8780 (mtmt) REVERT: B 1036 GLN cc_start: 0.8218 (tt0) cc_final: 0.7253 (mt0) REVERT: B 1038 LYS cc_start: 0.8779 (mppt) cc_final: 0.8570 (mmtt) REVERT: B 1039 ARG cc_start: 0.8095 (ptm160) cc_final: 0.7587 (ptm160) REVERT: B 1109 PHE cc_start: 0.9456 (t80) cc_final: 0.8546 (t80) REVERT: B 1111 GLU cc_start: 0.8796 (tp30) cc_final: 0.8306 (tp30) REVERT: C 314 GLN cc_start: 0.9230 (tm-30) cc_final: 0.9018 (tm-30) REVERT: C 646 ARG cc_start: 0.8113 (tpt170) cc_final: 0.7734 (tpt170) REVERT: C 741 TYR cc_start: 0.8922 (t80) cc_final: 0.8617 (t80) REVERT: C 755 GLN cc_start: 0.7614 (mt0) cc_final: 0.7263 (mt0) REVERT: C 762 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8700 (tp-100) REVERT: C 764 ASN cc_start: 0.8337 (m-40) cc_final: 0.7896 (m-40) REVERT: C 919 ASN cc_start: 0.9399 (t0) cc_final: 0.9018 (t0) REVERT: C 923 ILE cc_start: 0.9383 (mm) cc_final: 0.8979 (mt) REVERT: C 925 ASN cc_start: 0.9457 (t0) cc_final: 0.9185 (t0) REVERT: C 950 ASP cc_start: 0.8810 (m-30) cc_final: 0.8298 (m-30) REVERT: C 957 GLN cc_start: 0.9264 (tp40) cc_final: 0.9036 (tp40) REVERT: C 961 THR cc_start: 0.9529 (p) cc_final: 0.9067 (p) REVERT: C 964 LYS cc_start: 0.9281 (mttp) cc_final: 0.9062 (mttm) REVERT: C 965 GLN cc_start: 0.9549 (mm-40) cc_final: 0.9312 (mm-40) REVERT: C 1004 LEU cc_start: 0.9434 (tp) cc_final: 0.9160 (tp) REVERT: C 1005 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8684 (tm-30) REVERT: C 1006 THR cc_start: 0.9232 (p) cc_final: 0.8562 (p) REVERT: C 1010 GLN cc_start: 0.9091 (pm20) cc_final: 0.8654 (pm20) REVERT: C 1111 GLU cc_start: 0.8635 (tp30) cc_final: 0.8180 (tp30) REVERT: C 1113 GLN cc_start: 0.8908 (mp10) cc_final: 0.7893 (mp10) outliers start: 4 outliers final: 0 residues processed: 639 average time/residue: 0.1433 time to fit residues: 147.2274 Evaluate side-chains 543 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 541 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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: 8.9990 chunk 22 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1088 HIS B 87 ASN 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 954 GLN B 957 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN C 66 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 978 ASN C 992 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.171071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141385 restraints weight = 55439.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145634 restraints weight = 33352.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148531 restraints weight = 21337.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.150060 restraints weight = 14527.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150367 restraints weight = 12380.036| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24661 Z= 0.192 Angle : 0.861 19.863 33721 Z= 0.417 Chirality : 0.051 0.448 4035 Planarity : 0.005 0.074 4250 Dihedral : 6.511 35.331 3241 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.31 % Favored : 86.59 % Rotamer: Outliers : 0.16 % Allowed : 4.06 % Favored : 95.79 % 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 are not related in a simple way. whole: -3.97 (0.13), residues: 3006 helix: -0.85 (0.19), residues: 618 sheet: -2.43 (0.24), residues: 400 loop : -3.53 (0.12), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1019 TYR 0.030 0.002 TYR B 313 PHE 0.037 0.002 PHE B 559 TRP 0.031 0.002 TRP C 64 HIS 0.023 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (24570) covalent geometry : angle 0.81495 / 0.41 (33483) SS BOND : bond 0.00608 / 0.38 ( 35) SS BOND : angle 1.86155 / 1.21 ( 70) hydrogen bonds : bond 0.05125 / 3.42 ( 696) hydrogen bonds : angle 6.49685 / 4.37 ( 1932) link_ALPHA1-3 : bond 0.00253 / 0.13 ( 1) link_ALPHA1-3 : angle 2.10828 / 1.07 ( 3) link_ALPHA1-6 : bond 0.00522 / 0.27 ( 1) link_ALPHA1-6 : angle 1.66828 / 0.77 ( 3) link_BETA1-4 : bond 0.00402 / 0.25 ( 17) link_BETA1-4 : angle 3.00711 / 1.94 ( 51) link_BETA1-6 : bond 0.01295 / 0.68 ( 1) link_BETA1-6 : angle 1.79394 / 0.98 ( 3) link_NAG-ASN : bond 0.00700 / 0.41 ( 36) link_NAG-ASN : angle 4.30895 / 3.13 ( 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 634 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 630 time to evaluate : 0.943 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: A 48 LEU cc_start: 0.8245 (tp) cc_final: 0.7686 (tp) REVERT: A 49 HIS cc_start: 0.7446 (t70) cc_final: 0.6649 (t70) REVERT: A 153 MET cc_start: 0.5379 (ptt) cc_final: 0.4902 (tmm) REVERT: A 195 LYS cc_start: 0.8067 (ptmt) cc_final: 0.7839 (ptmt) REVERT: A 297 SER cc_start: 0.9474 (m) cc_final: 0.8967 (p) REVERT: A 369 TYR cc_start: 0.6036 (t80) cc_final: 0.5133 (m-80) REVERT: A 598 ILE cc_start: 0.8930 (mt) cc_final: 0.8711 (tt) REVERT: A 726 ILE cc_start: 0.9113 (pt) cc_final: 0.8580 (pt) REVERT: A 779 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8894 (tm-30) REVERT: A 790 LYS cc_start: 0.7282 (pttm) cc_final: 0.6695 (mmtm) REVERT: A 867 ASP cc_start: 0.9204 (p0) cc_final: 0.8873 (p0) REVERT: A 868 GLU cc_start: 0.7998 (pm20) cc_final: 0.7087 (tm-30) REVERT: A 948 LEU cc_start: 0.9340 (mt) cc_final: 0.8997 (mt) REVERT: A 983 ARG cc_start: 0.8817 (ptt90) cc_final: 0.8085 (ptt90) REVERT: A 1111 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8560 (mt-10) REVERT: A 1113 GLN cc_start: 0.8810 (mt0) cc_final: 0.8532 (mt0) REVERT: B 58 PHE cc_start: 0.7975 (m-10) cc_final: 0.7744 (m-80) REVERT: B 152 TRP cc_start: 0.7963 (t60) cc_final: 0.7390 (t60) REVERT: B 153 MET cc_start: 0.7899 (mtm) cc_final: 0.7038 (tpt) REVERT: B 378 LYS cc_start: 0.6254 (mmtt) cc_final: 0.5903 (mmmt) REVERT: B 776 LYS cc_start: 0.9238 (ttpp) cc_final: 0.8592 (tmmt) REVERT: B 780 GLU cc_start: 0.8534 (pt0) cc_final: 0.7635 (pt0) REVERT: B 825 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8675 (tptt) REVERT: B 895 GLN cc_start: 0.7096 (pm20) cc_final: 0.5752 (pp30) REVERT: B 902 MET cc_start: 0.7518 (mmp) cc_final: 0.6892 (mmp) REVERT: B 945 LEU cc_start: 0.8496 (mt) cc_final: 0.8156 (mt) REVERT: B 949 GLN cc_start: 0.8677 (tp40) cc_final: 0.7758 (tp-100) REVERT: B 953 ASN cc_start: 0.9270 (m110) cc_final: 0.9042 (m110) REVERT: B 969 ASN cc_start: 0.9014 (p0) cc_final: 0.8782 (p0) REVERT: B 1010 GLN cc_start: 0.9019 (mt0) cc_final: 0.8765 (mt0) REVERT: B 1028 LYS cc_start: 0.9004 (mttm) cc_final: 0.8766 (mtmt) REVERT: B 1038 LYS cc_start: 0.8830 (mppt) cc_final: 0.8590 (mmtt) REVERT: B 1039 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7467 (ptm160) REVERT: B 1095 PHE cc_start: 0.8726 (m-10) cc_final: 0.7717 (m-10) REVERT: B 1106 GLN cc_start: 0.8479 (pm20) cc_final: 0.8267 (pm20) REVERT: C 314 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8987 (tm-30) REVERT: C 646 ARG cc_start: 0.8128 (tpt170) cc_final: 0.7767 (tpt170) REVERT: C 725 GLU cc_start: 0.8011 (pm20) cc_final: 0.7511 (pm20) REVERT: C 741 TYR cc_start: 0.8852 (t80) cc_final: 0.8486 (t80) REVERT: C 755 GLN cc_start: 0.7568 (mt0) cc_final: 0.7302 (mt0) REVERT: C 764 ASN cc_start: 0.8309 (m-40) cc_final: 0.7903 (m-40) REVERT: C 913 GLN cc_start: 0.8264 (mt0) cc_final: 0.7941 (mt0) REVERT: C 919 ASN cc_start: 0.9423 (t0) cc_final: 0.9039 (t0) REVERT: C 923 ILE cc_start: 0.9375 (mm) cc_final: 0.9007 (mt) REVERT: C 925 ASN cc_start: 0.9418 (t0) cc_final: 0.9078 (t0) REVERT: C 1004 LEU cc_start: 0.9381 (tp) cc_final: 0.9127 (tp) REVERT: C 1005 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8546 (tm-30) REVERT: C 1006 THR cc_start: 0.9111 (p) cc_final: 0.8436 (p) REVERT: C 1010 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8778 (pm20) REVERT: C 1109 PHE cc_start: 0.8757 (t80) cc_final: 0.8522 (t80) REVERT: C 1111 GLU cc_start: 0.8674 (tp30) cc_final: 0.8141 (tp30) REVERT: C 1113 GLN cc_start: 0.8937 (mp10) cc_final: 0.7841 (mp10) outliers start: 4 outliers final: 1 residues processed: 632 average time/residue: 0.1553 time to fit residues: 157.0054 Evaluate side-chains 536 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 534 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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: 3.9990 chunk 123 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 285 optimal weight: 0.3980 chunk 284 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 293 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 301 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 920 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 542 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 66 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C 978 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.175278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143993 restraints weight = 55782.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148036 restraints weight = 33706.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.150814 restraints weight = 22858.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152730 restraints weight = 16920.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154075 restraints weight = 13442.386| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24661 Z= 0.150 Angle : 0.820 20.051 33721 Z= 0.393 Chirality : 0.050 0.432 4035 Planarity : 0.005 0.073 4250 Dihedral : 6.094 36.011 3241 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.54 % Favored : 87.36 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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 are not related in a simple way. whole: -3.58 (0.14), residues: 3006 helix: -0.42 (0.20), residues: 615 sheet: -2.08 (0.26), residues: 376 loop : -3.32 (0.12), residues: 2015 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 0.028 0.002 PHE B 559 TRP 0.021 0.002 TRP B 886 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (24570) covalent geometry : angle 0.77388 / 0.38 (33483) SS BOND : bond 0.00517 / 0.33 ( 35) SS BOND : angle 1.62579 / 1.09 ( 70) hydrogen bonds : bond 0.04676 / 3.11 ( 696) hydrogen bonds : angle 6.18205 / 4.14 ( 1932) link_ALPHA1-3 : bond 0.00578 / 0.30 ( 1) link_ALPHA1-3 : angle 1.96319 / 0.94 ( 3) link_ALPHA1-6 : bond 0.00580 / 0.31 ( 1) link_ALPHA1-6 : angle 1.39931 / 0.70 ( 3) link_BETA1-4 : bond 0.00529 / 0.34 ( 17) link_BETA1-4 : angle 2.82712 / 1.81 ( 51) link_BETA1-6 : bond 0.01382 / 0.73 ( 1) link_BETA1-6 : angle 1.82440 / 1.02 ( 3) link_NAG-ASN : bond 0.00764 / 0.46 ( 36) link_NAG-ASN : angle 4.28593 / 3.04 ( 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 626 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 0.809 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: A 48 LEU cc_start: 0.8179 (tp) cc_final: 0.7870 (tp) REVERT: A 49 HIS cc_start: 0.7151 (t70) cc_final: 0.6681 (t70) REVERT: A 145 TYR cc_start: 0.7217 (m-10) cc_final: 0.6875 (m-80) REVERT: A 153 MET cc_start: 0.5339 (ptt) cc_final: 0.4860 (tmm) REVERT: A 191 GLU cc_start: 0.6745 (mp0) cc_final: 0.6530 (mp0) REVERT: A 195 LYS cc_start: 0.7938 (ptmt) cc_final: 0.7719 (ptmt) REVERT: A 250 THR cc_start: 0.7828 (p) cc_final: 0.7504 (t) REVERT: A 297 SER cc_start: 0.9464 (m) cc_final: 0.9067 (p) REVERT: A 302 THR cc_start: 0.8570 (t) cc_final: 0.8367 (t) REVERT: A 369 TYR cc_start: 0.6011 (t80) cc_final: 0.5128 (m-80) REVERT: A 726 ILE cc_start: 0.9031 (pt) cc_final: 0.8526 (pt) REVERT: A 742 ILE cc_start: 0.9358 (tp) cc_final: 0.9090 (tp) REVERT: A 790 LYS cc_start: 0.7136 (pttm) cc_final: 0.6825 (mmtm) REVERT: A 867 ASP cc_start: 0.9146 (p0) cc_final: 0.8712 (p0) REVERT: A 868 GLU cc_start: 0.8079 (pm20) cc_final: 0.6871 (tm-30) REVERT: A 869 MET cc_start: 0.8798 (ptt) cc_final: 0.8529 (ppp) REVERT: A 902 MET cc_start: 0.8619 (mmp) cc_final: 0.8258 (mmp) REVERT: A 948 LEU cc_start: 0.9192 (mt) cc_final: 0.8849 (mt) REVERT: A 969 ASN cc_start: 0.9185 (m-40) cc_final: 0.8709 (m-40) REVERT: A 983 ARG cc_start: 0.8789 (ptt90) cc_final: 0.8259 (ptt90) REVERT: A 1113 GLN cc_start: 0.8611 (mt0) cc_final: 0.8389 (mt0) REVERT: B 152 TRP cc_start: 0.7927 (t60) cc_final: 0.7484 (t60) REVERT: B 153 MET cc_start: 0.7810 (mtm) cc_final: 0.7120 (tpt) REVERT: B 378 LYS cc_start: 0.6452 (mmtt) cc_final: 0.6041 (mmmt) REVERT: B 542 ASN cc_start: 0.7741 (m-40) cc_final: 0.6705 (t0) REVERT: B 727 LEU cc_start: 0.9326 (mt) cc_final: 0.8581 (mt) REVERT: B 731 MET cc_start: 0.7258 (ttt) cc_final: 0.6704 (ttt) REVERT: B 764 ASN cc_start: 0.8737 (m110) cc_final: 0.8429 (m110) REVERT: B 773 GLU cc_start: 0.9015 (tp30) cc_final: 0.8619 (tp30) REVERT: B 774 GLN cc_start: 0.8724 (tt0) cc_final: 0.8099 (tp-100) REVERT: B 776 LYS cc_start: 0.9243 (ttpp) cc_final: 0.8546 (tmmt) REVERT: B 780 GLU cc_start: 0.8440 (pt0) cc_final: 0.7698 (pt0) REVERT: B 802 PHE cc_start: 0.7526 (m-80) cc_final: 0.7112 (m-80) REVERT: B 805 ILE cc_start: 0.9403 (mp) cc_final: 0.9193 (mp) REVERT: B 825 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8542 (tptt) REVERT: B 861 LEU cc_start: 0.9604 (tt) cc_final: 0.9369 (tt) REVERT: B 902 MET cc_start: 0.7475 (mmp) cc_final: 0.6997 (mmp) REVERT: B 949 GLN cc_start: 0.8453 (tp40) cc_final: 0.7466 (tp-100) REVERT: B 969 ASN cc_start: 0.8941 (p0) cc_final: 0.8719 (p0) REVERT: B 1038 LYS cc_start: 0.8880 (mppt) cc_final: 0.8666 (mmtt) REVERT: B 1039 ARG cc_start: 0.8114 (ptm160) cc_final: 0.7625 (ptm160) REVERT: B 1052 PHE cc_start: 0.8153 (m-10) cc_final: 0.7844 (m-10) REVERT: B 1095 PHE cc_start: 0.8316 (m-10) cc_final: 0.7392 (m-10) REVERT: B 1109 PHE cc_start: 0.9196 (t80) cc_final: 0.8190 (t80) REVERT: C 152 TRP cc_start: 0.7014 (p-90) cc_final: 0.6264 (p-90) REVERT: C 153 MET cc_start: 0.6732 (ttm) cc_final: 0.6482 (ttm) REVERT: C 314 GLN cc_start: 0.9417 (tm-30) cc_final: 0.9085 (tm-30) REVERT: C 646 ARG cc_start: 0.7896 (tpt170) cc_final: 0.7655 (tpt170) REVERT: C 741 TYR cc_start: 0.8820 (t80) cc_final: 0.8357 (t80) REVERT: C 755 GLN cc_start: 0.7369 (mt0) cc_final: 0.7118 (mt0) REVERT: C 764 ASN cc_start: 0.8188 (m-40) cc_final: 0.7848 (m-40) REVERT: C 770 ILE cc_start: 0.8605 (pt) cc_final: 0.8210 (pt) REVERT: C 815 ARG cc_start: 0.8256 (tpm170) cc_final: 0.7931 (tpm170) REVERT: C 873 TYR cc_start: 0.8353 (m-10) cc_final: 0.7959 (m-80) REVERT: C 917 TYR cc_start: 0.7062 (m-10) cc_final: 0.5862 (m-10) REVERT: C 919 ASN cc_start: 0.9399 (t0) cc_final: 0.9157 (t0) REVERT: C 925 ASN cc_start: 0.9318 (t0) cc_final: 0.8976 (t0) REVERT: C 961 THR cc_start: 0.9353 (p) cc_final: 0.8890 (p) REVERT: C 964 LYS cc_start: 0.9258 (mttp) cc_final: 0.9033 (mttm) REVERT: C 1004 LEU cc_start: 0.9227 (tp) cc_final: 0.8936 (tp) REVERT: C 1005 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8492 (tm-30) REVERT: C 1006 THR cc_start: 0.8975 (p) cc_final: 0.8302 (p) REVERT: C 1010 GLN cc_start: 0.8806 (pm20) cc_final: 0.8548 (pm20) REVERT: C 1064 HIS cc_start: 0.7866 (m-70) cc_final: 0.7432 (m-70) REVERT: C 1109 PHE cc_start: 0.8611 (t80) cc_final: 0.8392 (t80) REVERT: C 1110 TYR cc_start: 0.9085 (t80) cc_final: 0.8836 (t80) REVERT: C 1111 GLU cc_start: 0.8499 (tp30) cc_final: 0.7897 (tp30) REVERT: C 1113 GLN cc_start: 0.8639 (mp10) cc_final: 0.7655 (mp10) outliers start: 0 outliers final: 0 residues processed: 626 average time/residue: 0.1497 time to fit residues: 149.9036 Evaluate side-chains 542 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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: 8.9990 chunk 192 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 264 optimal weight: 0.8980 chunk 260 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1064 HIS B 87 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 978 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.174733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143600 restraints weight = 55759.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147684 restraints weight = 33699.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150557 restraints weight = 22806.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152558 restraints weight = 16755.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.153871 restraints weight = 13208.619| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24661 Z= 0.163 Angle : 0.817 19.869 33721 Z= 0.393 Chirality : 0.051 0.667 4035 Planarity : 0.005 0.071 4250 Dihedral : 5.951 36.150 3241 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.54 % Favored : 87.36 % Rotamer: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % 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 are not related in a simple way. whole: -3.39 (0.14), residues: 3006 helix: -0.24 (0.20), residues: 618 sheet: -2.04 (0.26), residues: 375 loop : -3.19 (0.12), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1039 TYR 0.026 0.002 TYR B1007 PHE 0.036 0.002 PHE C 823 TRP 0.022 0.002 TRP C 64 HIS 0.013 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (24570) covalent geometry : angle 0.77009 / 0.38 (33483) SS BOND : bond 0.00430 / 0.27 ( 35) SS BOND : angle 1.81746 / 1.19 ( 70) hydrogen bonds : bond 0.04625 / 3.08 ( 696) hydrogen bonds : angle 6.13041 / 4.11 ( 1932) link_ALPHA1-3 : bond 0.00174 / 0.09 ( 1) link_ALPHA1-3 : angle 1.96729 / 1.00 ( 3) link_ALPHA1-6 : bond 0.00467 / 0.25 ( 1) link_ALPHA1-6 : angle 1.51571 / 0.74 ( 3) link_BETA1-4 : bond 0.00469 / 0.31 ( 17) link_BETA1-4 : angle 2.76470 / 1.77 ( 51) link_BETA1-6 : bond 0.01009 / 0.53 ( 1) link_BETA1-6 : angle 1.42662 / 0.74 ( 3) link_NAG-ASN : bond 0.00785 / 0.52 ( 36) link_NAG-ASN : angle 4.32865 / 3.10 ( 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 623 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 622 time to evaluate : 0.737 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: A 34 ARG cc_start: 0.8049 (mmp80) cc_final: 0.7686 (mmp80) REVERT: A 48 LEU cc_start: 0.8210 (tp) cc_final: 0.7811 (tp) REVERT: A 49 HIS cc_start: 0.7356 (t70) cc_final: 0.6650 (t70) REVERT: A 153 MET cc_start: 0.5290 (ptt) cc_final: 0.4837 (tmm) REVERT: A 250 THR cc_start: 0.7792 (p) cc_final: 0.7526 (t) REVERT: A 297 SER cc_start: 0.9444 (m) cc_final: 0.8975 (p) REVERT: A 369 TYR cc_start: 0.6082 (t80) cc_final: 0.5156 (m-80) REVERT: A 391 CYS cc_start: 0.2127 (OUTLIER) cc_final: 0.1876 (p) REVERT: A 726 ILE cc_start: 0.9110 (pt) cc_final: 0.8615 (pt) REVERT: A 867 ASP cc_start: 0.9156 (p0) cc_final: 0.8734 (p0) REVERT: A 868 GLU cc_start: 0.8055 (pm20) cc_final: 0.6818 (tm-30) REVERT: A 869 MET cc_start: 0.8866 (ptt) cc_final: 0.8492 (ppp) REVERT: A 901 GLN cc_start: 0.8796 (tt0) cc_final: 0.8575 (tt0) REVERT: A 902 MET cc_start: 0.8599 (mmp) cc_final: 0.8359 (mmp) REVERT: A 948 LEU cc_start: 0.9266 (mt) cc_final: 0.8929 (mt) REVERT: A 969 ASN cc_start: 0.9146 (m-40) cc_final: 0.8677 (m-40) REVERT: A 983 ARG cc_start: 0.8836 (ptt90) cc_final: 0.8415 (ptt90) REVERT: A 1039 ARG cc_start: 0.7974 (ptm-80) cc_final: 0.7726 (ptm-80) REVERT: A 1050 MET cc_start: 0.7919 (ptm) cc_final: 0.7501 (ptm) REVERT: A 1113 GLN cc_start: 0.8682 (mt0) cc_final: 0.8466 (mt0) REVERT: B 152 TRP cc_start: 0.7893 (t60) cc_final: 0.7690 (t60) REVERT: B 153 MET cc_start: 0.7817 (mtm) cc_final: 0.7147 (tpt) REVERT: B 210 ILE cc_start: 0.8442 (tt) cc_final: 0.8136 (mp) REVERT: B 318 PHE cc_start: 0.7836 (p90) cc_final: 0.7413 (p90) REVERT: B 378 LYS cc_start: 0.6493 (mmtt) cc_final: 0.6081 (mmmt) REVERT: B 542 ASN cc_start: 0.7718 (m-40) cc_final: 0.6756 (t0) REVERT: B 646 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7138 (tpp80) REVERT: B 727 LEU cc_start: 0.9269 (mt) cc_final: 0.8955 (mt) REVERT: B 731 MET cc_start: 0.7190 (ttt) cc_final: 0.6672 (ttt) REVERT: B 764 ASN cc_start: 0.8791 (m110) cc_final: 0.8541 (m110) REVERT: B 773 GLU cc_start: 0.9141 (tp30) cc_final: 0.8720 (tp30) REVERT: B 774 GLN cc_start: 0.8736 (tt0) cc_final: 0.8159 (tp-100) REVERT: B 776 LYS cc_start: 0.9255 (ttpp) cc_final: 0.8592 (tmmt) REVERT: B 780 GLU cc_start: 0.8544 (pt0) cc_final: 0.7796 (pt0) REVERT: B 802 PHE cc_start: 0.7828 (m-80) cc_final: 0.7436 (m-80) REVERT: B 825 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8645 (tptt) REVERT: B 861 LEU cc_start: 0.9637 (tt) cc_final: 0.9405 (tt) REVERT: B 902 MET cc_start: 0.7653 (mmp) cc_final: 0.7254 (mmp) REVERT: B 905 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.7999 (mmm-85) REVERT: B 945 LEU cc_start: 0.8435 (mt) cc_final: 0.8212 (mt) REVERT: B 949 GLN cc_start: 0.8462 (tp40) cc_final: 0.7879 (tp-100) REVERT: B 969 ASN cc_start: 0.8987 (p0) cc_final: 0.8759 (p0) REVERT: B 1039 ARG cc_start: 0.8250 (ptm160) cc_final: 0.7694 (ptm160) REVERT: B 1106 GLN cc_start: 0.8457 (pm20) cc_final: 0.8240 (pm20) REVERT: C 58 PHE cc_start: 0.6997 (m-80) cc_final: 0.6341 (m-80) REVERT: C 152 TRP cc_start: 0.7071 (p-90) cc_final: 0.6301 (p-90) REVERT: C 153 MET cc_start: 0.6572 (ttm) cc_final: 0.6323 (ttm) REVERT: C 307 THR cc_start: 0.7852 (t) cc_final: 0.7572 (t) REVERT: C 314 GLN cc_start: 0.9422 (tm-30) cc_final: 0.9089 (tm-30) REVERT: C 733 LYS cc_start: 0.9100 (pttm) cc_final: 0.8730 (pttm) REVERT: C 755 GLN cc_start: 0.7384 (mt0) cc_final: 0.7114 (mt0) REVERT: C 764 ASN cc_start: 0.8245 (m-40) cc_final: 0.7926 (m-40) REVERT: C 774 GLN cc_start: 0.8214 (tt0) cc_final: 0.7856 (tt0) REVERT: C 815 ARG cc_start: 0.8427 (tpm170) cc_final: 0.7994 (tpm170) REVERT: C 917 TYR cc_start: 0.7146 (m-10) cc_final: 0.5574 (m-10) REVERT: C 919 ASN cc_start: 0.9438 (t0) cc_final: 0.9190 (t0) REVERT: C 925 ASN cc_start: 0.9349 (t0) cc_final: 0.9010 (t0) REVERT: C 953 ASN cc_start: 0.8477 (m110) cc_final: 0.8263 (m-40) REVERT: C 961 THR cc_start: 0.9465 (p) cc_final: 0.8902 (p) REVERT: C 964 LYS cc_start: 0.9292 (mttp) cc_final: 0.9051 (mttm) REVERT: C 1000 ARG cc_start: 0.8995 (mtt180) cc_final: 0.8651 (mtt180) REVERT: C 1004 LEU cc_start: 0.9242 (tp) cc_final: 0.9003 (tp) REVERT: C 1005 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8512 (tm-30) REVERT: C 1006 THR cc_start: 0.9092 (p) cc_final: 0.8186 (p) REVERT: C 1010 GLN cc_start: 0.8864 (pm20) cc_final: 0.8536 (pm20) REVERT: C 1103 PHE cc_start: 0.8649 (m-10) cc_final: 0.8363 (m-10) REVERT: C 1109 PHE cc_start: 0.8693 (t80) cc_final: 0.8478 (t80) REVERT: C 1110 TYR cc_start: 0.9141 (t80) cc_final: 0.8885 (t80) REVERT: C 1111 GLU cc_start: 0.8510 (tp30) cc_final: 0.7889 (tp30) REVERT: C 1113 GLN cc_start: 0.8727 (mp10) cc_final: 0.7684 (mp10) REVERT: C 1114 ILE cc_start: 0.7473 (mm) cc_final: 0.7238 (mm) outliers start: 1 outliers final: 0 residues processed: 623 average time/residue: 0.1481 time to fit residues: 147.3370 Evaluate side-chains 533 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 532 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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: 9.9990 chunk 267 optimal weight: 0.9980 chunk 73 optimal weight: 0.0980 chunk 227 optimal weight: 0.8980 chunk 141 optimal weight: 0.0870 chunk 296 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 30.0000 chunk 119 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** 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 ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 66 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 901 GLN C 955 ASN C 978 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.179311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148273 restraints weight = 53854.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.152246 restraints weight = 33227.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155087 restraints weight = 22696.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.157070 restraints weight = 16816.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158445 restraints weight = 13313.047| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4398 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= 0.135 Angle : 0.792 20.002 33721 Z= 0.379 Chirality : 0.050 0.508 4035 Planarity : 0.005 0.071 4250 Dihedral : 5.639 36.522 3241 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.78 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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 are not related in a simple way. whole: -3.14 (0.14), residues: 3006 helix: 0.05 (0.20), residues: 618 sheet: -1.83 (0.26), residues: 369 loop : -3.06 (0.12), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.025 0.002 TYR A1007 PHE 0.027 0.002 PHE C 823 TRP 0.017 0.001 TRP C 64 HIS 0.013 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (24570) covalent geometry : angle 0.74964 / 0.37 (33483) SS BOND : bond 0.00511 / 0.34 ( 35) SS BOND : angle 1.67041 / 1.08 ( 70) hydrogen bonds : bond 0.04386 / 2.93 ( 696) hydrogen bonds : angle 5.91728 / 3.97 ( 1932) link_ALPHA1-3 : bond 0.00118 / 0.06 ( 1) link_ALPHA1-3 : angle 1.74811 / 0.89 ( 3) link_ALPHA1-6 : bond 0.00702 / 0.37 ( 1) link_ALPHA1-6 : angle 1.37107 / 0.72 ( 3) link_BETA1-4 : bond 0.00602 / 0.40 ( 17) link_BETA1-4 : angle 2.60232 / 1.65 ( 51) link_BETA1-6 : bond 0.00926 / 0.49 ( 1) link_BETA1-6 : angle 1.63200 / 0.91 ( 3) link_NAG-ASN : bond 0.00800 / 0.51 ( 36) link_NAG-ASN : angle 4.05123 / 2.89 ( 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 : 1.018 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 153 MET cc_start: 0.5202 (ptt) cc_final: 0.4861 (tmm) REVERT: A 250 THR cc_start: 0.7718 (p) cc_final: 0.7481 (t) REVERT: A 297 SER cc_start: 0.9454 (m) cc_final: 0.8964 (p) REVERT: A 369 TYR cc_start: 0.6026 (t80) cc_final: 0.5187 (m-80) REVERT: A 764 ASN cc_start: 0.9042 (m-40) cc_final: 0.8833 (m-40) REVERT: A 867 ASP cc_start: 0.9122 (p0) cc_final: 0.8692 (p0) REVERT: A 868 GLU cc_start: 0.7986 (pm20) cc_final: 0.6728 (tm-30) REVERT: A 869 MET cc_start: 0.8713 (ptt) cc_final: 0.8448 (ppp) REVERT: A 901 GLN cc_start: 0.8702 (tt0) cc_final: 0.8380 (tt0) REVERT: A 902 MET cc_start: 0.8529 (mmp) cc_final: 0.7707 (mmt) REVERT: A 923 ILE cc_start: 0.9184 (mt) cc_final: 0.8843 (mt) REVERT: A 926 GLN cc_start: 0.9047 (mt0) cc_final: 0.8547 (mp10) REVERT: A 969 ASN cc_start: 0.9050 (m-40) cc_final: 0.8524 (m-40) REVERT: A 983 ARG cc_start: 0.8948 (ptt90) cc_final: 0.8255 (ptt90) REVERT: A 1039 ARG cc_start: 0.7757 (ptm-80) cc_final: 0.7415 (ptm-80) REVERT: A 1113 GLN cc_start: 0.8726 (mt0) cc_final: 0.8480 (mt0) REVERT: B 104 TRP cc_start: 0.6924 (m-90) cc_final: 0.6522 (m-90) REVERT: B 153 MET cc_start: 0.7713 (mtm) cc_final: 0.7200 (tpt) REVERT: B 202 LYS cc_start: 0.8078 (pttt) cc_final: 0.7851 (pttp) REVERT: B 318 PHE cc_start: 0.7630 (p90) cc_final: 0.7188 (p90) REVERT: B 378 LYS cc_start: 0.6443 (mmtt) cc_final: 0.6055 (mmmt) REVERT: B 542 ASN cc_start: 0.7623 (m-40) cc_final: 0.6626 (t0) REVERT: B 726 ILE cc_start: 0.8185 (pt) cc_final: 0.7950 (pt) REVERT: B 727 LEU cc_start: 0.9261 (mt) cc_final: 0.8895 (mt) REVERT: B 731 MET cc_start: 0.7251 (ttt) cc_final: 0.6781 (ttt) REVERT: B 773 GLU cc_start: 0.9157 (tp30) cc_final: 0.8707 (tp30) REVERT: B 774 GLN cc_start: 0.8661 (tt0) cc_final: 0.8252 (tp-100) REVERT: B 776 LYS cc_start: 0.9327 (ttpp) cc_final: 0.8620 (tmmt) REVERT: B 780 GLU cc_start: 0.8429 (pt0) cc_final: 0.7663 (pt0) REVERT: B 802 PHE cc_start: 0.7829 (m-80) cc_final: 0.7110 (m-80) REVERT: B 825 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8681 (tttt) REVERT: B 861 LEU cc_start: 0.9626 (tt) cc_final: 0.9348 (tt) REVERT: B 949 GLN cc_start: 0.8333 (tp40) cc_final: 0.7731 (tp40) REVERT: B 969 ASN cc_start: 0.8854 (p0) cc_final: 0.8588 (p0) REVERT: B 1038 LYS cc_start: 0.8753 (mptt) cc_final: 0.8539 (mmtt) REVERT: C 58 PHE cc_start: 0.6680 (m-80) cc_final: 0.6173 (m-80) REVERT: C 152 TRP cc_start: 0.7169 (p-90) cc_final: 0.6421 (p-90) REVERT: C 153 MET cc_start: 0.6738 (ttm) cc_final: 0.6479 (ttm) REVERT: C 269 TYR cc_start: 0.7963 (m-10) cc_final: 0.7267 (m-10) REVERT: C 307 THR cc_start: 0.7797 (t) cc_final: 0.7485 (t) REVERT: C 314 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9094 (tm-30) REVERT: C 755 GLN cc_start: 0.7310 (mt0) cc_final: 0.7044 (mt0) REVERT: C 764 ASN cc_start: 0.8260 (m-40) cc_final: 0.7847 (m-40) REVERT: C 781 VAL cc_start: 0.9744 (t) cc_final: 0.9404 (t) REVERT: C 815 ARG cc_start: 0.8309 (tpm170) cc_final: 0.8005 (tpm170) REVERT: C 873 TYR cc_start: 0.8423 (m-10) cc_final: 0.7981 (m-80) REVERT: C 895 GLN cc_start: 0.8010 (pm20) cc_final: 0.7258 (pm20) REVERT: C 909 ILE cc_start: 0.8524 (mm) cc_final: 0.8047 (mm) REVERT: C 917 TYR cc_start: 0.7073 (m-10) cc_final: 0.5380 (m-10) REVERT: C 925 ASN cc_start: 0.9276 (t0) cc_final: 0.8888 (t0) REVERT: C 953 ASN cc_start: 0.8671 (m110) cc_final: 0.8399 (m-40) REVERT: C 961 THR cc_start: 0.9445 (p) cc_final: 0.8785 (p) REVERT: C 964 LYS cc_start: 0.9305 (mttp) cc_final: 0.9019 (mttm) REVERT: C 1000 ARG cc_start: 0.8944 (mtt180) cc_final: 0.8506 (mtt180) REVERT: C 1005 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8437 (tm-30) REVERT: C 1006 THR cc_start: 0.8913 (p) cc_final: 0.8350 (p) REVERT: C 1010 GLN cc_start: 0.8699 (pm20) cc_final: 0.8354 (pm20) REVERT: C 1064 HIS cc_start: 0.7573 (m-70) cc_final: 0.7256 (m-70) REVERT: C 1109 PHE cc_start: 0.8613 (t80) cc_final: 0.8342 (t80) REVERT: C 1110 TYR cc_start: 0.9062 (t80) cc_final: 0.8859 (t80) REVERT: C 1111 GLU cc_start: 0.8436 (tp30) cc_final: 0.7809 (tp30) REVERT: C 1113 GLN cc_start: 0.8673 (mp10) cc_final: 0.7599 (mp10) outliers start: 0 outliers final: 0 residues processed: 630 average time/residue: 0.1528 time to fit residues: 155.2265 Evaluate side-chains 549 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 549 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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: 0.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 226 optimal weight: 0.0570 chunk 250 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 128 optimal weight: 0.5980 chunk 290 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 978 ASN C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.179332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147293 restraints weight = 55746.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151486 restraints weight = 34022.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154350 restraints weight = 23174.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156302 restraints weight = 17169.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157749 restraints weight = 13660.842| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4611 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= 0.137 Angle : 0.780 19.882 33721 Z= 0.374 Chirality : 0.049 0.475 4035 Planarity : 0.005 0.077 4250 Dihedral : 5.562 36.346 3241 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.55 % Favored : 89.35 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % 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 are not related in a simple way. whole: -2.98 (0.14), residues: 3006 helix: 0.11 (0.21), residues: 620 sheet: -1.71 (0.27), residues: 359 loop : -2.93 (0.12), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 905 TYR 0.025 0.002 TYR B1007 PHE 0.028 0.002 PHE B 823 TRP 0.032 0.002 TRP B 152 HIS 0.011 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (24570) covalent geometry : angle 0.73943 / 0.36 (33483) SS BOND : bond 0.00500 / 0.33 ( 35) SS BOND : angle 1.62453 / 1.05 ( 70) hydrogen bonds : bond 0.04312 / 2.92 ( 696) hydrogen bonds : angle 5.82935 / 3.92 ( 1932) link_ALPHA1-3 : bond 0.00425 / 0.22 ( 1) link_ALPHA1-3 : angle 1.72684 / 0.83 ( 3) link_ALPHA1-6 : bond 0.00528 / 0.28 ( 1) link_ALPHA1-6 : angle 1.40600 / 0.72 ( 3) link_BETA1-4 : bond 0.00513 / 0.32 ( 17) link_BETA1-4 : angle 2.54654 / 1.62 ( 51) link_BETA1-6 : bond 0.00870 / 0.46 ( 1) link_BETA1-6 : angle 1.42792 / 0.79 ( 3) link_NAG-ASN : bond 0.00739 / 0.46 ( 36) link_NAG-ASN : angle 3.95770 / 2.81 ( 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: 0 poor density : 628 time to evaluate : 0.919 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 117 LEU cc_start: 0.8671 (tp) cc_final: 0.8405 (tp) REVERT: A 145 TYR cc_start: 0.7316 (m-80) cc_final: 0.7013 (m-80) REVERT: A 153 MET cc_start: 0.5028 (ptt) cc_final: 0.4822 (tmm) REVERT: A 250 THR cc_start: 0.7765 (p) cc_final: 0.7553 (t) REVERT: A 297 SER cc_start: 0.9544 (m) cc_final: 0.9069 (p) REVERT: A 369 TYR cc_start: 0.6166 (t80) cc_final: 0.5285 (m-80) REVERT: A 733 LYS cc_start: 0.8365 (mppt) cc_final: 0.7748 (mptt) REVERT: A 737 ASP cc_start: 0.8311 (p0) cc_final: 0.7894 (p0) REVERT: A 764 ASN cc_start: 0.9025 (m-40) cc_final: 0.8777 (m-40) REVERT: A 867 ASP cc_start: 0.9119 (p0) cc_final: 0.8658 (p0) REVERT: A 868 GLU cc_start: 0.8032 (pm20) cc_final: 0.6766 (tm-30) REVERT: A 869 MET cc_start: 0.8760 (ptt) cc_final: 0.8409 (ppp) REVERT: A 901 GLN cc_start: 0.8664 (tt0) cc_final: 0.8366 (tt0) REVERT: A 902 MET cc_start: 0.8530 (mmp) cc_final: 0.7726 (mmt) REVERT: A 969 ASN cc_start: 0.8997 (m-40) cc_final: 0.8497 (m-40) REVERT: A 983 ARG cc_start: 0.8962 (ptt90) cc_final: 0.8517 (ptt90) REVERT: A 1113 GLN cc_start: 0.8705 (mt0) cc_final: 0.8497 (mt0) REVERT: B 104 TRP cc_start: 0.6808 (m-90) cc_final: 0.6375 (m-90) REVERT: B 153 MET cc_start: 0.7658 (mtm) cc_final: 0.7021 (tpt) REVERT: B 318 PHE cc_start: 0.7717 (p90) cc_final: 0.7246 (p90) REVERT: B 378 LYS cc_start: 0.6480 (mmtt) cc_final: 0.6092 (mmmt) REVERT: B 542 ASN cc_start: 0.7625 (m-40) cc_final: 0.6677 (t0) REVERT: B 563 GLN cc_start: 0.7779 (mt0) cc_final: 0.6799 (mp10) REVERT: B 726 ILE cc_start: 0.8190 (pt) cc_final: 0.7979 (pt) REVERT: B 727 LEU cc_start: 0.9281 (mt) cc_final: 0.8913 (mt) REVERT: B 731 MET cc_start: 0.7234 (ttt) cc_final: 0.6999 (ttt) REVERT: B 764 ASN cc_start: 0.8788 (m110) cc_final: 0.8546 (m110) REVERT: B 773 GLU cc_start: 0.9234 (tp30) cc_final: 0.8753 (tp30) REVERT: B 774 GLN cc_start: 0.8657 (tt0) cc_final: 0.8313 (tp-100) REVERT: B 776 LYS cc_start: 0.9311 (ttpp) cc_final: 0.8643 (tmmt) REVERT: B 780 GLU cc_start: 0.8546 (pt0) cc_final: 0.7799 (pt0) REVERT: B 802 PHE cc_start: 0.7903 (m-80) cc_final: 0.7126 (m-80) REVERT: B 861 LEU cc_start: 0.9610 (tt) cc_final: 0.9351 (tt) REVERT: B 904 TYR cc_start: 0.8236 (t80) cc_final: 0.8030 (t80) REVERT: B 949 GLN cc_start: 0.8314 (tp40) cc_final: 0.7712 (tp40) REVERT: B 969 ASN cc_start: 0.8898 (p0) cc_final: 0.8600 (p0) REVERT: B 1027 THR cc_start: 0.9384 (m) cc_final: 0.8630 (p) REVERT: B 1106 GLN cc_start: 0.8416 (pm20) cc_final: 0.8044 (pm20) REVERT: C 58 PHE cc_start: 0.6691 (m-80) cc_final: 0.6162 (m-80) REVERT: C 152 TRP cc_start: 0.7104 (p-90) cc_final: 0.6338 (p-90) REVERT: C 153 MET cc_start: 0.6537 (ttm) cc_final: 0.6262 (ttm) REVERT: C 269 TYR cc_start: 0.7945 (m-10) cc_final: 0.7218 (m-80) REVERT: C 307 THR cc_start: 0.7790 (t) cc_final: 0.7507 (t) REVERT: C 314 GLN cc_start: 0.9416 (tm-30) cc_final: 0.9091 (tm-30) REVERT: C 357 ARG cc_start: 0.7230 (ttp-170) cc_final: 0.6947 (mtp180) REVERT: C 453 TYR cc_start: 0.8234 (p90) cc_final: 0.7356 (p90) REVERT: C 733 LYS cc_start: 0.9045 (pttm) cc_final: 0.8704 (pttm) REVERT: C 755 GLN cc_start: 0.7324 (mt0) cc_final: 0.7069 (mt0) REVERT: C 764 ASN cc_start: 0.8315 (m-40) cc_final: 0.7919 (m-40) REVERT: C 776 LYS cc_start: 0.9185 (tmmt) cc_final: 0.8733 (tmmt) REVERT: C 780 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8508 (mt-10) REVERT: C 815 ARG cc_start: 0.8405 (tpm170) cc_final: 0.8022 (tpm170) REVERT: C 873 TYR cc_start: 0.8464 (m-10) cc_final: 0.8131 (m-80) REVERT: C 917 TYR cc_start: 0.7198 (m-10) cc_final: 0.5573 (m-10) REVERT: C 925 ASN cc_start: 0.9281 (t0) cc_final: 0.8893 (t0) REVERT: C 953 ASN cc_start: 0.8715 (m110) cc_final: 0.8463 (m-40) REVERT: C 965 GLN cc_start: 0.9573 (mm-40) cc_final: 0.9163 (mm-40) REVERT: C 1000 ARG cc_start: 0.8943 (mtt180) cc_final: 0.8680 (mtt180) REVERT: C 1004 LEU cc_start: 0.9242 (tp) cc_final: 0.9015 (tp) REVERT: C 1005 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8531 (tm-30) REVERT: C 1006 THR cc_start: 0.9129 (p) cc_final: 0.8281 (p) REVERT: C 1010 GLN cc_start: 0.8887 (pm20) cc_final: 0.8669 (pm20) REVERT: C 1064 HIS cc_start: 0.7858 (m-70) cc_final: 0.7398 (m-70) REVERT: C 1109 PHE cc_start: 0.8641 (t80) cc_final: 0.8365 (t80) REVERT: C 1110 TYR cc_start: 0.9088 (t80) cc_final: 0.8872 (t80) REVERT: C 1111 GLU cc_start: 0.8418 (tp30) cc_final: 0.7841 (tp30) REVERT: C 1113 GLN cc_start: 0.8628 (mp10) cc_final: 0.7509 (mp10) outliers start: 0 outliers final: 0 residues processed: 628 average time/residue: 0.1563 time to fit residues: 157.9647 Evaluate side-chains 542 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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: 20.0000 chunk 3 optimal weight: 0.7980 chunk 284 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 211 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 283 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN B 87 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 B 953 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 774 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.177338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146280 restraints weight = 54119.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150238 restraints weight = 32857.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153122 restraints weight = 22416.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155153 restraints weight = 16511.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156458 restraints weight = 12980.037| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4686 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= 0.148 Angle : 0.782 19.804 33721 Z= 0.375 Chirality : 0.049 0.432 4035 Planarity : 0.005 0.080 4250 Dihedral : 5.514 36.332 3241 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.81 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % 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 are not related in a simple way. whole: -2.93 (0.14), residues: 3006 helix: 0.15 (0.21), residues: 620 sheet: -1.74 (0.27), residues: 358 loop : -2.88 (0.12), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 905 TYR 0.021 0.002 TYR A1110 PHE 0.029 0.002 PHE B 559 TRP 0.019 0.002 TRP B 152 HIS 0.006 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (24570) covalent geometry : angle 0.74111 / 0.37 (33483) SS BOND : bond 0.00490 / 0.31 ( 35) SS BOND : angle 1.56618 / 1.01 ( 70) hydrogen bonds : bond 0.04329 / 2.91 ( 696) hydrogen bonds : angle 5.81415 / 3.90 ( 1932) link_ALPHA1-3 : bond 0.00242 / 0.13 ( 1) link_ALPHA1-3 : angle 1.71375 / 0.84 ( 3) link_ALPHA1-6 : bond 0.00469 / 0.25 ( 1) link_ALPHA1-6 : angle 1.49940 / 0.75 ( 3) link_BETA1-4 : bond 0.00496 / 0.32 ( 17) link_BETA1-4 : angle 2.53042 / 1.60 ( 51) link_BETA1-6 : bond 0.01126 / 0.59 ( 1) link_BETA1-6 : angle 1.54243 / 0.83 ( 3) link_NAG-ASN : bond 0.00739 / 0.45 ( 36) link_NAG-ASN : angle 3.95266 / 2.80 ( 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 620 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 0.903 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 50 SER cc_start: 0.9220 (t) cc_final: 0.8702 (p) REVERT: A 51 THR cc_start: 0.9238 (p) cc_final: 0.9020 (p) REVERT: A 117 LEU cc_start: 0.8654 (tp) cc_final: 0.8405 (tp) REVERT: A 145 TYR cc_start: 0.7443 (m-80) cc_final: 0.7104 (m-80) REVERT: A 170 TYR cc_start: 0.8199 (t80) cc_final: 0.7980 (t80) REVERT: A 194 PHE cc_start: 0.7569 (p90) cc_final: 0.7360 (p90) REVERT: A 200 TYR cc_start: 0.5999 (m-80) cc_final: 0.5226 (m-80) REVERT: A 297 SER cc_start: 0.9516 (m) cc_final: 0.9079 (p) REVERT: A 369 TYR cc_start: 0.6104 (t80) cc_final: 0.5188 (m-80) REVERT: A 696 THR cc_start: 0.8145 (m) cc_final: 0.7905 (m) REVERT: A 737 ASP cc_start: 0.8273 (p0) cc_final: 0.7861 (p0) REVERT: A 764 ASN cc_start: 0.9026 (m-40) cc_final: 0.8799 (m-40) REVERT: A 867 ASP cc_start: 0.9124 (p0) cc_final: 0.8672 (p0) REVERT: A 868 GLU cc_start: 0.8011 (pm20) cc_final: 0.6727 (tm-30) REVERT: A 869 MET cc_start: 0.8753 (ptt) cc_final: 0.8394 (ppp) REVERT: A 901 GLN cc_start: 0.8672 (tt0) cc_final: 0.8335 (tt0) REVERT: A 902 MET cc_start: 0.8583 (mmp) cc_final: 0.8299 (mmp) REVERT: A 969 ASN cc_start: 0.9038 (m-40) cc_final: 0.8545 (m-40) REVERT: A 983 ARG cc_start: 0.8794 (ptt90) cc_final: 0.8473 (ptt90) REVERT: A 1113 GLN cc_start: 0.8585 (mt0) cc_final: 0.8351 (mt0) REVERT: B 104 TRP cc_start: 0.6947 (m-90) cc_final: 0.6470 (m-90) REVERT: B 153 MET cc_start: 0.7723 (mtm) cc_final: 0.7030 (tpt) REVERT: B 318 PHE cc_start: 0.7665 (p90) cc_final: 0.7157 (p90) REVERT: B 378 LYS cc_start: 0.6415 (mmtt) cc_final: 0.6023 (mmmt) REVERT: B 563 GLN cc_start: 0.6781 (mt0) cc_final: 0.6386 (mp10) REVERT: B 726 ILE cc_start: 0.8315 (pt) cc_final: 0.7990 (pt) REVERT: B 727 LEU cc_start: 0.9263 (mt) cc_final: 0.8850 (mt) REVERT: B 731 MET cc_start: 0.7099 (ttt) cc_final: 0.6607 (ttt) REVERT: B 764 ASN cc_start: 0.8766 (m110) cc_final: 0.8550 (m110) REVERT: B 773 GLU cc_start: 0.9205 (tp30) cc_final: 0.8731 (tp30) REVERT: B 774 GLN cc_start: 0.8620 (tt0) cc_final: 0.8304 (tp-100) REVERT: B 776 LYS cc_start: 0.9309 (ttpp) cc_final: 0.8571 (tmmt) REVERT: B 780 GLU cc_start: 0.8554 (pt0) cc_final: 0.7762 (pt0) REVERT: B 802 PHE cc_start: 0.7837 (m-80) cc_final: 0.7090 (m-80) REVERT: B 825 LYS cc_start: 0.8566 (tttt) cc_final: 0.7600 (tttm) REVERT: B 861 LEU cc_start: 0.9619 (tt) cc_final: 0.9303 (tt) REVERT: B 945 LEU cc_start: 0.8348 (mt) cc_final: 0.8090 (mt) REVERT: B 969 ASN cc_start: 0.8925 (p0) cc_final: 0.8597 (p0) REVERT: B 1106 GLN cc_start: 0.8396 (pm20) cc_final: 0.8117 (pm20) REVERT: C 58 PHE cc_start: 0.6841 (m-80) cc_final: 0.6270 (m-80) REVERT: C 269 TYR cc_start: 0.7949 (m-10) cc_final: 0.7195 (m-80) REVERT: C 307 THR cc_start: 0.7741 (t) cc_final: 0.7481 (t) REVERT: C 314 GLN cc_start: 0.9452 (tm-30) cc_final: 0.9122 (tm-30) REVERT: C 453 TYR cc_start: 0.8246 (p90) cc_final: 0.7335 (p90) REVERT: C 755 GLN cc_start: 0.7361 (mt0) cc_final: 0.7068 (mt0) REVERT: C 764 ASN cc_start: 0.8319 (m-40) cc_final: 0.7947 (m-40) REVERT: C 774 GLN cc_start: 0.8081 (tt0) cc_final: 0.7796 (tp40) REVERT: C 815 ARG cc_start: 0.8343 (tpm170) cc_final: 0.8000 (tpm170) REVERT: C 821 LEU cc_start: 0.8461 (mt) cc_final: 0.8132 (mt) REVERT: C 895 GLN cc_start: 0.8048 (pm20) cc_final: 0.7329 (pm20) REVERT: C 917 TYR cc_start: 0.7094 (m-10) cc_final: 0.6258 (m-10) REVERT: C 919 ASN cc_start: 0.9358 (t0) cc_final: 0.9005 (t0) REVERT: C 923 ILE cc_start: 0.9426 (mt) cc_final: 0.8637 (mt) REVERT: C 925 ASN cc_start: 0.9263 (t0) cc_final: 0.8999 (t0) REVERT: C 953 ASN cc_start: 0.8669 (m110) cc_final: 0.8438 (m-40) REVERT: C 965 GLN cc_start: 0.9546 (mm-40) cc_final: 0.9185 (mm-40) REVERT: C 1006 THR cc_start: 0.8955 (p) cc_final: 0.8190 (p) REVERT: C 1103 PHE cc_start: 0.8584 (m-10) cc_final: 0.8307 (m-10) REVERT: C 1109 PHE cc_start: 0.8644 (t80) cc_final: 0.8406 (t80) REVERT: C 1110 TYR cc_start: 0.9063 (t80) cc_final: 0.8859 (t80) REVERT: C 1111 GLU cc_start: 0.8402 (tp30) cc_final: 0.7767 (tp30) REVERT: C 1113 GLN cc_start: 0.8592 (mp10) cc_final: 0.7493 (mp10) REVERT: C 1114 ILE cc_start: 0.7416 (mm) cc_final: 0.7185 (mm) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.1616 time to fit residues: 160.8238 Evaluate side-chains 538 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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: 0.6980 chunk 299 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 279 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 242 optimal weight: 0.0050 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 774 GLN A 954 GLN A1023 ASN A1083 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** ** 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.180376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148887 restraints weight = 53499.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152976 restraints weight = 32542.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155872 restraints weight = 22155.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157824 restraints weight = 16349.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.159336 restraints weight = 12965.164| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.5009 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= 0.132 Angle : 0.781 19.933 33721 Z= 0.373 Chirality : 0.049 0.440 4035 Planarity : 0.005 0.082 4250 Dihedral : 5.398 36.461 3241 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.45 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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 are not related in a simple way. whole: -2.84 (0.14), residues: 3006 helix: 0.11 (0.21), residues: 628 sheet: -1.41 (0.27), residues: 365 loop : -2.86 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 905 TYR 0.025 0.001 TYR B 873 PHE 0.037 0.002 PHE B 275 TRP 0.023 0.002 TRP C 258 HIS 0.016 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (24570) covalent geometry : angle 0.74220 / 0.36 (33483) SS BOND : bond 0.00393 / 0.25 ( 35) SS BOND : angle 1.47807 / 0.95 ( 70) hydrogen bonds : bond 0.04275 / 2.89 ( 696) hydrogen bonds : angle 5.76600 / 3.89 ( 1932) link_ALPHA1-3 : bond 0.00364 / 0.19 ( 1) link_ALPHA1-3 : angle 1.63874 / 0.79 ( 3) link_ALPHA1-6 : bond 0.00445 / 0.23 ( 1) link_ALPHA1-6 : angle 1.28402 / 0.67 ( 3) link_BETA1-4 : bond 0.00619 / 0.37 ( 17) link_BETA1-4 : angle 2.43312 / 1.54 ( 51) link_BETA1-6 : bond 0.00400 / 0.21 ( 1) link_BETA1-6 : angle 1.44587 / 0.84 ( 3) link_NAG-ASN : bond 0.00771 / 0.47 ( 36) link_NAG-ASN : angle 3.90479 / 2.75 ( 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 627 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 0.869 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 30 ASN cc_start: 0.9105 (t0) cc_final: 0.8889 (t0) REVERT: A 117 LEU cc_start: 0.8800 (tp) cc_final: 0.8572 (tp) REVERT: A 145 TYR cc_start: 0.7439 (m-80) cc_final: 0.7103 (m-80) REVERT: A 200 TYR cc_start: 0.6085 (m-80) cc_final: 0.4832 (m-80) REVERT: A 297 SER cc_start: 0.9466 (m) cc_final: 0.8982 (p) REVERT: A 369 TYR cc_start: 0.6091 (t80) cc_final: 0.5212 (m-80) REVERT: A 697 MET cc_start: 0.8746 (ptm) cc_final: 0.8264 (ttm) REVERT: A 699 LEU cc_start: 0.8963 (mt) cc_final: 0.8729 (pt) REVERT: A 737 ASP cc_start: 0.8202 (p0) cc_final: 0.7790 (p0) REVERT: A 764 ASN cc_start: 0.8994 (m-40) cc_final: 0.8718 (m-40) REVERT: A 768 THR cc_start: 0.9210 (t) cc_final: 0.9007 (t) REVERT: A 867 ASP cc_start: 0.9076 (p0) cc_final: 0.8613 (p0) REVERT: A 868 GLU cc_start: 0.7997 (pm20) cc_final: 0.6800 (tm-30) REVERT: A 901 GLN cc_start: 0.8668 (tt0) cc_final: 0.8357 (tt0) REVERT: A 902 MET cc_start: 0.8540 (mmp) cc_final: 0.7729 (mmt) REVERT: A 923 ILE cc_start: 0.9166 (mt) cc_final: 0.8917 (pt) REVERT: A 926 GLN cc_start: 0.9063 (mt0) cc_final: 0.8539 (mp10) REVERT: A 969 ASN cc_start: 0.8947 (m-40) cc_final: 0.8490 (m-40) REVERT: A 983 ARG cc_start: 0.8762 (ptt90) cc_final: 0.8487 (ptt90) REVERT: B 104 TRP cc_start: 0.6870 (m-90) cc_final: 0.6426 (m-90) REVERT: B 153 MET cc_start: 0.7699 (mtm) cc_final: 0.7073 (tpt) REVERT: B 318 PHE cc_start: 0.7581 (p90) cc_final: 0.7008 (p90) REVERT: B 378 LYS cc_start: 0.6429 (mmtt) cc_final: 0.6035 (mmmt) REVERT: B 542 ASN cc_start: 0.7589 (m-40) cc_final: 0.6644 (t0) REVERT: B 563 GLN cc_start: 0.7442 (mt0) cc_final: 0.6797 (mp10) REVERT: B 727 LEU cc_start: 0.9307 (mt) cc_final: 0.8882 (mt) REVERT: B 764 ASN cc_start: 0.8728 (m110) cc_final: 0.8512 (m110) REVERT: B 773 GLU cc_start: 0.9159 (tp30) cc_final: 0.8791 (tp30) REVERT: B 774 GLN cc_start: 0.8652 (tt0) cc_final: 0.8427 (tp40) REVERT: B 776 LYS cc_start: 0.9335 (ttpp) cc_final: 0.8634 (tmmt) REVERT: B 780 GLU cc_start: 0.8515 (pt0) cc_final: 0.7766 (pt0) REVERT: B 825 LYS cc_start: 0.8609 (tttt) cc_final: 0.8135 (tttp) REVERT: B 861 LEU cc_start: 0.9625 (tt) cc_final: 0.9345 (tt) REVERT: B 969 ASN cc_start: 0.8873 (p0) cc_final: 0.8640 (p0) REVERT: B 1106 GLN cc_start: 0.8420 (pm20) cc_final: 0.8096 (pm20) REVERT: C 58 PHE cc_start: 0.6738 (m-80) cc_final: 0.6170 (m-80) REVERT: C 307 THR cc_start: 0.7827 (t) cc_final: 0.7569 (t) REVERT: C 314 GLN cc_start: 0.9463 (tm-30) cc_final: 0.8889 (tm-30) REVERT: C 453 TYR cc_start: 0.8182 (p90) cc_final: 0.7252 (p90) REVERT: C 664 ILE cc_start: 0.8820 (mt) cc_final: 0.8342 (pt) REVERT: C 764 ASN cc_start: 0.8296 (m-40) cc_final: 0.7942 (m-40) REVERT: C 776 LYS cc_start: 0.9173 (tmmt) cc_final: 0.8736 (tmmt) REVERT: C 780 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8521 (mt-10) REVERT: C 815 ARG cc_start: 0.8332 (tpm170) cc_final: 0.7996 (tpm170) REVERT: C 873 TYR cc_start: 0.8382 (m-10) cc_final: 0.8082 (m-80) REVERT: C 895 GLN cc_start: 0.7955 (pm20) cc_final: 0.7534 (pm20) REVERT: C 917 TYR cc_start: 0.7378 (m-10) cc_final: 0.5945 (m-10) REVERT: C 919 ASN cc_start: 0.9332 (t0) cc_final: 0.8993 (t0) REVERT: C 923 ILE cc_start: 0.9404 (mt) cc_final: 0.8585 (mt) REVERT: C 925 ASN cc_start: 0.9224 (t0) cc_final: 0.8845 (t0) REVERT: C 953 ASN cc_start: 0.8691 (m110) cc_final: 0.8471 (m-40) REVERT: C 965 GLN cc_start: 0.9497 (mm-40) cc_final: 0.9148 (mm-40) REVERT: C 1000 ARG cc_start: 0.9042 (mtt180) cc_final: 0.8630 (mtp85) REVERT: C 1006 THR cc_start: 0.8955 (p) cc_final: 0.8154 (p) REVERT: C 1109 PHE cc_start: 0.8588 (t80) cc_final: 0.8339 (t80) REVERT: C 1111 GLU cc_start: 0.8337 (tp30) cc_final: 0.7768 (tp30) REVERT: C 1113 GLN cc_start: 0.8579 (mp10) cc_final: 0.7452 (mp10) REVERT: C 1114 ILE cc_start: 0.7376 (mm) cc_final: 0.7142 (mm) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.1578 time to fit residues: 158.0461 Evaluate side-chains 540 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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: 10.0000 chunk 206 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 252 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 197 optimal weight: 0.1980 chunk 253 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN A 606 ASN A 655 HIS A 774 GLN A 901 GLN 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 955 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.177413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.146144 restraints weight = 53846.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150231 restraints weight = 33045.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153042 restraints weight = 22512.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154973 restraints weight = 16621.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156365 restraints weight = 13189.620| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24661 Z= 0.155 Angle : 0.788 19.953 33721 Z= 0.380 Chirality : 0.049 0.398 4035 Planarity : 0.005 0.082 4250 Dihedral : 5.419 36.151 3241 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.81 % Favored : 89.09 % Rotamer: Outliers : 0.04 % Allowed : 0.36 % Favored : 99.60 % 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 are not related in a simple way. whole: -2.82 (0.14), residues: 3006 helix: 0.11 (0.21), residues: 625 sheet: -1.52 (0.26), residues: 383 loop : -2.81 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1091 TYR 0.027 0.002 TYR B1007 PHE 0.026 0.002 PHE B 559 TRP 0.017 0.002 TRP C 64 HIS 0.011 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (24570) covalent geometry : angle 0.74922 / 0.37 (33483) SS BOND : bond 0.00414 / 0.26 ( 35) SS BOND : angle 1.51141 / 0.98 ( 70) hydrogen bonds : bond 0.04369 / 2.98 ( 696) hydrogen bonds : angle 5.84728 / 3.96 ( 1932) link_ALPHA1-3 : bond 0.00239 / 0.13 ( 1) link_ALPHA1-3 : angle 1.67866 / 0.80 ( 3) link_ALPHA1-6 : bond 0.00422 / 0.22 ( 1) link_ALPHA1-6 : angle 1.52970 / 0.77 ( 3) link_BETA1-4 : bond 0.00500 / 0.34 ( 17) link_BETA1-4 : angle 2.44267 / 1.54 ( 51) link_BETA1-6 : bond 0.01204 / 0.63 ( 1) link_BETA1-6 : angle 1.44677 / 0.76 ( 3) link_NAG-ASN : bond 0.00707 / 0.43 ( 36) link_NAG-ASN : angle 3.91343 / 2.76 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4397.94 seconds wall clock time: 77 minutes 5.10 seconds (4625.10 seconds total)