Starting phenix.real_space_refine on Wed Feb 4 04:24:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xog_33347/02_2026/7xog_33347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xog_33347/02_2026/7xog_33347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xog_33347/02_2026/7xog_33347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xog_33347/02_2026/7xog_33347.map" model { file = "/net/cci-nas-00/data/ceres_data/7xog_33347/02_2026/7xog_33347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xog_33347/02_2026/7xog_33347.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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 36 5.16 5 C 5469 2.51 5 N 1416 2.21 5 O 1887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8808 Number of models: 1 Model: "" Number of chains: 21 Chain: "C" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2688 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 11, 'TRANS': 336} Chain breaks: 5 Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2688 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 11, 'TRANS': 336} Chain breaks: 4 Chain: "B" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2688 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 11, 'TRANS': 336} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: 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: "G" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: 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: "L" 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: "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: 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: "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: 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: "Q" 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: "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: "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 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: "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 Time building chain proxies: 2.38, per 1000 atoms: 0.27 Number of scatterers: 8808 At special positions: 0 Unit cell: (78.1, 75.9, 231, 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 36 16.00 O 1887 8.00 N 1416 7.00 C 5469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.04 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.88 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.02 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.02 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.04 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.63 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.02 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.02 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.04 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.77 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.02 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 E 3 " - " MAN E 4 " " MAN F 3 " - " MAN F 4 " " MAN J 3 " - " MAN J 4 " " MAN K 3 " - " MAN K 4 " " MAN O 3 " - " MAN O 4 " " MAN P 3 " - " MAN P 4 " ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " " NAG G 2 " - " MAN G 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG L 2 " - " MAN L 3 " " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 3 " " NAG Q 2 " - " MAN Q 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 A1303 " - " ASN A 706 " " NAG A1304 " - " ASN A 714 " " NAG B1304 " - " ASN B 706 " " NAG B1305 " - " ASN B 714 " " NAG C1302 " - " ASN C 706 " " NAG C1303 " - " ASN C 714 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 305.6 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 52.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.737A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 766 removed outlier: 3.637A pdb=" N ALA C 763 " --> pdb=" O GLN C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 988 removed outlier: 3.524A pdb=" N ASN C 950 " --> pdb=" O GLN C 946 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1031 removed outlier: 3.617A pdb=" N GLN C 999 " --> pdb=" O THR C 995 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C1000 " --> pdb=" O GLY C 996 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C1017 " --> pdb=" O ALA C1013 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS C1029 " --> pdb=" O LYS C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1144 through 1151 Processing helix chain 'C' and resid 1165 through 1169 Processing helix chain 'C' and resid 1178 through 1190 Processing helix chain 'C' and resid 1191 through 1194 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.739A pdb=" N LEU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 766 removed outlier: 3.637A pdb=" N ALA A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 988 removed outlier: 3.524A pdb=" N ASN A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1031 removed outlier: 3.617A pdb=" N GLN A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A1000 " --> pdb=" O GLY A 996 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS A1029 " --> pdb=" O LYS A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1151 Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1191 through 1194 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.739A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 766 removed outlier: 3.638A pdb=" N ALA B 763 " --> pdb=" O GLN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 987 removed outlier: 3.524A pdb=" N ASN B 950 " --> pdb=" O GLN B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1031 removed outlier: 3.617A pdb=" N GLN B 999 " --> pdb=" O THR B 995 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B1000 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B1017 " --> pdb=" O ALA B1013 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS B1029 " --> pdb=" O LYS B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1151 Processing helix chain 'B' and resid 1165 through 1169 Processing helix chain 'B' and resid 1178 through 1190 Processing helix chain 'B' and resid 1191 through 1194 Processing sheet with id=AA1, first strand: chain 'C' and resid 707 through 711 removed outlier: 4.715A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 1044 through 1053 removed outlier: 5.578A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 1078 through 1080 Processing sheet with id=AA4, first strand: chain 'C' and resid 1126 through 1131 removed outlier: 6.066A pdb=" N VAL C1126 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR B 721 " --> pdb=" O VAL C1126 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY C1128 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE B 723 " --> pdb=" O GLY C1128 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C1130 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 707 through 711 removed outlier: 4.713A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1044 through 1053 removed outlier: 5.577A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N VAL B1126 " --> pdb=" O PHE A 715 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 717 " --> pdb=" O VAL B1126 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLY B1128 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 719 " --> pdb=" O GLY B1128 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL B1130 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR A 721 " --> pdb=" O VAL B1130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1078 through 1080 Processing sheet with id=AA8, first strand: chain 'B' and resid 707 through 711 removed outlier: 4.714A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1078 through 1080 525 hydrogen bonds defined for protein. 1491 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: 1.33 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.55: 8815 1.55 - 1.90: 98 1.90 - 2.25: 0 2.25 - 2.60: 5 2.60 - 2.95: 7 Bond restraints: 8925 Sorted by residual: bond pdb=" C THR B 713 " pdb=" N ASN B 714 " ideal model delta sigma weight residual 1.331 2.927 -1.596 1.22e-02 6.72e+03 1.71e+04 bond pdb=" C GLN C1068 " pdb=" N GLU C1069 " ideal model delta sigma weight residual 1.331 2.946 -1.615 1.25e-02 6.40e+03 1.67e+04 bond pdb=" C GLN A1068 " pdb=" N GLU A1069 " ideal model delta sigma weight residual 1.331 2.929 -1.598 1.24e-02 6.50e+03 1.66e+04 bond pdb=" C THR C 713 " pdb=" N ASN C 714 " ideal model delta sigma weight residual 1.331 2.703 -1.372 1.22e-02 6.72e+03 1.26e+04 bond pdb=" C GLY A1032 " pdb=" N GLN A1033 " ideal model delta sigma weight residual 1.330 2.897 -1.567 1.41e-02 5.03e+03 1.23e+04 ... (remaining 8920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.97: 12073 11.97 - 23.94: 8 23.94 - 35.92: 12 35.92 - 47.89: 6 47.89 - 59.86: 6 Bond angle restraints: 12105 Sorted by residual: angle pdb=" O GLU B 987 " pdb=" C GLU B 987 " pdb=" N VAL B 988 " ideal model delta sigma weight residual 122.59 62.73 59.86 1.33e+00 5.65e-01 2.03e+03 angle pdb=" O GLU A 987 " pdb=" C GLU A 987 " pdb=" N VAL A 988 " ideal model delta sigma weight residual 122.59 70.20 52.39 1.33e+00 5.65e-01 1.55e+03 angle pdb=" O GLY A1032 " pdb=" C GLY A1032 " pdb=" N GLN A1033 " ideal model delta sigma weight residual 123.37 90.29 33.08 8.80e-01 1.29e+00 1.41e+03 angle pdb=" CA GLU B 987 " pdb=" C GLU B 987 " pdb=" N VAL B 988 " ideal model delta sigma weight residual 116.84 175.25 -58.41 1.71e+00 3.42e-01 1.17e+03 angle pdb=" O GLU C 987 " pdb=" C GLU C 987 " pdb=" N VAL C 988 " ideal model delta sigma weight residual 122.59 79.56 43.03 1.33e+00 5.65e-01 1.05e+03 ... (remaining 12100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 5700 24.83 - 49.65: 335 49.65 - 74.48: 40 74.48 - 99.30: 54 99.30 - 124.13: 9 Dihedral angle restraints: 6138 sinusoidal: 3102 harmonic: 3036 Sorted by residual: dihedral pdb=" CA GLU B 987 " pdb=" C GLU B 987 " pdb=" N VAL B 988 " pdb=" CA VAL B 988 " ideal model delta harmonic sigma weight residual -180.00 -111.30 -68.70 0 5.00e+00 4.00e-02 1.89e+02 dihedral pdb=" CB CYS C1029 " pdb=" SG CYS C1029 " pdb=" SG CYS C1040 " pdb=" CB CYS C1040 " ideal model delta sinusoidal sigma weight residual 93.00 167.73 -74.73 1 1.00e+01 1.00e-02 7.07e+01 dihedral pdb=" N ASN A 706 " pdb=" C ASN A 706 " pdb=" CA ASN A 706 " pdb=" CB ASN A 706 " ideal model delta harmonic sigma weight residual 122.80 141.19 -18.39 0 2.50e+00 1.60e-01 5.41e+01 ... (remaining 6135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 1464 0.170 - 0.340: 106 0.340 - 0.510: 8 0.510 - 0.679: 3 0.679 - 0.849: 3 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA ASN A 706 " pdb=" N ASN A 706 " pdb=" C ASN A 706 " pdb=" CB ASN A 706 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" CA ASN B 706 " pdb=" N ASN B 706 " pdb=" C ASN B 706 " pdb=" CB ASN B 706 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.79e+01 chirality pdb=" CA ASN C 706 " pdb=" N ASN C 706 " pdb=" C ASN C 706 " pdb=" CB ASN C 706 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.85 2.00e-01 2.50e+01 1.79e+01 ... (remaining 1581 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A1152 " -0.131 2.00e-02 2.50e+03 1.66e-01 2.76e+02 pdb=" C TYR A1152 " 0.284 2.00e-02 2.50e+03 pdb=" O TYR A1152 " -0.098 2.00e-02 2.50e+03 pdb=" N PHE A1153 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B1152 " 0.123 2.00e-02 2.50e+03 1.61e-01 2.59e+02 pdb=" C TYR B1152 " -0.276 2.00e-02 2.50e+03 pdb=" O TYR B1152 " 0.091 2.00e-02 2.50e+03 pdb=" N PHE B1153 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1032 " -0.120 2.00e-02 2.50e+03 1.59e-01 2.53e+02 pdb=" C GLY A1032 " 0.271 2.00e-02 2.50e+03 pdb=" O GLY A1032 " -0.104 2.00e-02 2.50e+03 pdb=" N GLN A1033 " -0.047 2.00e-02 2.50e+03 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 6 2.17 - 2.85: 2284 2.85 - 3.53: 12313 3.53 - 4.22: 19098 4.22 - 4.90: 32772 Nonbonded interactions: 66473 Sorted by model distance: nonbonded pdb=" CB ASN B1131 " pdb=" C6 MAN P 4 " model vdw 1.481 3.840 nonbonded pdb=" CB ASN B1131 " pdb=" O6 MAN P 4 " model vdw 1.614 3.440 nonbonded pdb=" CG2 ILE B 723 " pdb=" O6 MAN F 4 " model vdw 2.122 3.460 nonbonded pdb=" O ASP C1143 " pdb=" NH2 ARG B 997 " model vdw 2.131 3.120 nonbonded pdb=" CG1 ILE B 723 " pdb=" O6 MAN F 4 " model vdw 2.159 3.440 ... (remaining 66468 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.600 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.040 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 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 : 0.052 1.615 8973 Z= 3.931 Angle : 2.941 59.862 12237 Z= 1.858 Chirality : 0.107 0.849 1584 Planarity : 0.014 0.166 1479 Dihedral : 17.977 124.127 4122 Min Nonbonded Distance : 1.481 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.61 % Allowed : 7.82 % Favored : 89.58 % Cbeta Deviations : 1.82 % 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: -2.67 (0.22), residues: 984 helix: -1.88 (0.18), residues: 474 sheet: 0.38 (0.56), residues: 72 loop : -1.90 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1011 TYR 0.120 0.031 TYR A 704 PHE 0.046 0.010 PHE A1100 TRP 0.115 0.048 TRP C1099 HIS 0.015 0.003 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.05060 ( 8925) covalent geometry : angle 2.66344 (12105) SS BOND : bond 0.36764 ( 12) SS BOND : angle 22.69612 ( 24) hydrogen bonds : bond 0.21224 ( 525) hydrogen bonds : angle 8.41590 ( 1491) link_ALPHA1-3 : bond 0.00653 ( 6) link_ALPHA1-3 : angle 1.85201 ( 18) link_ALPHA1-4 : bond 0.00505 ( 9) link_ALPHA1-4 : angle 2.49407 ( 27) link_BETA1-4 : bond 0.00789 ( 15) link_BETA1-4 : angle 1.54171 ( 45) link_NAG-ASN : bond 0.19930 ( 6) link_NAG-ASN : angle 20.06876 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 3 residues processed: 220 average time/residue: 0.0844 time to fit residues: 26.8202 Evaluate side-chains 101 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1071 ASN Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain B residue 1071 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 700 ASN C 748 ASN C 917 GLN C 922 ASN ** C1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 HIS C1098 HIS A 700 ASN A 748 ASN A 922 ASN A 925 ASN A1002 GLN ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 HIS B 700 ASN B 748 ASN B 922 ASN B1061 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.086875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.070450 restraints weight = 42103.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.072373 restraints weight = 21989.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.073649 restraints weight = 14505.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.074547 restraints weight = 11026.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.075095 restraints weight = 9114.531| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8973 Z= 0.224 Angle : 0.936 12.176 12237 Z= 0.464 Chirality : 0.052 0.458 1584 Planarity : 0.005 0.045 1479 Dihedral : 14.326 111.073 2253 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.75 % Allowed : 11.29 % Favored : 82.95 % 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: -0.13 (0.25), residues: 1008 helix: 0.84 (0.22), residues: 495 sheet: -0.01 (0.44), residues: 127 loop : -1.30 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 762 TYR 0.019 0.002 TYR A1152 PHE 0.018 0.003 PHE A1145 TRP 0.011 0.004 TRP B1099 HIS 0.004 0.001 HIS C1098 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 8925) covalent geometry : angle 0.88102 (12105) SS BOND : bond 0.00328 ( 12) SS BOND : angle 3.63944 ( 24) hydrogen bonds : bond 0.05627 ( 525) hydrogen bonds : angle 5.47877 ( 1491) link_ALPHA1-3 : bond 0.01079 ( 6) link_ALPHA1-3 : angle 1.78619 ( 18) link_ALPHA1-4 : bond 0.01061 ( 9) link_ALPHA1-4 : angle 2.84404 ( 27) link_BETA1-4 : bond 0.00298 ( 15) link_BETA1-4 : angle 0.92900 ( 45) link_NAG-ASN : bond 0.00764 ( 6) link_NAG-ASN : angle 6.17509 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 94 time to evaluate : 0.352 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: A 743 SER cc_start: 0.6634 (OUTLIER) cc_final: 0.6418 (t) REVERT: A 1086 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.9163 (p90) REVERT: B 704 TYR cc_start: 0.8326 (m-80) cc_final: 0.8119 (m-80) REVERT: B 731 THR cc_start: 0.7953 (p) cc_final: 0.7719 (t) outliers start: 53 outliers final: 24 residues processed: 141 average time/residue: 0.0837 time to fit residues: 17.0908 Evaluate side-chains 97 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1005 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1071 ASN Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1134 VAL Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1193 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 759 GLN ** C1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1095 ASN A 759 GLN A1007 GLN A1098 HIS B 759 GLN B 910 GLN B1098 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.074509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.057360 restraints weight = 41790.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.059076 restraints weight = 22281.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.060215 restraints weight = 15171.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.060957 restraints weight = 11957.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.061432 restraints weight = 10261.262| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 8973 Z= 0.294 Angle : 0.945 11.652 12237 Z= 0.464 Chirality : 0.052 0.434 1584 Planarity : 0.005 0.041 1479 Dihedral : 13.385 112.733 2253 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.80 % Allowed : 16.50 % Favored : 79.70 % 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: 0.55 (0.26), residues: 1008 helix: 1.52 (0.22), residues: 474 sheet: 0.12 (0.43), residues: 139 loop : -0.94 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1182 TYR 0.019 0.002 TYR A1064 PHE 0.026 0.004 PHE A1092 TRP 0.015 0.004 TRP C1099 HIS 0.006 0.002 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00655 ( 8925) covalent geometry : angle 0.90027 (12105) SS BOND : bond 0.00892 ( 12) SS BOND : angle 3.10410 ( 24) hydrogen bonds : bond 0.06949 ( 525) hydrogen bonds : angle 5.13919 ( 1491) link_ALPHA1-3 : bond 0.00615 ( 6) link_ALPHA1-3 : angle 1.62135 ( 18) link_ALPHA1-4 : bond 0.00946 ( 9) link_ALPHA1-4 : angle 2.63163 ( 27) link_BETA1-4 : bond 0.00344 ( 15) link_BETA1-4 : angle 1.57527 ( 45) link_NAG-ASN : bond 0.01303 ( 6) link_NAG-ASN : angle 5.42538 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 731 THR cc_start: 0.8716 (p) cc_final: 0.8335 (t) REVERT: B 724 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8669 (mp) outliers start: 35 outliers final: 18 residues processed: 98 average time/residue: 0.0962 time to fit residues: 12.9878 Evaluate side-chains 71 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 909 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1007 GLN A1098 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.075112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.057783 restraints weight = 43176.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.059571 restraints weight = 22422.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.060744 restraints weight = 15157.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.061497 restraints weight = 11885.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.061969 restraints weight = 10185.775| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8973 Z= 0.172 Angle : 0.783 11.049 12237 Z= 0.375 Chirality : 0.045 0.394 1584 Planarity : 0.004 0.036 1479 Dihedral : 12.386 108.839 2247 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.45 % Allowed : 15.96 % Favored : 79.59 % 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: 1.03 (0.26), residues: 1008 helix: 2.26 (0.22), residues: 477 sheet: 0.25 (0.43), residues: 139 loop : -1.21 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B1182 TYR 0.011 0.001 TYR A1064 PHE 0.011 0.002 PHE B1039 TRP 0.014 0.003 TRP B1099 HIS 0.003 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8925) covalent geometry : angle 0.73460 (12105) SS BOND : bond 0.00532 ( 12) SS BOND : angle 2.46875 ( 24) hydrogen bonds : bond 0.06093 ( 525) hydrogen bonds : angle 4.70045 ( 1491) link_ALPHA1-3 : bond 0.00657 ( 6) link_ALPHA1-3 : angle 1.45819 ( 18) link_ALPHA1-4 : bond 0.01432 ( 9) link_ALPHA1-4 : angle 2.96984 ( 27) link_BETA1-4 : bond 0.00302 ( 15) link_BETA1-4 : angle 0.92497 ( 45) link_NAG-ASN : bond 0.00919 ( 6) link_NAG-ASN : angle 5.26860 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 61 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 731 THR cc_start: 0.8734 (p) cc_final: 0.8492 (t) REVERT: B 724 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8648 (mp) outliers start: 41 outliers final: 23 residues processed: 96 average time/residue: 0.0835 time to fit residues: 11.7524 Evaluate side-chains 81 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 914 TYR Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 0.1980 chunk 68 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.072786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.055618 restraints weight = 40780.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.057340 restraints weight = 21564.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.058485 restraints weight = 14589.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.059226 restraints weight = 11404.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.059697 restraints weight = 9749.596| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.7487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8973 Z= 0.161 Angle : 0.757 11.007 12237 Z= 0.356 Chirality : 0.044 0.369 1584 Planarity : 0.004 0.032 1479 Dihedral : 11.697 105.605 2247 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.91 % Allowed : 17.48 % Favored : 78.61 % 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: 1.25 (0.26), residues: 1008 helix: 2.51 (0.22), residues: 477 sheet: 0.25 (0.43), residues: 139 loop : -1.15 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1088 TYR 0.010 0.001 TYR A1064 PHE 0.017 0.002 PHE C 924 TRP 0.010 0.002 TRP B1099 HIS 0.002 0.001 HIS A1098 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8925) covalent geometry : angle 0.70772 (12105) SS BOND : bond 0.00507 ( 12) SS BOND : angle 2.30197 ( 24) hydrogen bonds : bond 0.05904 ( 525) hydrogen bonds : angle 4.56423 ( 1491) link_ALPHA1-3 : bond 0.00594 ( 6) link_ALPHA1-3 : angle 1.49479 ( 18) link_ALPHA1-4 : bond 0.01517 ( 9) link_ALPHA1-4 : angle 3.16324 ( 27) link_BETA1-4 : bond 0.00291 ( 15) link_BETA1-4 : angle 0.98046 ( 45) link_NAG-ASN : bond 0.01025 ( 6) link_NAG-ASN : angle 5.15207 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 55 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: C 731 THR cc_start: 0.8754 (p) cc_final: 0.8498 (t) REVERT: A 743 SER cc_start: 0.7386 (OUTLIER) cc_final: 0.6960 (t) REVERT: B 724 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8639 (mp) REVERT: B 1031 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8543 (mt) outliers start: 36 outliers final: 23 residues processed: 85 average time/residue: 0.0886 time to fit residues: 10.8847 Evaluate side-chains 77 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 914 TYR Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 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 925 ASN ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.071940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054782 restraints weight = 40387.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.056497 restraints weight = 21585.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.057643 restraints weight = 14708.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.058369 restraints weight = 11569.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.058843 restraints weight = 9943.669| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.7857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8973 Z= 0.160 Angle : 0.742 10.969 12237 Z= 0.348 Chirality : 0.044 0.368 1584 Planarity : 0.003 0.032 1479 Dihedral : 11.126 104.323 2247 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.23 % Allowed : 18.02 % Favored : 77.74 % 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: 1.18 (0.26), residues: 1008 helix: 2.57 (0.22), residues: 477 sheet: -0.21 (0.43), residues: 139 loop : -1.17 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1182 TYR 0.010 0.001 TYR B1064 PHE 0.021 0.002 PHE C 924 TRP 0.009 0.002 TRP B1099 HIS 0.003 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8925) covalent geometry : angle 0.69114 (12105) SS BOND : bond 0.00590 ( 12) SS BOND : angle 2.09327 ( 24) hydrogen bonds : bond 0.05791 ( 525) hydrogen bonds : angle 4.50454 ( 1491) link_ALPHA1-3 : bond 0.00596 ( 6) link_ALPHA1-3 : angle 1.49355 ( 18) link_ALPHA1-4 : bond 0.01645 ( 9) link_ALPHA1-4 : angle 3.30493 ( 27) link_BETA1-4 : bond 0.00226 ( 15) link_BETA1-4 : angle 0.93761 ( 45) link_NAG-ASN : bond 0.00981 ( 6) link_NAG-ASN : angle 5.12736 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 53 time to evaluate : 0.321 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: A 743 SER cc_start: 0.7285 (OUTLIER) cc_final: 0.6931 (t) REVERT: B 724 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8711 (mp) REVERT: B 1031 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8583 (mt) outliers start: 39 outliers final: 26 residues processed: 86 average time/residue: 0.0916 time to fit residues: 11.1519 Evaluate side-chains 77 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 48 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 914 TYR Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 761 ASN C1131 ASN ** C1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1156 HIS A 952 ASN A1131 ASN A1184 ASN ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** 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 = 0.3608 r_free = 0.3608 target = 0.067713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.051108 restraints weight = 40233.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.052701 restraints weight = 22110.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.053771 restraints weight = 15345.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.054456 restraints weight = 12196.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.054902 restraints weight = 10565.196| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.8724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 8973 Z= 0.287 Angle : 0.880 12.346 12237 Z= 0.424 Chirality : 0.049 0.427 1584 Planarity : 0.005 0.059 1479 Dihedral : 11.868 109.634 2247 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.10 % Allowed : 17.92 % Favored : 76.98 % 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: 0.80 (0.25), residues: 1008 helix: 1.98 (0.22), residues: 477 sheet: -0.15 (0.40), residues: 139 loop : -1.05 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1182 TYR 0.021 0.002 TYR A1064 PHE 0.030 0.003 PHE C 924 TRP 0.004 0.002 TRP B1099 HIS 0.008 0.002 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 8925) covalent geometry : angle 0.83184 (12105) SS BOND : bond 0.01028 ( 12) SS BOND : angle 2.20974 ( 24) hydrogen bonds : bond 0.07088 ( 525) hydrogen bonds : angle 4.87178 ( 1491) link_ALPHA1-3 : bond 0.00512 ( 6) link_ALPHA1-3 : angle 1.66951 ( 18) link_ALPHA1-4 : bond 0.01466 ( 9) link_ALPHA1-4 : angle 3.17724 ( 27) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 1.63222 ( 45) link_NAG-ASN : bond 0.01068 ( 6) link_NAG-ASN : angle 5.49755 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 49 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 SER cc_start: 0.7392 (OUTLIER) cc_final: 0.7019 (t) REVERT: B 930 LYS cc_start: 0.7368 (tptt) cc_final: 0.7152 (tptt) REVERT: B 1031 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8689 (mt) outliers start: 47 outliers final: 30 residues processed: 91 average time/residue: 0.0709 time to fit residues: 9.3005 Evaluate side-chains 76 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 44 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 925 ASN A1131 ASN ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.070366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.053240 restraints weight = 42357.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.054952 restraints weight = 22421.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.056072 restraints weight = 15362.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.056813 restraints weight = 12169.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.057267 restraints weight = 10498.863| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.8774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8973 Z= 0.161 Angle : 0.784 11.415 12237 Z= 0.374 Chirality : 0.045 0.378 1584 Planarity : 0.004 0.032 1479 Dihedral : 11.221 107.136 2247 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.69 % Allowed : 19.54 % Favored : 76.76 % 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: 1.01 (0.26), residues: 1008 helix: 2.17 (0.22), residues: 477 sheet: 0.12 (0.41), residues: 139 loop : -1.05 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1182 TYR 0.012 0.001 TYR B1004 PHE 0.012 0.002 PHE C 924 TRP 0.008 0.002 TRP B1099 HIS 0.002 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8925) covalent geometry : angle 0.73416 (12105) SS BOND : bond 0.00507 ( 12) SS BOND : angle 2.17019 ( 24) hydrogen bonds : bond 0.06431 ( 525) hydrogen bonds : angle 4.67059 ( 1491) link_ALPHA1-3 : bond 0.00635 ( 6) link_ALPHA1-3 : angle 1.50218 ( 18) link_ALPHA1-4 : bond 0.01594 ( 9) link_ALPHA1-4 : angle 3.22924 ( 27) link_BETA1-4 : bond 0.00255 ( 15) link_BETA1-4 : angle 0.99260 ( 45) link_NAG-ASN : bond 0.01047 ( 6) link_NAG-ASN : angle 5.37178 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 46 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 SER cc_start: 0.7182 (OUTLIER) cc_final: 0.6818 (t) REVERT: B 1031 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8654 (mt) outliers start: 34 outliers final: 25 residues processed: 78 average time/residue: 0.0737 time to fit residues: 8.4858 Evaluate side-chains 70 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 914 TYR Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1155 ASN ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.070311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.053601 restraints weight = 41496.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.055260 restraints weight = 22089.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.056345 restraints weight = 15144.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.057043 restraints weight = 11996.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.057498 restraints weight = 10355.418| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.8879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8973 Z= 0.154 Angle : 0.771 11.199 12237 Z= 0.366 Chirality : 0.044 0.363 1584 Planarity : 0.004 0.031 1479 Dihedral : 10.696 103.364 2247 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 3.26 % Allowed : 20.74 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.06 (0.26), residues: 1008 helix: 2.39 (0.22), residues: 480 sheet: -0.23 (0.42), residues: 139 loop : -1.15 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1182 TYR 0.011 0.001 TYR B1004 PHE 0.010 0.001 PHE B1086 TRP 0.010 0.002 TRP B1099 HIS 0.005 0.001 HIS A1080 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8925) covalent geometry : angle 0.72140 (12105) SS BOND : bond 0.00576 ( 12) SS BOND : angle 2.05096 ( 24) hydrogen bonds : bond 0.06105 ( 525) hydrogen bonds : angle 4.52097 ( 1491) link_ALPHA1-3 : bond 0.00585 ( 6) link_ALPHA1-3 : angle 1.50410 ( 18) link_ALPHA1-4 : bond 0.01602 ( 9) link_ALPHA1-4 : angle 3.31342 ( 27) link_BETA1-4 : bond 0.00253 ( 15) link_BETA1-4 : angle 0.95181 ( 45) link_NAG-ASN : bond 0.01088 ( 6) link_NAG-ASN : angle 5.24576 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 SER cc_start: 0.7400 (OUTLIER) cc_final: 0.7064 (t) REVERT: B 1031 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8677 (mt) outliers start: 30 outliers final: 24 residues processed: 68 average time/residue: 0.0882 time to fit residues: 8.8644 Evaluate side-chains 67 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 41 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 914 TYR Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.0000 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1131 ASN ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.069414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.052824 restraints weight = 41644.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.054458 restraints weight = 22124.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.055551 restraints weight = 15180.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.056248 restraints weight = 12016.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.056702 restraints weight = 10371.033| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.9120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8973 Z= 0.169 Angle : 0.778 11.200 12237 Z= 0.369 Chirality : 0.045 0.369 1584 Planarity : 0.004 0.031 1479 Dihedral : 10.526 101.422 2247 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 2.93 % Allowed : 21.39 % Favored : 75.68 % 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: 1.10 (0.26), residues: 1008 helix: 2.43 (0.22), residues: 480 sheet: -0.24 (0.42), residues: 139 loop : -1.12 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1182 TYR 0.012 0.001 TYR B 914 PHE 0.011 0.002 PHE B1086 TRP 0.006 0.002 TRP B1099 HIS 0.003 0.001 HIS A1080 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8925) covalent geometry : angle 0.73070 (12105) SS BOND : bond 0.00701 ( 12) SS BOND : angle 1.95373 ( 24) hydrogen bonds : bond 0.06155 ( 525) hydrogen bonds : angle 4.55505 ( 1491) link_ALPHA1-3 : bond 0.00540 ( 6) link_ALPHA1-3 : angle 1.53022 ( 18) link_ALPHA1-4 : bond 0.01483 ( 9) link_ALPHA1-4 : angle 3.21598 ( 27) link_BETA1-4 : bond 0.00218 ( 15) link_BETA1-4 : angle 1.04336 ( 45) link_NAG-ASN : bond 0.01090 ( 6) link_NAG-ASN : angle 5.18411 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 SER cc_start: 0.7317 (OUTLIER) cc_final: 0.6993 (t) REVERT: B 1031 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8680 (mt) outliers start: 27 outliers final: 24 residues processed: 69 average time/residue: 0.0815 time to fit residues: 8.1454 Evaluate side-chains 66 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.068437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.051925 restraints weight = 41669.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.053568 restraints weight = 22362.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.054638 restraints weight = 15403.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.055328 restraints weight = 12229.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.055776 restraints weight = 10578.061| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.9476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8973 Z= 0.182 Angle : 0.796 11.274 12237 Z= 0.377 Chirality : 0.045 0.373 1584 Planarity : 0.004 0.033 1479 Dihedral : 10.548 102.219 2247 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 3.37 % Allowed : 21.17 % Favored : 75.46 % 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: 1.00 (0.26), residues: 1008 helix: 2.39 (0.22), residues: 480 sheet: -0.30 (0.41), residues: 139 loop : -1.23 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1182 TYR 0.012 0.001 TYR C1064 PHE 0.011 0.002 PHE B1086 TRP 0.007 0.002 TRP B1099 HIS 0.005 0.001 HIS A1080 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8925) covalent geometry : angle 0.74867 (12105) SS BOND : bond 0.00552 ( 12) SS BOND : angle 2.12557 ( 24) hydrogen bonds : bond 0.06272 ( 525) hydrogen bonds : angle 4.60936 ( 1491) link_ALPHA1-3 : bond 0.00546 ( 6) link_ALPHA1-3 : angle 1.52310 ( 18) link_ALPHA1-4 : bond 0.01468 ( 9) link_ALPHA1-4 : angle 3.17871 ( 27) link_BETA1-4 : bond 0.00176 ( 15) link_BETA1-4 : angle 1.10579 ( 45) link_NAG-ASN : bond 0.01057 ( 6) link_NAG-ASN : angle 5.20900 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.34 seconds wall clock time: 29 minutes 51.66 seconds (1791.66 seconds total)