Starting phenix.real_space_refine on Wed Jan 14 05:08:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fdw_29016/01_2026/8fdw_29016_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fdw_29016/01_2026/8fdw_29016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fdw_29016/01_2026/8fdw_29016_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fdw_29016/01_2026/8fdw_29016_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fdw_29016/01_2026/8fdw_29016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fdw_29016/01_2026/8fdw_29016.map" } resolution = 2.9 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= 0.001 sd= 0.023 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 84 5.16 5 C 7833 2.51 5 N 1986 2.21 5 O 2553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12456 Number of models: 1 Model: "" Number of chains: 21 Chain: "B" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3904 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 15, 'TRANS': 492} Chain breaks: 1 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3904 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 15, 'TRANS': 492} Chain breaks: 1 Chain: "C" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3904 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 15, 'TRANS': 492} Chain breaks: 1 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.28, per 1000 atoms: 0.26 Number of scatterers: 12456 At special positions: 0 Unit cell: (74.25, 80.85, 285.45, 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 84 16.00 O 2553 8.00 N 1986 7.00 C 7833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 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=2.05 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN D 3 " - " MAN D 4 " " MAN E 3 " - " MAN E 4 " " MAN I 3 " - " MAN I 4 " " MAN J 3 " - " MAN J 4 " " MAN N 3 " - " MAN N 4 " " MAN O 3 " - " MAN O 4 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " " NAG I 2 " - " MAN I 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG N 2 " - " MAN N 3 " " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1402 " - " ASN A 709 " " NAG A1403 " - " ASN A 717 " " NAG A1404 " - " ASN A1173 " " NAG B1402 " - " ASN B 709 " " NAG B1403 " - " ASN B 717 " " NAG B1404 " - " ASN B1173 " " NAG C1402 " - " ASN C 709 " " NAG C1403 " - " ASN C 717 " " NAG C1404 " - " ASN C1173 " " NAG D 1 " - " ASN B1098 " " NAG E 1 " - " ASN B1134 " " NAG F 1 " - " ASN B1158 " " NAG G 1 " - " ASN B1074 " " NAG H 1 " - " ASN B1194 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN A1158 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1194 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C1158 " " NAG Q 1 " - " ASN C1074 " " NAG R 1 " - " ASN C1194 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 627.8 milliseconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2850 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 13 sheets defined 53.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.644A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 Processing helix chain 'B' and resid 833 through 842 Processing helix chain 'B' and resid 844 through 849 removed outlier: 4.302A pdb=" N LEU B 849 " --> pdb=" O ALA B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 887 removed outlier: 4.115A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP B 886 " --> pdb=" O ILE B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 894 Processing helix chain 'B' and resid 895 through 1031 removed outlier: 3.781A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1147 through 1153 Processing helix chain 'B' and resid 1168 through 1172 removed outlier: 4.249A pdb=" N GLY B1171 " --> pdb=" O ASP B1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1193 Processing helix chain 'B' and resid 1218 through 1234 removed outlier: 3.510A pdb=" N ILE B1232 " --> pdb=" O VAL B1228 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B1233 " --> pdb=" O MET B1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 1237 through 1249 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.748A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 768 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 866 through 887 removed outlier: 4.115A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 895 through 1031 removed outlier: 3.781A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1147 through 1153 Processing helix chain 'A' and resid 1168 through 1172 removed outlier: 4.250A pdb=" N GLY A1171 " --> pdb=" O ASP A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1193 Processing helix chain 'A' and resid 1194 through 1197 Processing helix chain 'A' and resid 1218 through 1234 removed outlier: 3.511A pdb=" N ILE A1232 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A1233 " --> pdb=" O MET A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1249 Processing helix chain 'C' and resid 704 through 708 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 5.073A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 768 Processing helix chain 'C' and resid 833 through 842 Processing helix chain 'C' and resid 844 through 849 removed outlier: 4.120A pdb=" N LEU C 849 " --> pdb=" O ALA C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 887 removed outlier: 4.115A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP C 886 " --> pdb=" O ILE C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 894 Processing helix chain 'C' and resid 895 through 1031 removed outlier: 3.782A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C1027 " --> pdb=" O ASN C1023 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1147 through 1153 Processing helix chain 'C' and resid 1168 through 1172 removed outlier: 4.248A pdb=" N GLY C1171 " --> pdb=" O ASP C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1179 through 1193 Processing helix chain 'C' and resid 1194 through 1197 Processing helix chain 'C' and resid 1218 through 1234 removed outlier: 3.511A pdb=" N ILE C1232 " --> pdb=" O VAL C1228 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET C1233 " --> pdb=" O MET C1229 " (cutoff:3.500A) Processing helix chain 'C' and resid 1237 through 1249 Processing sheet with id=AA1, first strand: chain 'B' and resid 1047 through 1050 removed outlier: 5.743A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1047 through 1050 removed outlier: 5.743A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 853 through 855 Processing sheet with id=AA4, first strand: chain 'B' and resid 1081 through 1083 Processing sheet with id=AA5, first strand: chain 'B' and resid 1094 through 1098 removed outlier: 3.756A pdb=" N ASN B1098 " --> pdb=" O HIS B1101 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1129 through 1134 removed outlier: 6.036A pdb=" N VAL B1129 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N THR A 724 " --> pdb=" O VAL B1129 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY B1131 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE A 726 " --> pdb=" O GLY B1131 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B1133 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 5.693A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A1098 " --> pdb=" O HIS A1101 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 853 through 855 Processing sheet with id=AA9, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB1, first strand: chain 'A' and resid 1129 through 1134 removed outlier: 6.016A pdb=" N VAL A1129 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR C 724 " --> pdb=" O VAL A1129 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY A1131 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE C 726 " --> pdb=" O GLY A1131 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A1133 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1047 through 1048 removed outlier: 5.203A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN C1098 " --> pdb=" O HIS C1101 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 853 through 855 Processing sheet with id=AB4, first strand: chain 'C' and resid 1081 through 1083 712 hydrogen bonds defined for protein. 2010 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: 2.07 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2157 1.32 - 1.45: 3199 1.45 - 1.57: 7190 1.57 - 1.70: 0 1.70 - 1.83: 117 Bond restraints: 12663 Sorted by residual: bond pdb=" C3 MAN E 3 " pdb=" O3 MAN E 3 " ideal model delta sigma weight residual 1.408 1.488 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C3 MAN J 3 " pdb=" O3 MAN J 3 " ideal model delta sigma weight residual 1.408 1.488 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C3 MAN O 3 " pdb=" O3 MAN O 3 " ideal model delta sigma weight residual 1.408 1.487 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C3 MAN N 3 " pdb=" O3 MAN N 3 " ideal model delta sigma weight residual 1.408 1.486 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C3 MAN D 3 " pdb=" O3 MAN D 3 " ideal model delta sigma weight residual 1.408 1.486 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 12658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 14159 2.21 - 4.42: 2873 4.42 - 6.62: 151 6.62 - 8.83: 14 8.83 - 11.04: 5 Bond angle restraints: 17202 Sorted by residual: angle pdb=" N TYR B1206 " pdb=" CA TYR B1206 " pdb=" C TYR B1206 " ideal model delta sigma weight residual 110.91 121.17 -10.26 1.17e+00 7.31e-01 7.69e+01 angle pdb=" N LYS B1211 " pdb=" CA LYS B1211 " pdb=" C LYS B1211 " ideal model delta sigma weight residual 110.28 120.93 -10.65 1.48e+00 4.57e-01 5.18e+01 angle pdb=" N VAL C 729 " pdb=" CA VAL C 729 " pdb=" C VAL C 729 " ideal model delta sigma weight residual 113.71 107.65 6.06 9.50e-01 1.11e+00 4.07e+01 angle pdb=" CA GLY B1046 " pdb=" C GLY B1046 " pdb=" O GLY B1046 " ideal model delta sigma weight residual 122.22 118.28 3.94 6.50e-01 2.37e+00 3.68e+01 angle pdb=" CB GLU C 868 " pdb=" CG GLU C 868 " pdb=" CD GLU C 868 " ideal model delta sigma weight residual 112.60 122.25 -9.65 1.70e+00 3.46e-01 3.22e+01 ... (remaining 17197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.11: 7820 24.11 - 48.22: 366 48.22 - 72.33: 97 72.33 - 96.44: 27 96.44 - 120.54: 21 Dihedral angle restraints: 8331 sinusoidal: 3912 harmonic: 4419 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -177.45 -89.55 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual 93.00 179.89 -86.89 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 179.51 -86.51 1 1.00e+01 1.00e-02 9.02e+01 ... (remaining 8328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 1971 0.153 - 0.307: 191 0.307 - 0.460: 12 0.460 - 0.614: 4 0.614 - 0.767: 6 Chirality restraints: 2184 Sorted by residual: chirality pdb=" C1 MAN N 3 " pdb=" O4 NAG N 2 " pdb=" C2 MAN N 3 " pdb=" O5 MAN N 3 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.66e+02 chirality pdb=" C1 MAN D 3 " pdb=" O4 NAG D 2 " pdb=" C2 MAN D 3 " pdb=" O5 MAN D 3 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.66e+02 chirality pdb=" C1 MAN I 3 " pdb=" O4 NAG I 2 " pdb=" C2 MAN I 3 " pdb=" O5 MAN I 3 " both_signs ideal model delta sigma weight residual False 2.40 2.15 0.25 2.00e-02 2.50e+03 1.61e+02 ... (remaining 2181 not shown) Planarity restraints: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " -0.346 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG J 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.143 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " 0.528 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.345 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG E 1 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.526 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " -0.344 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG O 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.117 2.00e-02 2.50e+03 ... (remaining 2142 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 4554 2.88 - 3.39: 12658 3.39 - 3.89: 20512 3.89 - 4.40: 23107 4.40 - 4.90: 37320 Nonbonded interactions: 98151 Sorted by model distance: nonbonded pdb=" N GLU C 868 " pdb=" OE1 GLU C 868 " model vdw 2.379 3.120 nonbonded pdb=" OG1 THR B 866 " pdb=" OE1 GLU B 868 " model vdw 2.382 3.040 nonbonded pdb=" N GLU B 868 " pdb=" OE1 GLU B 868 " model vdw 2.383 3.120 nonbonded pdb=" OG1 THR C 866 " pdb=" OE1 GLU C 868 " model vdw 2.390 3.040 nonbonded pdb=" OE2 GLU A 868 " pdb=" N TRP C1212 " model vdw 2.397 3.120 ... (remaining 98146 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 23.650 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: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.480 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 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 : 0.013 0.080 12732 Z= 0.816 Angle : 1.699 18.375 17394 Z= 1.115 Chirality : 0.104 0.767 2184 Planarity : 0.021 0.333 2121 Dihedral : 16.179 120.544 5436 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.07 % Favored : 91.80 % Rotamer: Outliers : 1.92 % Allowed : 7.13 % Favored : 90.96 % 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: -2.79 (0.19), residues: 1512 helix: -1.34 (0.16), residues: 723 sheet: -1.21 (0.38), residues: 159 loop : -2.57 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 995 TYR 0.046 0.007 TYR C 917 PHE 0.052 0.009 PHE C1095 TRP 0.076 0.018 TRP A 886 HIS 0.010 0.003 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.01299 (12663) covalent geometry : angle 1.62657 (17202) SS BOND : bond 0.00772 ( 15) SS BOND : angle 1.33104 ( 30) hydrogen bonds : bond 0.19188 ( 710) hydrogen bonds : angle 8.58690 ( 2010) link_ALPHA1-3 : bond 0.02872 ( 6) link_ALPHA1-3 : angle 3.12830 ( 18) link_ALPHA1-4 : bond 0.01815 ( 9) link_ALPHA1-4 : angle 4.68672 ( 27) link_BETA1-4 : bond 0.01267 ( 15) link_BETA1-4 : angle 3.19996 ( 45) link_NAG-ASN : bond 0.01303 ( 24) link_NAG-ASN : angle 6.91084 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 407 time to evaluate : 0.327 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: B 697 MET cc_start: 0.7042 (tmm) cc_final: 0.6538 (tmm) REVERT: B 730 SER cc_start: 0.8032 (m) cc_final: 0.7551 (p) REVERT: B 907 ASN cc_start: 0.2871 (m-40) cc_final: 0.2490 (m-40) REVERT: B 1028 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7883 (tttt) REVERT: B 1154 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8643 (ttmm) REVERT: A 1028 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8037 (tttm) REVERT: A 1107 ARG cc_start: 0.8096 (tpt90) cc_final: 0.7869 (tmt170) REVERT: A 1135 ASN cc_start: 0.8156 (m-40) cc_final: 0.7910 (m-40) REVERT: A 1139 ASP cc_start: 0.8261 (t0) cc_final: 0.8006 (t0) REVERT: A 1154 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8712 (tttm) REVERT: C 849 LEU cc_start: 0.5990 (tp) cc_final: 0.5770 (mp) outliers start: 25 outliers final: 8 residues processed: 426 average time/residue: 0.5414 time to fit residues: 251.6385 Evaluate side-chains 221 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 213 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 1210 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS A 755 GLN A 949 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1023 ASN A1048 HIS A1064 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN C 914 ASN C1011 GLN C1054 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.119299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.097347 restraints weight = 32949.386| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.62 r_work: 0.3610 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12732 Z= 0.208 Angle : 0.957 14.357 17394 Z= 0.444 Chirality : 0.054 0.672 2184 Planarity : 0.004 0.036 2121 Dihedral : 12.784 107.928 2779 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 6.59 % Allowed : 20.38 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.65 (0.21), residues: 1512 helix: 1.00 (0.18), residues: 717 sheet: -0.46 (0.41), residues: 159 loop : -2.17 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1000 TYR 0.029 0.003 TYR C 904 PHE 0.016 0.002 PHE A1121 TRP 0.019 0.002 TRP C1214 HIS 0.014 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00442 (12663) covalent geometry : angle 0.88309 (17202) SS BOND : bond 0.01952 ( 15) SS BOND : angle 2.18343 ( 30) hydrogen bonds : bond 0.05180 ( 710) hydrogen bonds : angle 5.44647 ( 2010) link_ALPHA1-3 : bond 0.00713 ( 6) link_ALPHA1-3 : angle 2.26462 ( 18) link_ALPHA1-4 : bond 0.01404 ( 9) link_ALPHA1-4 : angle 3.39154 ( 27) link_BETA1-4 : bond 0.00489 ( 15) link_BETA1-4 : angle 2.04932 ( 45) link_NAG-ASN : bond 0.01143 ( 24) link_NAG-ASN : angle 4.97359 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 238 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 730 SER cc_start: 0.8736 (m) cc_final: 0.8405 (p) REVERT: B 859 THR cc_start: 0.7667 (m) cc_final: 0.6836 (t) REVERT: B 861 LEU cc_start: 0.6842 (mt) cc_final: 0.6583 (mm) REVERT: B 902 MET cc_start: 0.7414 (ttp) cc_final: 0.6905 (ttp) REVERT: B 904 TYR cc_start: 0.8389 (m-10) cc_final: 0.8185 (m-80) REVERT: B 905 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7085 (ptp90) REVERT: B 909 ILE cc_start: 0.8765 (mt) cc_final: 0.8421 (pp) REVERT: B 915 VAL cc_start: 0.8421 (p) cc_final: 0.7981 (m) REVERT: B 1045 LYS cc_start: 0.8519 (tptp) cc_final: 0.8269 (tptt) REVERT: B 1057 PRO cc_start: 0.8261 (Cg_exo) cc_final: 0.8060 (Cg_endo) REVERT: A 904 TYR cc_start: 0.7828 (m-10) cc_final: 0.7502 (m-10) REVERT: A 905 ARG cc_start: 0.7193 (ptp90) cc_final: 0.6718 (ptp90) REVERT: A 909 ILE cc_start: 0.8873 (mt) cc_final: 0.8568 (pp) REVERT: A 915 VAL cc_start: 0.8723 (p) cc_final: 0.6801 (m) REVERT: A 919 ASN cc_start: 0.7795 (m-40) cc_final: 0.6550 (m110) REVERT: A 1125 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7676 (t0) REVERT: A 1127 ASP cc_start: 0.8729 (m-30) cc_final: 0.8475 (m-30) REVERT: A 1135 ASN cc_start: 0.8382 (m-40) cc_final: 0.8073 (m-40) REVERT: C 697 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.5751 (tmm) REVERT: C 1038 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8718 (mtmm) REVERT: C 1054 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: C 1055 SER cc_start: 0.9227 (m) cc_final: 0.8996 (t) REVERT: C 1135 ASN cc_start: 0.8320 (m-40) cc_final: 0.8009 (m110) REVERT: C 1139 ASP cc_start: 0.8811 (t0) cc_final: 0.8543 (p0) REVERT: C 1205 LYS cc_start: 0.8244 (mppt) cc_final: 0.7962 (mppt) REVERT: C 1233 MET cc_start: 0.5369 (tpt) cc_final: 0.4755 (ttp) outliers start: 86 outliers final: 31 residues processed: 288 average time/residue: 0.4561 time to fit residues: 145.9951 Evaluate side-chains 239 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 905 ARG Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain B residue 1240 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1169 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 23 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 44 optimal weight: 0.3980 chunk 111 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 949 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS B1064 HIS B1135 ASN A 901 GLN A 935 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN C 914 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1036 GLN C1064 HIS C1159 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.113655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.090955 restraints weight = 33513.225| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.69 r_work: 0.3481 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12732 Z= 0.237 Angle : 0.904 12.522 17394 Z= 0.426 Chirality : 0.052 0.454 2184 Planarity : 0.004 0.034 2121 Dihedral : 12.089 108.456 2771 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 6.59 % Allowed : 22.22 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.30 (0.21), residues: 1512 helix: 1.41 (0.18), residues: 729 sheet: -0.42 (0.40), residues: 159 loop : -2.20 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 847 TYR 0.026 0.003 TYR C 904 PHE 0.026 0.002 PHE B 927 TRP 0.019 0.002 TRP B 886 HIS 0.015 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00522 (12663) covalent geometry : angle 0.84308 (17202) SS BOND : bond 0.01136 ( 15) SS BOND : angle 2.13347 ( 30) hydrogen bonds : bond 0.04790 ( 710) hydrogen bonds : angle 4.95924 ( 2010) link_ALPHA1-3 : bond 0.00697 ( 6) link_ALPHA1-3 : angle 1.78190 ( 18) link_ALPHA1-4 : bond 0.01625 ( 9) link_ALPHA1-4 : angle 3.18227 ( 27) link_BETA1-4 : bond 0.00319 ( 15) link_BETA1-4 : angle 1.92830 ( 45) link_NAG-ASN : bond 0.00814 ( 24) link_NAG-ASN : angle 4.32817 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 213 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 861 LEU cc_start: 0.7387 (mt) cc_final: 0.7104 (mt) REVERT: B 902 MET cc_start: 0.7470 (ttt) cc_final: 0.6953 (ttp) REVERT: B 909 ILE cc_start: 0.8845 (mt) cc_final: 0.8515 (tt) REVERT: B 928 ASN cc_start: 0.8909 (t0) cc_final: 0.8671 (t0) REVERT: B 949 GLN cc_start: 0.8638 (tt0) cc_final: 0.8239 (tt0) REVERT: A 909 ILE cc_start: 0.8815 (mt) cc_final: 0.8493 (pp) REVERT: A 927 PHE cc_start: 0.8479 (t80) cc_final: 0.8202 (t80) REVERT: A 990 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8277 (mt-10) REVERT: A 1127 ASP cc_start: 0.8828 (m-30) cc_final: 0.8620 (m-30) REVERT: A 1135 ASN cc_start: 0.8333 (m-40) cc_final: 0.7931 (m-40) REVERT: C 927 PHE cc_start: 0.8321 (t80) cc_final: 0.7888 (t80) REVERT: C 1038 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8819 (mtmm) REVERT: C 1054 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8659 (pm20) REVERT: C 1125 ASN cc_start: 0.8396 (t0) cc_final: 0.8163 (t0) REVERT: C 1135 ASN cc_start: 0.8305 (m-40) cc_final: 0.7981 (m110) REVERT: C 1136 THR cc_start: 0.8710 (m) cc_final: 0.8505 (p) REVERT: C 1139 ASP cc_start: 0.8879 (t0) cc_final: 0.8665 (p0) REVERT: C 1212 TRP cc_start: 0.4218 (OUTLIER) cc_final: 0.2718 (m-10) outliers start: 86 outliers final: 26 residues processed: 266 average time/residue: 0.4207 time to fit residues: 125.3792 Evaluate side-chains 221 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain B residue 1240 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1212 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 10 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 chunk 109 optimal weight: 0.0170 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 62 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN C 935 GLN C 949 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.113532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.090524 restraints weight = 32899.482| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.70 r_work: 0.3482 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12732 Z= 0.180 Angle : 0.863 12.914 17394 Z= 0.398 Chirality : 0.049 0.547 2184 Planarity : 0.004 0.050 2121 Dihedral : 11.503 110.014 2768 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.06 % Allowed : 23.98 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.06 (0.21), residues: 1512 helix: 1.61 (0.19), residues: 729 sheet: -0.36 (0.39), residues: 159 loop : -2.06 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 905 TYR 0.033 0.002 TYR C 904 PHE 0.024 0.002 PHE B 927 TRP 0.020 0.001 TRP B 886 HIS 0.015 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00395 (12663) covalent geometry : angle 0.80141 (17202) SS BOND : bond 0.00906 ( 15) SS BOND : angle 2.39142 ( 30) hydrogen bonds : bond 0.04248 ( 710) hydrogen bonds : angle 4.76330 ( 2010) link_ALPHA1-3 : bond 0.00597 ( 6) link_ALPHA1-3 : angle 1.71984 ( 18) link_ALPHA1-4 : bond 0.01567 ( 9) link_ALPHA1-4 : angle 3.07883 ( 27) link_BETA1-4 : bond 0.00374 ( 15) link_BETA1-4 : angle 1.75854 ( 45) link_NAG-ASN : bond 0.00693 ( 24) link_NAG-ASN : angle 4.22097 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 191 time to evaluate : 0.461 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: B 861 LEU cc_start: 0.7551 (mt) cc_final: 0.7226 (mt) REVERT: B 902 MET cc_start: 0.7705 (ttt) cc_final: 0.7153 (ttp) REVERT: B 909 ILE cc_start: 0.8820 (mt) cc_final: 0.8480 (tt) REVERT: B 928 ASN cc_start: 0.8918 (t0) cc_final: 0.8645 (t0) REVERT: B 1197 LEU cc_start: 0.8802 (mm) cc_final: 0.8346 (tp) REVERT: A 909 ILE cc_start: 0.8850 (mt) cc_final: 0.8519 (pp) REVERT: A 990 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8426 (mt-10) REVERT: A 1127 ASP cc_start: 0.8822 (m-30) cc_final: 0.8599 (m-30) REVERT: A 1135 ASN cc_start: 0.8355 (m-40) cc_final: 0.7909 (m-40) REVERT: A 1208 GLN cc_start: 0.3967 (OUTLIER) cc_final: 0.3309 (pp30) REVERT: C 770 ILE cc_start: 0.9148 (tp) cc_final: 0.8782 (pp) REVERT: C 849 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8613 (mm) REVERT: C 873 TYR cc_start: 0.6465 (m-80) cc_final: 0.6080 (m-80) REVERT: C 905 ARG cc_start: 0.7877 (ptp90) cc_final: 0.7542 (ptp90) REVERT: C 919 ASN cc_start: 0.7563 (m110) cc_final: 0.7304 (m-40) REVERT: C 927 PHE cc_start: 0.8342 (t80) cc_final: 0.8051 (t80) REVERT: C 951 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8807 (m) REVERT: C 1038 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8835 (mtmm) REVERT: C 1125 ASN cc_start: 0.8365 (t0) cc_final: 0.8034 (t0) REVERT: C 1135 ASN cc_start: 0.8270 (m-40) cc_final: 0.7973 (m110) REVERT: C 1139 ASP cc_start: 0.8854 (t0) cc_final: 0.8653 (p0) REVERT: C 1203 LEU cc_start: 0.9033 (tt) cc_final: 0.8783 (tm) REVERT: C 1233 MET cc_start: 0.5756 (tpt) cc_final: 0.4984 (ttp) outliers start: 66 outliers final: 30 residues processed: 234 average time/residue: 0.4437 time to fit residues: 115.7072 Evaluate side-chains 218 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1193 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 14 optimal weight: 0.0370 chunk 72 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN B1048 HIS B1054 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN B1135 ASN A 901 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.112462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.089485 restraints weight = 33289.574| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.68 r_work: 0.3456 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12732 Z= 0.184 Angle : 0.855 11.927 17394 Z= 0.395 Chirality : 0.048 0.457 2184 Planarity : 0.004 0.032 2121 Dihedral : 11.331 111.207 2768 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.06 % Allowed : 24.75 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.20 (0.22), residues: 1512 helix: 1.78 (0.19), residues: 723 sheet: -0.43 (0.39), residues: 159 loop : -1.76 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1185 TYR 0.031 0.002 TYR C 904 PHE 0.020 0.002 PHE A 927 TRP 0.022 0.001 TRP B 886 HIS 0.016 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00405 (12663) covalent geometry : angle 0.79987 (17202) SS BOND : bond 0.00763 ( 15) SS BOND : angle 1.97227 ( 30) hydrogen bonds : bond 0.04050 ( 710) hydrogen bonds : angle 4.63492 ( 2010) link_ALPHA1-3 : bond 0.00586 ( 6) link_ALPHA1-3 : angle 1.68054 ( 18) link_ALPHA1-4 : bond 0.01675 ( 9) link_ALPHA1-4 : angle 3.05123 ( 27) link_BETA1-4 : bond 0.00305 ( 15) link_BETA1-4 : angle 1.64495 ( 45) link_NAG-ASN : bond 0.00548 ( 24) link_NAG-ASN : angle 4.02257 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 184 time to evaluate : 0.539 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: B 902 MET cc_start: 0.7643 (ttt) cc_final: 0.6971 (ttp) REVERT: B 909 ILE cc_start: 0.8777 (mt) cc_final: 0.8365 (tt) REVERT: B 928 ASN cc_start: 0.8975 (t0) cc_final: 0.8728 (t0) REVERT: B 1139 ASP cc_start: 0.8789 (t0) cc_final: 0.8439 (p0) REVERT: B 1197 LEU cc_start: 0.8777 (mm) cc_final: 0.8365 (tp) REVERT: A 909 ILE cc_start: 0.8844 (mt) cc_final: 0.8592 (pp) REVERT: A 1135 ASN cc_start: 0.8319 (m-40) cc_final: 0.7850 (m-40) REVERT: A 1194 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8517 (t0) REVERT: A 1197 LEU cc_start: 0.8831 (mm) cc_final: 0.8627 (tm) REVERT: A 1208 GLN cc_start: 0.3889 (OUTLIER) cc_final: 0.3030 (pp30) REVERT: C 697 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.5696 (tmm) REVERT: C 770 ILE cc_start: 0.9163 (tp) cc_final: 0.8844 (pp) REVERT: C 849 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8651 (mm) REVERT: C 873 TYR cc_start: 0.6818 (m-80) cc_final: 0.6496 (m-80) REVERT: C 905 ARG cc_start: 0.7950 (ptp90) cc_final: 0.7635 (ptp-170) REVERT: C 906 PHE cc_start: 0.7708 (m-80) cc_final: 0.7249 (m-80) REVERT: C 1038 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8817 (mtmm) REVERT: C 1125 ASN cc_start: 0.8267 (t0) cc_final: 0.7900 (t0) REVERT: C 1135 ASN cc_start: 0.8261 (m-40) cc_final: 0.7971 (m110) REVERT: C 1139 ASP cc_start: 0.8846 (t0) cc_final: 0.8618 (p0) REVERT: C 1203 LEU cc_start: 0.9044 (tt) cc_final: 0.8797 (tm) outliers start: 66 outliers final: 32 residues processed: 232 average time/residue: 0.4627 time to fit residues: 119.1408 Evaluate side-chains 205 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1227 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 920 GLN B1048 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN A1208 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.109809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.086741 restraints weight = 33038.562| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.62 r_work: 0.3394 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12732 Z= 0.246 Angle : 0.889 12.721 17394 Z= 0.413 Chirality : 0.051 0.456 2184 Planarity : 0.004 0.030 2121 Dihedral : 11.507 115.588 2768 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.29 % Allowed : 25.75 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.18 (0.22), residues: 1512 helix: 1.66 (0.19), residues: 747 sheet: -0.57 (0.39), residues: 159 loop : -1.72 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 905 TYR 0.031 0.003 TYR C 904 PHE 0.016 0.002 PHE A 898 TRP 0.023 0.002 TRP B 886 HIS 0.017 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00544 (12663) covalent geometry : angle 0.83805 (17202) SS BOND : bond 0.01030 ( 15) SS BOND : angle 2.16443 ( 30) hydrogen bonds : bond 0.04186 ( 710) hydrogen bonds : angle 4.65504 ( 2010) link_ALPHA1-3 : bond 0.00503 ( 6) link_ALPHA1-3 : angle 1.69253 ( 18) link_ALPHA1-4 : bond 0.01751 ( 9) link_ALPHA1-4 : angle 3.07791 ( 27) link_BETA1-4 : bond 0.00220 ( 15) link_BETA1-4 : angle 1.54609 ( 45) link_NAG-ASN : bond 0.00513 ( 24) link_NAG-ASN : angle 3.91467 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 193 time to evaluate : 0.485 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: B 902 MET cc_start: 0.7836 (ttt) cc_final: 0.7432 (ttp) REVERT: B 909 ILE cc_start: 0.8789 (mt) cc_final: 0.8392 (tt) REVERT: B 928 ASN cc_start: 0.9008 (t0) cc_final: 0.8774 (t0) REVERT: B 1139 ASP cc_start: 0.8875 (t70) cc_final: 0.8489 (p0) REVERT: B 1197 LEU cc_start: 0.8777 (mm) cc_final: 0.8428 (tm) REVERT: A 727 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 905 ARG cc_start: 0.7983 (ptp90) cc_final: 0.7497 (ptp90) REVERT: A 909 ILE cc_start: 0.8851 (mt) cc_final: 0.8579 (pp) REVERT: A 1135 ASN cc_start: 0.8267 (m110) cc_final: 0.7782 (m-40) REVERT: C 770 ILE cc_start: 0.9188 (tp) cc_final: 0.8898 (pp) REVERT: C 905 ARG cc_start: 0.8062 (ptp90) cc_final: 0.7839 (ptp-170) REVERT: C 906 PHE cc_start: 0.7762 (m-80) cc_final: 0.7349 (m-80) REVERT: C 951 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8854 (m) REVERT: C 1038 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8814 (mtmm) REVERT: C 1125 ASN cc_start: 0.8246 (t0) cc_final: 0.7924 (t0) REVERT: C 1135 ASN cc_start: 0.8312 (m-40) cc_final: 0.7974 (m110) REVERT: C 1139 ASP cc_start: 0.8881 (t0) cc_final: 0.8681 (p0) REVERT: C 1203 LEU cc_start: 0.9078 (tt) cc_final: 0.8827 (tm) outliers start: 69 outliers final: 33 residues processed: 244 average time/residue: 0.4438 time to fit residues: 120.6167 Evaluate side-chains 215 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1054 GLN Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1153 ASP Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1227 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 27 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 112 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1048 HIS B1054 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN A1054 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN A1208 GLN C1088 HIS C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.110201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.087411 restraints weight = 32807.369| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.59 r_work: 0.3412 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12732 Z= 0.206 Angle : 0.872 12.339 17394 Z= 0.402 Chirality : 0.050 0.570 2184 Planarity : 0.004 0.062 2121 Dihedral : 11.326 113.649 2768 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.83 % Allowed : 27.43 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.31 (0.22), residues: 1512 helix: 1.76 (0.19), residues: 747 sheet: -0.81 (0.38), residues: 171 loop : -1.56 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 905 TYR 0.033 0.002 TYR C 917 PHE 0.019 0.002 PHE A1220 TRP 0.026 0.002 TRP B 886 HIS 0.018 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00455 (12663) covalent geometry : angle 0.81809 (17202) SS BOND : bond 0.00850 ( 15) SS BOND : angle 1.90438 ( 30) hydrogen bonds : bond 0.03949 ( 710) hydrogen bonds : angle 4.60819 ( 2010) link_ALPHA1-3 : bond 0.00529 ( 6) link_ALPHA1-3 : angle 1.70193 ( 18) link_ALPHA1-4 : bond 0.01746 ( 9) link_ALPHA1-4 : angle 3.03283 ( 27) link_BETA1-4 : bond 0.00237 ( 15) link_BETA1-4 : angle 1.49545 ( 45) link_NAG-ASN : bond 0.00617 ( 24) link_NAG-ASN : angle 4.07709 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 194 time to evaluate : 0.587 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: B 902 MET cc_start: 0.7861 (ttt) cc_final: 0.7460 (ttt) REVERT: B 909 ILE cc_start: 0.8696 (mt) cc_final: 0.8319 (tt) REVERT: B 928 ASN cc_start: 0.8995 (t0) cc_final: 0.8762 (t0) REVERT: B 954 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8674 (tm-30) REVERT: B 1139 ASP cc_start: 0.8835 (t70) cc_final: 0.8467 (p0) REVERT: B 1197 LEU cc_start: 0.8752 (mm) cc_final: 0.8423 (tm) REVERT: A 902 MET cc_start: 0.7932 (ttt) cc_final: 0.7518 (ttt) REVERT: A 905 ARG cc_start: 0.8119 (ptp90) cc_final: 0.7243 (ptp90) REVERT: A 909 ILE cc_start: 0.8804 (mt) cc_final: 0.8545 (pp) REVERT: A 1135 ASN cc_start: 0.8187 (m110) cc_final: 0.7687 (m-40) REVERT: A 1208 GLN cc_start: 0.3757 (OUTLIER) cc_final: 0.3001 (pp30) REVERT: C 770 ILE cc_start: 0.9196 (tp) cc_final: 0.8966 (pp) REVERT: C 905 ARG cc_start: 0.8165 (ptp90) cc_final: 0.7859 (ptp-170) REVERT: C 906 PHE cc_start: 0.7806 (m-80) cc_final: 0.7302 (m-80) REVERT: C 951 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8699 (m) REVERT: C 1038 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8815 (mtmm) REVERT: C 1125 ASN cc_start: 0.8181 (t0) cc_final: 0.7917 (t0) REVERT: C 1135 ASN cc_start: 0.8274 (m-40) cc_final: 0.7949 (m110) REVERT: C 1139 ASP cc_start: 0.8863 (t0) cc_final: 0.8662 (p0) REVERT: C 1203 LEU cc_start: 0.9039 (tt) cc_final: 0.8785 (tm) REVERT: C 1205 LYS cc_start: 0.8263 (mppt) cc_final: 0.7732 (mppt) outliers start: 63 outliers final: 35 residues processed: 242 average time/residue: 0.4545 time to fit residues: 122.3030 Evaluate side-chains 218 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1227 ILE Chi-restraints excluded: chain C residue 1244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1048 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 965 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN C1088 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.109643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.086294 restraints weight = 32507.733| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.60 r_work: 0.3396 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12732 Z= 0.234 Angle : 0.902 12.397 17394 Z= 0.418 Chirality : 0.051 0.548 2184 Planarity : 0.004 0.040 2121 Dihedral : 11.324 115.466 2768 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.52 % Allowed : 27.97 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.36 (0.22), residues: 1512 helix: 1.78 (0.19), residues: 750 sheet: -0.87 (0.38), residues: 171 loop : -1.48 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 847 TYR 0.021 0.002 TYR C 917 PHE 0.017 0.002 PHE A1220 TRP 0.029 0.002 TRP B 886 HIS 0.020 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00518 (12663) covalent geometry : angle 0.85236 (17202) SS BOND : bond 0.00966 ( 15) SS BOND : angle 1.94747 ( 30) hydrogen bonds : bond 0.04092 ( 710) hydrogen bonds : angle 4.62907 ( 2010) link_ALPHA1-3 : bond 0.00497 ( 6) link_ALPHA1-3 : angle 1.69780 ( 18) link_ALPHA1-4 : bond 0.01766 ( 9) link_ALPHA1-4 : angle 3.08239 ( 27) link_BETA1-4 : bond 0.00205 ( 15) link_BETA1-4 : angle 1.47064 ( 45) link_NAG-ASN : bond 0.00505 ( 24) link_NAG-ASN : angle 3.94564 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.450 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: B 902 MET cc_start: 0.7988 (ttt) cc_final: 0.7500 (ttp) REVERT: B 909 ILE cc_start: 0.8708 (mt) cc_final: 0.8344 (tt) REVERT: B 928 ASN cc_start: 0.8978 (t0) cc_final: 0.8762 (t0) REVERT: B 954 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8621 (tm-30) REVERT: B 1139 ASP cc_start: 0.8844 (t70) cc_final: 0.8459 (p0) REVERT: B 1197 LEU cc_start: 0.8728 (mm) cc_final: 0.8417 (tm) REVERT: A 905 ARG cc_start: 0.8114 (ptp90) cc_final: 0.7280 (ptp90) REVERT: A 909 ILE cc_start: 0.8815 (mt) cc_final: 0.8560 (pp) REVERT: A 1135 ASN cc_start: 0.8213 (m110) cc_final: 0.7705 (m-40) REVERT: A 1139 ASP cc_start: 0.8890 (t0) cc_final: 0.8433 (p0) REVERT: C 770 ILE cc_start: 0.9193 (tp) cc_final: 0.8983 (pp) REVERT: C 905 ARG cc_start: 0.8211 (ptp90) cc_final: 0.7886 (ptp-170) REVERT: C 906 PHE cc_start: 0.7868 (m-80) cc_final: 0.7342 (m-80) REVERT: C 1038 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8822 (mtmm) REVERT: C 1125 ASN cc_start: 0.8150 (t0) cc_final: 0.7936 (t0) REVERT: C 1135 ASN cc_start: 0.8299 (m-40) cc_final: 0.7874 (m-40) REVERT: C 1139 ASP cc_start: 0.8875 (t0) cc_final: 0.8641 (p0) REVERT: C 1144 GLU cc_start: 0.8361 (tt0) cc_final: 0.7572 (tm-30) REVERT: C 1166 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8819 (mp) REVERT: C 1203 LEU cc_start: 0.9071 (tt) cc_final: 0.8819 (tm) outliers start: 59 outliers final: 37 residues processed: 226 average time/residue: 0.4395 time to fit residues: 110.5222 Evaluate side-chains 217 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1054 GLN Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1153 ASP Chi-restraints excluded: chain B residue 1175 SER Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1166 LEU Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1227 ILE Chi-restraints excluded: chain C residue 1244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 5 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 89 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 913 GLN B 969 ASN B1048 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1054 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS A1208 GLN C1088 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.109872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.086398 restraints weight = 32744.986| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.64 r_work: 0.3401 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.7098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12732 Z= 0.201 Angle : 0.916 14.888 17394 Z= 0.419 Chirality : 0.050 0.568 2184 Planarity : 0.004 0.033 2121 Dihedral : 11.121 114.111 2768 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.91 % Allowed : 28.20 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.37 (0.22), residues: 1512 helix: 1.76 (0.19), residues: 750 sheet: -0.90 (0.38), residues: 171 loop : -1.44 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 905 TYR 0.021 0.002 TYR C 917 PHE 0.021 0.002 PHE A1220 TRP 0.032 0.002 TRP B 886 HIS 0.021 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00444 (12663) covalent geometry : angle 0.86357 (17202) SS BOND : bond 0.00822 ( 15) SS BOND : angle 1.83238 ( 30) hydrogen bonds : bond 0.03996 ( 710) hydrogen bonds : angle 4.64324 ( 2010) link_ALPHA1-3 : bond 0.00513 ( 6) link_ALPHA1-3 : angle 1.70492 ( 18) link_ALPHA1-4 : bond 0.01790 ( 9) link_ALPHA1-4 : angle 3.05751 ( 27) link_BETA1-4 : bond 0.00233 ( 15) link_BETA1-4 : angle 1.40394 ( 45) link_NAG-ASN : bond 0.00537 ( 24) link_NAG-ASN : angle 4.17836 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.363 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: B 905 ARG cc_start: 0.8129 (ptp90) cc_final: 0.7838 (ptp90) REVERT: B 909 ILE cc_start: 0.8663 (mt) cc_final: 0.8292 (tt) REVERT: B 928 ASN cc_start: 0.9019 (t0) cc_final: 0.8758 (t0) REVERT: B 954 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8674 (tp40) REVERT: B 1139 ASP cc_start: 0.8859 (t70) cc_final: 0.8444 (p0) REVERT: B 1197 LEU cc_start: 0.8725 (mm) cc_final: 0.8412 (tm) REVERT: A 869 MET cc_start: 0.8091 (ptp) cc_final: 0.7871 (pmm) REVERT: A 905 ARG cc_start: 0.8150 (ptp90) cc_final: 0.7144 (ptp90) REVERT: A 909 ILE cc_start: 0.8773 (mt) cc_final: 0.8524 (pp) REVERT: A 1135 ASN cc_start: 0.8134 (m110) cc_final: 0.7606 (m-40) REVERT: A 1139 ASP cc_start: 0.8911 (t0) cc_final: 0.8447 (p0) REVERT: C 864 LEU cc_start: 0.7961 (mp) cc_final: 0.7645 (mp) REVERT: C 905 ARG cc_start: 0.8229 (ptp90) cc_final: 0.7832 (ptp-170) REVERT: C 906 PHE cc_start: 0.7878 (m-80) cc_final: 0.7433 (m-80) REVERT: C 951 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8707 (m) REVERT: C 1038 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8839 (mtmm) REVERT: C 1135 ASN cc_start: 0.8266 (m110) cc_final: 0.7850 (m-40) REVERT: C 1139 ASP cc_start: 0.8880 (t0) cc_final: 0.8606 (p0) REVERT: C 1144 GLU cc_start: 0.8346 (tt0) cc_final: 0.7557 (tm-30) REVERT: C 1205 LYS cc_start: 0.8292 (mppt) cc_final: 0.7744 (mppt) outliers start: 51 outliers final: 30 residues processed: 224 average time/residue: 0.4562 time to fit residues: 113.1315 Evaluate side-chains 212 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1054 GLN Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1153 ASP Chi-restraints excluded: chain B residue 1175 SER Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1227 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 90 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 117 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN B1048 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN C1088 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.109217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.085666 restraints weight = 32874.969| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.63 r_work: 0.3387 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.7281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12732 Z= 0.226 Angle : 0.941 13.750 17394 Z= 0.430 Chirality : 0.052 0.605 2184 Planarity : 0.004 0.032 2121 Dihedral : 11.052 115.458 2766 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.30 % Allowed : 29.58 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.42 (0.22), residues: 1512 helix: 1.81 (0.19), residues: 753 sheet: -0.94 (0.38), residues: 171 loop : -1.41 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 905 TYR 0.021 0.002 TYR C 917 PHE 0.019 0.002 PHE A1220 TRP 0.035 0.002 TRP B 886 HIS 0.021 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00501 (12663) covalent geometry : angle 0.88764 (17202) SS BOND : bond 0.00904 ( 15) SS BOND : angle 1.92606 ( 30) hydrogen bonds : bond 0.04033 ( 710) hydrogen bonds : angle 4.63713 ( 2010) link_ALPHA1-3 : bond 0.00470 ( 6) link_ALPHA1-3 : angle 1.72629 ( 18) link_ALPHA1-4 : bond 0.01816 ( 9) link_ALPHA1-4 : angle 3.11651 ( 27) link_BETA1-4 : bond 0.00216 ( 15) link_BETA1-4 : angle 1.46130 ( 45) link_NAG-ASN : bond 0.00618 ( 24) link_NAG-ASN : angle 4.26699 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.485 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: B 770 ILE cc_start: 0.8987 (mp) cc_final: 0.8728 (pp) REVERT: B 909 ILE cc_start: 0.8674 (mt) cc_final: 0.8312 (tt) REVERT: B 928 ASN cc_start: 0.8992 (t0) cc_final: 0.8732 (t0) REVERT: B 954 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8671 (tp40) REVERT: B 1139 ASP cc_start: 0.8857 (t70) cc_final: 0.8443 (p0) REVERT: B 1197 LEU cc_start: 0.8725 (mm) cc_final: 0.8422 (tm) REVERT: A 869 MET cc_start: 0.8183 (ptp) cc_final: 0.7798 (pmm) REVERT: A 905 ARG cc_start: 0.8097 (ptp90) cc_final: 0.7258 (ptp90) REVERT: A 909 ILE cc_start: 0.8770 (mt) cc_final: 0.8514 (pp) REVERT: A 1038 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8918 (mttm) REVERT: A 1135 ASN cc_start: 0.8152 (m110) cc_final: 0.7626 (m-40) REVERT: A 1139 ASP cc_start: 0.8916 (t0) cc_final: 0.8469 (p0) REVERT: C 905 ARG cc_start: 0.8109 (ptp90) cc_final: 0.7803 (ptp-170) REVERT: C 906 PHE cc_start: 0.7825 (m-80) cc_final: 0.7372 (m-80) REVERT: C 1038 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8839 (mtmm) REVERT: C 1135 ASN cc_start: 0.8239 (m110) cc_final: 0.7813 (m-40) REVERT: C 1139 ASP cc_start: 0.8884 (t0) cc_final: 0.8560 (p0) REVERT: C 1144 GLU cc_start: 0.8305 (tt0) cc_final: 0.7566 (tm-30) REVERT: C 1205 LYS cc_start: 0.8290 (mppt) cc_final: 0.7740 (mppt) REVERT: C 1229 MET cc_start: 0.7894 (tmm) cc_final: 0.7667 (tpp) outliers start: 43 outliers final: 35 residues processed: 215 average time/residue: 0.4716 time to fit residues: 112.1441 Evaluate side-chains 217 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1054 GLN Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1153 ASP Chi-restraints excluded: chain B residue 1169 ILE Chi-restraints excluded: chain B residue 1175 SER Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1175 SER Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1227 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 103 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN B1048 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN C1088 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.109161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.085628 restraints weight = 33089.088| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.63 r_work: 0.3388 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.7371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12732 Z= 0.227 Angle : 0.942 13.457 17394 Z= 0.431 Chirality : 0.052 0.584 2184 Planarity : 0.004 0.087 2121 Dihedral : 11.008 115.447 2766 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.22 % Allowed : 29.43 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.36 (0.22), residues: 1512 helix: 1.75 (0.19), residues: 753 sheet: -0.99 (0.38), residues: 171 loop : -1.41 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 905 TYR 0.020 0.002 TYR C 917 PHE 0.019 0.002 PHE B1220 TRP 0.033 0.002 TRP B 886 HIS 0.021 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00502 (12663) covalent geometry : angle 0.89016 (17202) SS BOND : bond 0.00908 ( 15) SS BOND : angle 1.91527 ( 30) hydrogen bonds : bond 0.04051 ( 710) hydrogen bonds : angle 4.67955 ( 2010) link_ALPHA1-3 : bond 0.00480 ( 6) link_ALPHA1-3 : angle 1.74318 ( 18) link_ALPHA1-4 : bond 0.01871 ( 9) link_ALPHA1-4 : angle 3.16143 ( 27) link_BETA1-4 : bond 0.00209 ( 15) link_BETA1-4 : angle 1.47054 ( 45) link_NAG-ASN : bond 0.00526 ( 24) link_NAG-ASN : angle 4.19599 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.28 seconds wall clock time: 81 minutes 20.95 seconds (4880.95 seconds total)