Starting phenix.real_space_refine on Sat Jul 26 22:46:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xog_33347/07_2025/7xog_33347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xog_33347/07_2025/7xog_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_33347/07_2025/7xog_33347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xog_33347/07_2025/7xog_33347.map" model { file = "/net/cci-nas-00/data/ceres_data/7xog_33347/07_2025/7xog_33347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xog_33347/07_2025/7xog_33347.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.31, per 1000 atoms: 0.94 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: 2.93 Conformation dependent library (CDL) restraints added in 969.3 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: 0.88 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: 2.49 Time building geometry restraints manager: 3.37 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: 0.00 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: 6.970 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 26.470 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.115 0.048 TRP C1099 HIS 0.015 0.003 HIS B1045 PHE 0.046 0.010 PHE A1100 TYR 0.120 0.031 TYR A 704 ARG 0.004 0.001 ARG A1011 Details of bonding type rmsd link_NAG-ASN : bond 0.19930 ( 6) link_NAG-ASN : angle 20.06876 ( 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_ALPHA1-3 : bond 0.00653 ( 6) link_ALPHA1-3 : angle 1.85201 ( 18) hydrogen bonds : bond 0.21224 ( 525) hydrogen bonds : angle 8.41590 ( 1491) SS BOND : bond 0.36764 ( 12) SS BOND : angle 22.69612 ( 24) covalent geometry : bond 0.05060 ( 8925) covalent geometry : angle 2.66344 (12105) *********************** 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 : 0.989 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: 0.1877 time to fit residues: 58.5684 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 : 1.016 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 922 ASN ** C1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 HIS C1098 HIS A 700 ASN A 748 ASN A 759 GLN A 922 ASN A 925 ASN A1002 GLN ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 HIS A1098 HIS B 700 ASN B 748 ASN B 922 ASN B1061 HIS B1098 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.085861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.069514 restraints weight = 41450.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.071429 restraints weight = 21733.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.072698 restraints weight = 14326.340| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8973 Z= 0.237 Angle : 0.951 11.881 12237 Z= 0.471 Chirality : 0.053 0.442 1584 Planarity : 0.006 0.044 1479 Dihedral : 14.216 109.549 2253 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.65 % Allowed : 12.05 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1008 helix: 0.82 (0.22), residues: 495 sheet: 0.06 (0.44), residues: 127 loop : -1.30 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B1099 HIS 0.005 0.001 HIS C1098 PHE 0.028 0.003 PHE B 715 TYR 0.021 0.002 TYR A1152 ARG 0.004 0.001 ARG C1088 Details of bonding type rmsd link_NAG-ASN : bond 0.00810 ( 6) link_NAG-ASN : angle 5.99989 ( 18) link_ALPHA1-4 : bond 0.01096 ( 9) link_ALPHA1-4 : angle 2.83665 ( 27) link_BETA1-4 : bond 0.00333 ( 15) link_BETA1-4 : angle 0.93896 ( 45) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 1.82563 ( 18) hydrogen bonds : bond 0.05674 ( 525) hydrogen bonds : angle 5.44572 ( 1491) SS BOND : bond 0.00458 ( 12) SS BOND : angle 3.26773 ( 24) covalent geometry : bond 0.00507 ( 8925) covalent geometry : angle 0.90139 (12105) *********************** 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 149 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 0.925 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: 0.6609 (OUTLIER) cc_final: 0.6395 (t) REVERT: B 731 THR cc_start: 0.8045 (p) cc_final: 0.7813 (t) outliers start: 52 outliers final: 23 residues processed: 142 average time/residue: 0.1910 time to fit residues: 38.4330 Evaluate side-chains 95 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 913 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1134 VAL 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 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 1193 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN B 910 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.083229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.066264 restraints weight = 42544.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.068070 restraints weight = 22874.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.069249 restraints weight = 15560.376| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8973 Z= 0.170 Angle : 0.805 11.547 12237 Z= 0.393 Chirality : 0.045 0.383 1584 Planarity : 0.004 0.040 1479 Dihedral : 12.812 108.772 2253 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.15 % Allowed : 15.74 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1008 helix: 1.99 (0.23), residues: 495 sheet: 0.78 (0.47), residues: 109 loop : -1.24 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C1099 HIS 0.005 0.001 HIS C1080 PHE 0.014 0.002 PHE A1092 TYR 0.012 0.001 TYR C1152 ARG 0.004 0.001 ARG B1182 Details of bonding type rmsd link_NAG-ASN : bond 0.01033 ( 6) link_NAG-ASN : angle 5.53481 ( 18) link_ALPHA1-4 : bond 0.01375 ( 9) link_ALPHA1-4 : angle 2.88922 ( 27) link_BETA1-4 : bond 0.00321 ( 15) link_BETA1-4 : angle 0.87056 ( 45) link_ALPHA1-3 : bond 0.00702 ( 6) link_ALPHA1-3 : angle 1.55826 ( 18) hydrogen bonds : bond 0.05275 ( 525) hydrogen bonds : angle 4.88276 ( 1491) SS BOND : bond 0.00600 ( 12) SS BOND : angle 3.41010 ( 24) covalent geometry : bond 0.00348 ( 8925) covalent geometry : angle 0.74964 (12105) *********************** 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 104 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 731 THR cc_start: 0.8286 (p) cc_final: 0.7898 (t) REVERT: A 731 THR cc_start: 0.8575 (p) cc_final: 0.8325 (t) outliers start: 29 outliers final: 18 residues processed: 99 average time/residue: 0.2227 time to fit residues: 30.1058 Evaluate side-chains 81 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 1015 ILE Chi-restraints excluded: chain C residue 1071 ASN 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 909 THR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 914 TYR Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1193 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.0020 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 761 ASN C 923 GLN ** C1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.077111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.059956 restraints weight = 42147.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.061714 restraints weight = 22254.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.062871 restraints weight = 15085.457| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8973 Z= 0.212 Angle : 0.798 11.015 12237 Z= 0.387 Chirality : 0.046 0.398 1584 Planarity : 0.004 0.038 1479 Dihedral : 12.234 108.035 2249 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 3.80 % Allowed : 16.18 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1008 helix: 2.39 (0.23), residues: 477 sheet: 0.31 (0.43), residues: 139 loop : -1.22 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C1099 HIS 0.005 0.001 HIS A1080 PHE 0.022 0.002 PHE C 924 TYR 0.015 0.002 TYR A1064 ARG 0.004 0.001 ARG A 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00930 ( 6) link_NAG-ASN : angle 5.14924 ( 18) link_ALPHA1-4 : bond 0.01345 ( 9) link_ALPHA1-4 : angle 3.10050 ( 27) link_BETA1-4 : bond 0.00208 ( 15) link_BETA1-4 : angle 1.14882 ( 45) link_ALPHA1-3 : bond 0.00601 ( 6) link_ALPHA1-3 : angle 1.56941 ( 18) hydrogen bonds : bond 0.05736 ( 525) hydrogen bonds : angle 4.63755 ( 1491) SS BOND : bond 0.00638 ( 12) SS BOND : angle 2.04655 ( 24) covalent geometry : bond 0.00458 ( 8925) covalent geometry : angle 0.75236 (12105) *********************** 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 97 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 731 THR cc_start: 0.8544 (p) cc_final: 0.8067 (t) REVERT: A 731 THR cc_start: 0.8650 (p) cc_final: 0.8420 (t) REVERT: A 738 TYR cc_start: 0.8888 (t80) cc_final: 0.8676 (t80) outliers start: 35 outliers final: 21 residues processed: 92 average time/residue: 0.2093 time to fit residues: 27.1287 Evaluate side-chains 76 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1161 VAL 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 979 SER Chi-restraints excluded: chain A residue 988 VAL 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 1193 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 914 TYR 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 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 71 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 96 optimal weight: 0.0870 chunk 88 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1007 GLN A1007 GLN ** B1095 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 = 0.3790 r_free = 0.3790 target = 0.076155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.059162 restraints weight = 41604.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.060903 restraints weight = 22197.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.062046 restraints weight = 15111.724| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.6867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8973 Z= 0.165 Angle : 0.755 10.822 12237 Z= 0.360 Chirality : 0.044 0.372 1584 Planarity : 0.004 0.032 1479 Dihedral : 11.645 107.144 2247 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.58 % Allowed : 16.94 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1008 helix: 2.60 (0.22), residues: 477 sheet: -0.10 (0.44), residues: 139 loop : -1.20 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A1099 HIS 0.002 0.001 HIS C1080 PHE 0.024 0.002 PHE C 924 TYR 0.011 0.001 TYR A1064 ARG 0.002 0.000 ARG B1011 Details of bonding type rmsd link_NAG-ASN : bond 0.00979 ( 6) link_NAG-ASN : angle 5.04461 ( 18) link_ALPHA1-4 : bond 0.01615 ( 9) link_ALPHA1-4 : angle 3.13336 ( 27) link_BETA1-4 : bond 0.00248 ( 15) link_BETA1-4 : angle 0.88455 ( 45) link_ALPHA1-3 : bond 0.00599 ( 6) link_ALPHA1-3 : angle 1.45399 ( 18) hydrogen bonds : bond 0.05554 ( 525) hydrogen bonds : angle 4.46842 ( 1491) SS BOND : bond 0.00662 ( 12) SS BOND : angle 2.33241 ( 24) covalent geometry : bond 0.00345 ( 8925) covalent geometry : angle 0.70720 (12105) *********************** 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 88 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 1.034 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: 0.8700 (p) cc_final: 0.8388 (t) REVERT: C 740 CYS cc_start: 0.6334 (OUTLIER) cc_final: 0.6021 (t) REVERT: A 743 SER cc_start: 0.7286 (OUTLIER) cc_final: 0.6940 (t) REVERT: B 724 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8428 (mp) outliers start: 33 outliers final: 19 residues processed: 84 average time/residue: 0.1911 time to fit residues: 23.4942 Evaluate side-chains 71 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 1193 SER 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 1031 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1125 VAL 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 82 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1131 ASN ** C1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1156 HIS ** 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 = 0.3680 r_free = 0.3680 target = 0.070901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.053868 restraints weight = 42026.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.055528 restraints weight = 22862.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.056593 restraints weight = 15865.567| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.8125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8973 Z= 0.262 Angle : 0.858 11.393 12237 Z= 0.412 Chirality : 0.048 0.433 1584 Planarity : 0.004 0.032 1479 Dihedral : 11.844 108.518 2247 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.78 % Allowed : 17.26 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1008 helix: 2.18 (0.22), residues: 480 sheet: -0.35 (0.43), residues: 139 loop : -1.36 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP B1099 HIS 0.005 0.002 HIS B1085 PHE 0.019 0.003 PHE C 924 TYR 0.020 0.002 TYR A1064 ARG 0.005 0.001 ARG B1016 Details of bonding type rmsd link_NAG-ASN : bond 0.01008 ( 6) link_NAG-ASN : angle 5.36715 ( 18) link_ALPHA1-4 : bond 0.01489 ( 9) link_ALPHA1-4 : angle 3.17344 ( 27) link_BETA1-4 : bond 0.00367 ( 15) link_BETA1-4 : angle 1.50674 ( 45) link_ALPHA1-3 : bond 0.00487 ( 6) link_ALPHA1-3 : angle 1.65360 ( 18) hydrogen bonds : bond 0.06863 ( 525) hydrogen bonds : angle 4.72674 ( 1491) SS BOND : bond 0.00637 ( 12) SS BOND : angle 2.34747 ( 24) covalent geometry : bond 0.00574 ( 8925) covalent geometry : angle 0.80931 (12105) *********************** 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 95 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 51 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 SER cc_start: 0.7117 (OUTLIER) cc_final: 0.6675 (t) REVERT: A 751 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9399 (mm) REVERT: A 1089 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: B 1031 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8617 (mt) outliers start: 44 outliers final: 27 residues processed: 89 average time/residue: 0.1983 time to fit residues: 25.4212 Evaluate side-chains 78 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 47 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 751 LEU Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1089 GLU 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 735 CYS Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 764 LEU 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 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3700 r_free = 0.3700 target = 0.071712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.054710 restraints weight = 41773.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.056427 restraints weight = 22387.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.057535 restraints weight = 15305.924| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.8309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8973 Z= 0.170 Angle : 0.775 11.290 12237 Z= 0.369 Chirality : 0.045 0.379 1584 Planarity : 0.004 0.039 1479 Dihedral : 11.267 107.550 2247 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.80 % Allowed : 18.35 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1008 helix: 2.17 (0.22), residues: 480 sheet: -0.22 (0.43), residues: 139 loop : -1.20 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1099 HIS 0.002 0.001 HIS C1085 PHE 0.016 0.002 PHE C 924 TYR 0.011 0.001 TYR B 738 ARG 0.007 0.001 ARG C1182 Details of bonding type rmsd link_NAG-ASN : bond 0.01011 ( 6) link_NAG-ASN : angle 5.25642 ( 18) link_ALPHA1-4 : bond 0.01627 ( 9) link_ALPHA1-4 : angle 3.24535 ( 27) link_BETA1-4 : bond 0.00264 ( 15) link_BETA1-4 : angle 0.94479 ( 45) link_ALPHA1-3 : bond 0.00641 ( 6) link_ALPHA1-3 : angle 1.47470 ( 18) hydrogen bonds : bond 0.06287 ( 525) hydrogen bonds : angle 4.60440 ( 1491) SS BOND : bond 0.00573 ( 12) SS BOND : angle 2.51654 ( 24) covalent geometry : bond 0.00354 ( 8925) covalent geometry : angle 0.72332 (12105) *********************** 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 85 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 50 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 SER cc_start: 0.7009 (OUTLIER) cc_final: 0.6620 (t) REVERT: B 909 THR cc_start: 0.4817 (OUTLIER) cc_final: 0.4598 (p) REVERT: B 1031 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8626 (mt) outliers start: 35 outliers final: 21 residues processed: 81 average time/residue: 0.1748 time to fit residues: 20.9897 Evaluate side-chains 69 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 735 CYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1089 GLU 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 909 THR 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 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 71 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 925 ASN C1156 HIS ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.070892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.053786 restraints weight = 42486.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.055449 restraints weight = 23026.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.056544 restraints weight = 15934.353| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.8606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8973 Z= 0.185 Angle : 0.779 11.342 12237 Z= 0.373 Chirality : 0.045 0.381 1584 Planarity : 0.004 0.035 1479 Dihedral : 11.007 103.643 2247 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.02 % Allowed : 18.89 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1008 helix: 2.12 (0.22), residues: 480 sheet: -0.20 (0.42), residues: 139 loop : -1.33 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B1099 HIS 0.004 0.001 HIS B1085 PHE 0.047 0.002 PHE B 924 TYR 0.012 0.001 TYR A1064 ARG 0.006 0.000 ARG C1182 Details of bonding type rmsd link_NAG-ASN : bond 0.01053 ( 6) link_NAG-ASN : angle 5.22852 ( 18) link_ALPHA1-4 : bond 0.01493 ( 9) link_ALPHA1-4 : angle 3.29273 ( 27) link_BETA1-4 : bond 0.00172 ( 15) link_BETA1-4 : angle 1.08822 ( 45) link_ALPHA1-3 : bond 0.00540 ( 6) link_ALPHA1-3 : angle 1.53992 ( 18) hydrogen bonds : bond 0.06267 ( 525) hydrogen bonds : angle 4.59178 ( 1491) SS BOND : bond 0.00654 ( 12) SS BOND : angle 2.29990 ( 24) covalent geometry : bond 0.00396 ( 8925) covalent geometry : angle 0.72850 (12105) *********************** 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 85 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 48 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 SER cc_start: 0.7390 (OUTLIER) cc_final: 0.7018 (t) REVERT: B 1031 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8589 (mt) outliers start: 37 outliers final: 26 residues processed: 80 average time/residue: 0.1823 time to fit residues: 21.3197 Evaluate side-chains 70 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 42 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 750 LEU 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 735 CYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 979 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 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 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 10 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 0.0270 overall best weight: 0.9242 ------------------------------------------------------------------------------- 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** ** 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 = 0.3674 r_free = 0.3674 target = 0.070538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.053426 restraints weight = 42307.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.055124 restraints weight = 22796.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.056194 restraints weight = 15700.953| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.8830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8973 Z= 0.181 Angle : 0.799 11.320 12237 Z= 0.379 Chirality : 0.045 0.379 1584 Planarity : 0.004 0.034 1479 Dihedral : 10.893 104.172 2247 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Rotamer: Outliers : 3.37 % Allowed : 19.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1008 helix: 2.26 (0.22), residues: 480 sheet: -0.20 (0.43), residues: 139 loop : -1.22 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B1099 HIS 0.004 0.001 HIS A1080 PHE 0.040 0.002 PHE B 924 TYR 0.012 0.001 TYR A1064 ARG 0.003 0.000 ARG C1182 Details of bonding type rmsd link_NAG-ASN : bond 0.01018 ( 6) link_NAG-ASN : angle 5.24138 ( 18) link_ALPHA1-4 : bond 0.01534 ( 9) link_ALPHA1-4 : angle 3.22633 ( 27) link_BETA1-4 : bond 0.00194 ( 15) link_BETA1-4 : angle 1.02137 ( 45) link_ALPHA1-3 : bond 0.00567 ( 6) link_ALPHA1-3 : angle 1.50137 ( 18) hydrogen bonds : bond 0.06248 ( 525) hydrogen bonds : angle 4.55936 ( 1491) SS BOND : bond 0.00643 ( 12) SS BOND : angle 2.20544 ( 24) covalent geometry : bond 0.00385 ( 8925) covalent geometry : angle 0.75148 (12105) *********************** 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 75 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 44 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 SER cc_start: 0.7212 (OUTLIER) cc_final: 0.6899 (t) REVERT: B 1031 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8645 (mt) REVERT: B 1047 MET cc_start: 0.8435 (tpp) cc_final: 0.8232 (tpp) outliers start: 31 outliers final: 27 residues processed: 71 average time/residue: 0.1784 time to fit residues: 19.0808 Evaluate side-chains 69 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 40 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 750 LEU 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 735 CYS 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 979 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.069164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.052088 restraints weight = 42868.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.053781 restraints weight = 23122.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.054865 restraints weight = 15997.628| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.9209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8973 Z= 0.206 Angle : 0.816 11.379 12237 Z= 0.388 Chirality : 0.046 0.388 1584 Planarity : 0.004 0.035 1479 Dihedral : 10.965 104.044 2247 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 3.04 % Allowed : 20.63 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1008 helix: 2.17 (0.22), residues: 480 sheet: -0.34 (0.41), residues: 139 loop : -1.16 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1099 HIS 0.007 0.001 HIS A1045 PHE 0.035 0.002 PHE B 924 TYR 0.014 0.001 TYR B1064 ARG 0.005 0.001 ARG B1182 Details of bonding type rmsd link_NAG-ASN : bond 0.01044 ( 6) link_NAG-ASN : angle 5.28029 ( 18) link_ALPHA1-4 : bond 0.01472 ( 9) link_ALPHA1-4 : angle 3.15961 ( 27) link_BETA1-4 : bond 0.00220 ( 15) link_BETA1-4 : angle 1.20258 ( 45) link_ALPHA1-3 : bond 0.00609 ( 6) link_ALPHA1-3 : angle 1.58001 ( 18) hydrogen bonds : bond 0.06503 ( 525) hydrogen bonds : angle 4.68172 ( 1491) SS BOND : bond 0.00764 ( 12) SS BOND : angle 2.24934 ( 24) covalent geometry : bond 0.00448 ( 8925) covalent geometry : angle 0.76843 (12105) ********************** 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 71 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 43 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 SER cc_start: 0.7506 (OUTLIER) cc_final: 0.7194 (t) REVERT: B 1031 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8729 (mt) REVERT: B 1182 ARG cc_start: 0.8647 (tpp80) cc_final: 0.8180 (ttt180) outliers start: 28 outliers final: 25 residues processed: 69 average time/residue: 0.1857 time to fit residues: 19.4070 Evaluate side-chains 63 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 36 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 750 LEU 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 735 CYS 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 979 SER 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 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 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 39 optimal weight: 0.0770 chunk 64 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1131 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 = 0.3670 r_free = 0.3670 target = 0.070221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.053284 restraints weight = 42198.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.054976 restraints weight = 22577.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.056099 restraints weight = 15521.316| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.9255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8973 Z= 0.154 Angle : 0.778 11.190 12237 Z= 0.366 Chirality : 0.044 0.363 1584 Planarity : 0.004 0.038 1479 Dihedral : 10.481 103.401 2247 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.54 % Rotamer: Outliers : 2.50 % Allowed : 21.06 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1008 helix: 2.44 (0.22), residues: 480 sheet: -0.21 (0.42), residues: 139 loop : -1.15 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1099 HIS 0.004 0.001 HIS A1080 PHE 0.043 0.002 PHE B 924 TYR 0.011 0.001 TYR B1004 ARG 0.004 0.000 ARG A1088 Details of bonding type rmsd link_NAG-ASN : bond 0.01108 ( 6) link_NAG-ASN : angle 5.26698 ( 18) link_ALPHA1-4 : bond 0.01612 ( 9) link_ALPHA1-4 : angle 3.23679 ( 27) link_BETA1-4 : bond 0.00293 ( 15) link_BETA1-4 : angle 0.95489 ( 45) link_ALPHA1-3 : bond 0.00606 ( 6) link_ALPHA1-3 : angle 1.49180 ( 18) hydrogen bonds : bond 0.06053 ( 525) hydrogen bonds : angle 4.51853 ( 1491) SS BOND : bond 0.00560 ( 12) SS BOND : angle 2.05463 ( 24) covalent geometry : bond 0.00308 ( 8925) covalent geometry : angle 0.72907 (12105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4009.80 seconds wall clock time: 72 minutes 26.40 seconds (4346.40 seconds total)