Starting phenix.real_space_refine on Sat Dec 28 18:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xog_33347/12_2024/7xog_33347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xog_33347/12_2024/7xog_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_33347/12_2024/7xog_33347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xog_33347/12_2024/7xog_33347.map" model { file = "/net/cci-nas-00/data/ceres_data/7xog_33347/12_2024/7xog_33347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xog_33347/12_2024/7xog_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-5532/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: 8.29, 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: 2.71 Conformation dependent library (CDL) restraints added in 955.3 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: 0.86 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: 2.61 Time building geometry restraints manager: 3.04 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: 8.710 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.530 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.160 ------------------------------------------------------------------------------- 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 : 0.051 1.615 8925 Z= 3.223 Angle : 2.663 59.862 12105 Z= 1.786 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 *********************** 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 : 0.865 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: 0.1866 time to fit residues: 58.0175 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 : 1.012 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.5980 chunk 92 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B 700 ASN B 748 ASN B 922 ASN B1061 HIS B1098 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8925 Z= 0.312 Angle : 0.885 8.305 12105 Z= 0.452 Chirality : 0.052 0.438 1584 Planarity : 0.005 0.043 1479 Dihedral : 14.204 109.968 2253 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.43 % Allowed : 12.16 % Favored : 82.41 % 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: -0.08 (0.25), residues: 1008 helix: 0.86 (0.22), residues: 495 sheet: 0.14 (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 0.004 0.001 HIS C1098 PHE 0.022 0.003 PHE C1153 TYR 0.016 0.002 TYR A1152 ARG 0.003 0.001 ARG C1088 *********************** 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 145 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 95 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 23 residues processed: 139 average time/residue: 0.1851 time to fit residues: 36.9575 Evaluate side-chains 93 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 913 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1193 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 100 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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** A1098 HIS B 759 GLN B 910 GLN B1184 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8925 Z= 0.316 Angle : 0.840 9.884 12105 Z= 0.425 Chirality : 0.048 0.399 1584 Planarity : 0.005 0.041 1479 Dihedral : 12.849 111.270 2253 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.37 % Allowed : 16.61 % 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: 0.80 (0.26), residues: 1008 helix: 2.03 (0.23), residues: 474 sheet: -0.12 (0.41), residues: 145 loop : -1.13 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP C1099 HIS 0.007 0.001 HIS C1080 PHE 0.023 0.003 PHE A1092 TYR 0.015 0.002 TYR C1152 ARG 0.003 0.001 ARG B1016 *********************** 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 99 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 94 average time/residue: 0.2280 time to fit residues: 29.7939 Evaluate side-chains 69 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 735 CYS 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 1193 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN A1098 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.6799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8925 Z= 0.251 Angle : 0.722 8.176 12105 Z= 0.357 Chirality : 0.045 0.388 1584 Planarity : 0.004 0.035 1479 Dihedral : 12.160 107.906 2247 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.80 % Allowed : 17.16 % Favored : 79.04 % 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: 2.47 (0.22), residues: 477 sheet: 0.28 (0.43), residues: 139 loop : -1.18 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B1099 HIS 0.003 0.001 HIS A1098 PHE 0.011 0.002 PHE B 924 TYR 0.012 0.001 TYR A1064 ARG 0.003 0.000 ARG A1016 *********************** 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 90 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 55 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 740 CYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7218 (t) REVERT: B 724 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8004 (mp) outliers start: 35 outliers final: 20 residues processed: 86 average time/residue: 0.2073 time to fit residues: 25.3525 Evaluate side-chains 70 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 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 1015 ILE Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1112 ILE 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 914 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 68 optimal weight: 0.1980 chunk 0 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1007 GLN ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8925 Z= 0.205 Angle : 0.694 8.615 12105 Z= 0.341 Chirality : 0.043 0.367 1584 Planarity : 0.004 0.032 1479 Dihedral : 11.525 105.944 2247 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.58 % Allowed : 17.70 % Favored : 78.72 % 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: 1.25 (0.26), residues: 1008 helix: 2.62 (0.23), residues: 477 sheet: -0.14 (0.43), residues: 139 loop : -1.14 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1099 HIS 0.002 0.001 HIS C1061 PHE 0.022 0.002 PHE B 924 TYR 0.010 0.001 TYR B1004 ARG 0.004 0.000 ARG B1088 *********************** 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 83 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 50 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 22 residues processed: 78 average time/residue: 0.1972 time to fit residues: 22.2663 Evaluate side-chains 70 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 731 THR 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 1015 ILE 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 1134 VAL Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 735 CYS 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 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 57 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 923 GLN C1131 ASN ** C1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1156 HIS A 952 ASN ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.8370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8925 Z= 0.392 Angle : 0.843 9.119 12105 Z= 0.416 Chirality : 0.049 0.438 1584 Planarity : 0.005 0.045 1479 Dihedral : 12.081 110.384 2247 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.45 % Allowed : 18.24 % Favored : 77.31 % 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: 0.80 (0.26), residues: 1008 helix: 1.96 (0.22), residues: 477 sheet: 0.00 (0.41), residues: 139 loop : -1.10 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A1099 HIS 0.007 0.002 HIS B1085 PHE 0.025 0.003 PHE C 924 TYR 0.022 0.002 TYR A1064 ARG 0.004 0.001 ARG B1182 *********************** 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 94 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 53 time to evaluate : 0.929 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 outliers start: 41 outliers final: 28 residues processed: 88 average time/residue: 0.2071 time to fit residues: 25.8184 Evaluate side-chains 77 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 49 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 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 1015 ILE Chi-restraints excluded: chain A residue 1089 GLU 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 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 1042 LYS Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1125 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 72 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1156 HIS 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.8506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8925 Z= 0.224 Angle : 0.729 11.628 12105 Z= 0.356 Chirality : 0.045 0.383 1584 Planarity : 0.004 0.035 1479 Dihedral : 11.349 107.625 2247 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.69 % Allowed : 19.44 % Favored : 76.87 % 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: 1.01 (0.26), residues: 1008 helix: 2.27 (0.22), residues: 480 sheet: 0.27 (0.45), residues: 109 loop : -1.19 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1099 HIS 0.002 0.001 HIS B1080 PHE 0.047 0.002 PHE A 924 TYR 0.012 0.001 TYR B1004 ARG 0.002 0.000 ARG A1016 *********************** 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 89 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 55 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 TYR cc_start: 0.6973 (t80) cc_final: 0.6716 (t80) outliers start: 34 outliers final: 20 residues processed: 85 average time/residue: 0.2009 time to fit residues: 24.6194 Evaluate side-chains 69 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 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 740 CYS Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 979 SER 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 19 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 925 ASN ** C1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.8812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8925 Z= 0.293 Angle : 0.757 10.305 12105 Z= 0.374 Chirality : 0.046 0.390 1584 Planarity : 0.004 0.035 1479 Dihedral : 11.240 104.801 2247 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.69 % Allowed : 19.44 % Favored : 76.87 % 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: 0.83 (0.25), residues: 1008 helix: 2.03 (0.22), residues: 477 sheet: -0.10 (0.40), residues: 139 loop : -1.09 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B1099 HIS 0.003 0.001 HIS A1098 PHE 0.050 0.002 PHE C 924 TYR 0.014 0.001 TYR A1064 ARG 0.004 0.000 ARG B1088 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 46 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 28 residues processed: 77 average time/residue: 0.2215 time to fit residues: 24.2008 Evaluate side-chains 66 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 38 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 735 CYS 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 1161 VAL Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 1015 ILE 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 736 THR 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 1015 ILE Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.8945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8925 Z= 0.249 Angle : 0.749 12.285 12105 Z= 0.369 Chirality : 0.045 0.373 1584 Planarity : 0.005 0.126 1479 Dihedral : 10.995 104.757 2247 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 3.37 % Allowed : 19.76 % Favored : 76.87 % 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: 0.78 (0.25), residues: 1008 helix: 2.10 (0.22), residues: 480 sheet: -0.34 (0.41), residues: 139 loop : -1.21 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B1099 HIS 0.004 0.001 HIS A1080 PHE 0.015 0.002 PHE B 924 TYR 0.011 0.001 TYR A1064 ARG 0.021 0.001 ARG C1182 *********************** 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 71 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 40 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 26 residues processed: 70 average time/residue: 0.2020 time to fit residues: 20.7288 Evaluate side-chains 63 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 37 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 735 CYS 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 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 1161 VAL 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 1015 ILE Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1154 LYS 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 101 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.0770 chunk 74 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.9116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8925 Z= 0.221 Angle : 0.727 10.398 12105 Z= 0.354 Chirality : 0.044 0.365 1584 Planarity : 0.004 0.034 1479 Dihedral : 10.545 102.325 2247 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.63 % Rotamer: Outliers : 2.71 % Allowed : 20.20 % 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: 0.95 (0.26), residues: 1008 helix: 2.26 (0.22), residues: 480 sheet: -0.31 (0.41), residues: 139 loop : -1.15 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B1099 HIS 0.003 0.001 HIS C1045 PHE 0.015 0.002 PHE B 924 TYR 0.010 0.001 TYR B1004 ARG 0.010 0.001 ARG A1182 ********************** 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 66 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 41 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 21 residues processed: 65 average time/residue: 0.1977 time to fit residues: 18.7166 Evaluate side-chains 57 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 735 CYS 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 1161 VAL Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1154 LYS 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 22 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 chunk 4 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.068258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.051670 restraints weight = 41230.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.053276 restraints weight = 22232.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054330 restraints weight = 15437.819| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.9398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8925 Z= 0.284 Angle : 0.757 10.375 12105 Z= 0.368 Chirality : 0.046 0.379 1584 Planarity : 0.004 0.048 1479 Dihedral : 10.686 101.902 2247 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 2.71 % Allowed : 20.63 % Favored : 76.66 % 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: 0.91 (0.25), residues: 1008 helix: 2.23 (0.22), residues: 480 sheet: -0.39 (0.41), residues: 139 loop : -1.13 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1099 HIS 0.005 0.001 HIS A1080 PHE 0.026 0.002 PHE B 924 TYR 0.013 0.001 TYR B1064 ARG 0.007 0.001 ARG A1182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1973.34 seconds wall clock time: 37 minutes 29.65 seconds (2249.65 seconds total)