Starting phenix.real_space_refine on Fri Jul 19 20:26:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xog_33347/07_2024/7xog_33347.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xog_33347/07_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xog_33347/07_2024/7xog_33347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xog_33347/07_2024/7xog_33347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xog_33347/07_2024/7xog_33347.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xog_33347/07_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 Residue "C TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 742": "OD1" <-> "OD2" Residue "C TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 762": "NH1" <-> "NH2" Residue "C ASP 933": "OD1" <-> "OD2" Residue "C PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 987": "OE1" <-> "OE2" Residue "C ASP 991": "OD1" <-> "OD2" Residue "C ARG 1011": "NH1" <-> "NH2" Residue "C GLU 1014": "OE1" <-> "OE2" Residue "C ASP 1038": "OD1" <-> "OD2" Residue "C ASP 1081": "OD1" <-> "OD2" Residue "C PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1088": "NH1" <-> "NH2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "C ARG 1104": "NH1" <-> "NH2" Residue "C PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1143": "OD1" <-> "OD2" Residue "C PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1181": "OD1" <-> "OD2" Residue "C GLU 1185": "OE1" <-> "OE2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 742": "OD1" <-> "OD2" Residue "A TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ASP 933": "OD1" <-> "OD2" Residue "A PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 987": "OE1" <-> "OE2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A ARG 1011": "NH1" <-> "NH2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "A ASP 1038": "OD1" <-> "OD2" Residue "A ASP 1081": "OD1" <-> "OD2" Residue "A PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1088": "NH1" <-> "NH2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1143": "OD1" <-> "OD2" Residue "A PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1181": "OD1" <-> "OD2" Residue "A GLU 1185": "OE1" <-> "OE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 742": "OD1" <-> "OD2" Residue "B TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 762": "NH1" <-> "NH2" Residue "B ASP 933": "OD1" <-> "OD2" Residue "B PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 987": "OE1" <-> "OE2" Residue "B ASP 991": "OD1" <-> "OD2" Residue "B ARG 1011": "NH1" <-> "NH2" Residue "B GLU 1014": "OE1" <-> "OE2" Residue "B ASP 1038": "OD1" <-> "OD2" Residue "B ASP 1081": "OD1" <-> "OD2" Residue "B PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1088": "NH1" <-> "NH2" Residue "B GLU 1089": "OE1" <-> "OE2" Residue "B ARG 1104": "NH1" <-> "NH2" Residue "B PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1143": "OD1" <-> "OD2" Residue "B PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1181": "OD1" <-> "OD2" Residue "B GLU 1185": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.50, per 1000 atoms: 0.85 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 - 3.50 Amino acid : False - 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: 4.41 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.90 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: 2.59 Time building geometry restraints manager: 4.74 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: 62.73 - 85.23: 6 85.23 - 107.74: 553 107.74 - 130.24: 11516 130.24 - 152.75: 24 152.75 - 175.25: 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 2.520 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 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: 9.960 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.610 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.050 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.920 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 0.970 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: 0.1818 time to fit residues: 56.6773 Evaluate side-chains 101 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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: 0.6980 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8925 Z= 0.283 Angle : 0.859 8.425 12105 Z= 0.439 Chirality : 0.052 0.430 1584 Planarity : 0.005 0.043 1479 Dihedral : 14.139 109.561 2253 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.10 % Allowed : 12.16 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.22), residues: 495 sheet: 0.83 (0.46), residues: 110 loop : -1.41 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B1099 HIS 0.004 0.001 HIS C1098 PHE 0.023 0.003 PHE B 715 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 147 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 100 time to evaluate : 1.004 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: 47 outliers final: 23 residues processed: 142 average time/residue: 0.1900 time to fit residues: 38.0835 Evaluate side-chains 92 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1005 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1071 ASN Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1134 VAL Chi-restraints excluded: chain C residue 1193 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 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 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: 3.9990 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 0.0470 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1095 ASN ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 HIS A1098 HIS B 759 GLN B 910 GLN B1098 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8925 Z= 0.317 Angle : 0.835 8.755 12105 Z= 0.421 Chirality : 0.048 0.377 1584 Planarity : 0.005 0.044 1479 Dihedral : 12.935 110.120 2253 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.54 % Rotamer: Outliers : 3.69 % Allowed : 16.29 % 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: 0.78 (0.26), residues: 1008 helix: 1.87 (0.22), residues: 477 sheet: 0.78 (0.45), residues: 115 loop : -1.20 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP C1099 HIS 0.007 0.001 HIS C1080 PHE 0.023 0.003 PHE A1092 TYR 0.014 0.002 TYR C1152 ARG 0.004 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 107 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 73 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 21 residues processed: 102 average time/residue: 0.2388 time to fit residues: 32.6285 Evaluate side-chains 80 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 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 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 B residue 724 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 757 CYS 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 1154 LYS 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: 0.6980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7548 moved from start: 0.6780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8925 Z= 0.225 Angle : 0.703 8.224 12105 Z= 0.343 Chirality : 0.044 0.379 1584 Planarity : 0.004 0.030 1479 Dihedral : 12.206 108.672 2251 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.02 % Allowed : 16.83 % Favored : 79.15 % 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: 1.10 (0.26), residues: 1008 helix: 2.34 (0.22), residues: 474 sheet: 0.86 (0.47), residues: 109 loop : -1.27 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B1099 HIS 0.002 0.001 HIS A1098 PHE 0.011 0.002 PHE B1086 TYR 0.011 0.001 TYR A1064 ARG 0.003 0.000 ARG B 762 *********************** 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 96 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 59 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 TYR cc_start: 0.7047 (t80) cc_final: 0.6804 (t80) outliers start: 37 outliers final: 23 residues processed: 91 average time/residue: 0.2168 time to fit residues: 27.3089 Evaluate side-chains 75 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 52 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 931 ILE 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 979 SER Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN C1007 GLN C1131 ASN C1156 HIS ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1184 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.7882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8925 Z= 0.323 Angle : 0.772 8.813 12105 Z= 0.383 Chirality : 0.047 0.402 1584 Planarity : 0.004 0.041 1479 Dihedral : 12.082 108.151 2247 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.10 % Allowed : 17.92 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.26), residues: 1008 helix: 2.10 (0.22), residues: 477 sheet: 0.50 (0.46), residues: 109 loop : -1.15 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A1099 HIS 0.005 0.001 HIS A1085 PHE 0.018 0.003 PHE B 924 TYR 0.016 0.002 TYR A1064 ARG 0.005 0.001 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 105 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 58 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 724 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8301 (mp) outliers start: 47 outliers final: 29 residues processed: 99 average time/residue: 0.2088 time to fit residues: 28.9155 Evaluate side-chains 80 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 50 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 935 LEU 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 979 SER Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 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 1134 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 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 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1156 HIS ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** 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: 0.7736 moved from start: 0.8221 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 : 0.735 11.573 12105 Z= 0.359 Chirality : 0.045 0.388 1584 Planarity : 0.004 0.033 1479 Dihedral : 11.627 108.432 2247 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.91 % Allowed : 19.65 % 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: 0.84 (0.25), residues: 1008 helix: 2.08 (0.22), residues: 480 sheet: 0.43 (0.46), residues: 109 loop : -1.28 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1099 HIS 0.003 0.001 HIS B1085 PHE 0.017 0.002 PHE B 924 TYR 0.013 0.001 TYR B1064 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 88 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 52 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 27 residues processed: 84 average time/residue: 0.2175 time to fit residues: 25.4445 Evaluate side-chains 76 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 49 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 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 979 SER Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1154 LYS Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1042 LYS 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 72 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 0.0470 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** 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: 0.7696 moved from start: 0.8374 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= 0.199 Angle : 0.686 9.591 12105 Z= 0.333 Chirality : 0.043 0.364 1584 Planarity : 0.003 0.030 1479 Dihedral : 10.881 105.503 2247 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.37 % Allowed : 20.30 % 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: 0.85 (0.26), residues: 1008 helix: 2.37 (0.22), residues: 459 sheet: -0.14 (0.43), residues: 139 loop : -1.35 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1099 HIS 0.001 0.000 HIS A1098 PHE 0.033 0.002 PHE C 924 TYR 0.011 0.001 TYR B1004 ARG 0.013 0.001 ARG C1182 *********************** 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 fitting. rotamer outliers: 31 poor density : 54 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 82 average time/residue: 0.2106 time to fit residues: 24.5007 Evaluate side-chains 68 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 959 LEU 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 1015 ILE Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 0.0060 chunk 55 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.8550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8925 Z= 0.213 Angle : 0.698 10.377 12105 Z= 0.340 Chirality : 0.043 0.358 1584 Planarity : 0.003 0.029 1479 Dihedral : 10.670 104.101 2247 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 3.91 % Allowed : 20.63 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.45 (0.22), residues: 462 sheet: -0.11 (0.43), residues: 139 loop : -1.32 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B1099 HIS 0.004 0.001 HIS A1080 PHE 0.013 0.002 PHE B 924 TYR 0.010 0.001 TYR B1064 ARG 0.003 0.000 ARG C1182 *********************** 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 83 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 47 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 29 residues processed: 79 average time/residue: 0.2041 time to fit residues: 23.0434 Evaluate side-chains 70 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 41 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 911 ASN Chi-restraints excluded: chain C residue 925 ASN Chi-restraints excluded: chain C residue 959 LEU 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 740 CYS Chi-restraints excluded: chain A residue 914 TYR Chi-restraints excluded: chain A residue 979 SER 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 740 CYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** 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: 0.7719 moved from start: 0.8676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8925 Z= 0.214 Angle : 0.699 9.657 12105 Z= 0.337 Chirality : 0.043 0.353 1584 Planarity : 0.003 0.029 1479 Dihedral : 10.505 103.275 2247 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.63 % Rotamer: Outliers : 3.58 % Allowed : 21.28 % Favored : 75.14 % 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: 1.03 (0.26), residues: 1008 helix: 2.28 (0.22), residues: 480 sheet: -0.12 (0.42), residues: 139 loop : -1.10 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B1099 HIS 0.002 0.001 HIS C1080 PHE 0.016 0.002 PHE C 924 TYR 0.010 0.001 TYR B1004 ARG 0.002 0.000 ARG C 762 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 39 time to evaluate : 1.000 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: 29 residues processed: 68 average time/residue: 0.2001 time to fit residues: 19.9673 Evaluate side-chains 67 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 38 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 750 LEU Chi-restraints excluded: chain C residue 914 TYR Chi-restraints excluded: chain C residue 924 PHE Chi-restraints excluded: chain C residue 959 LEU 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 740 CYS Chi-restraints excluded: chain A residue 914 TYR Chi-restraints excluded: chain A residue 979 SER 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 B residue 735 CYS Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain B residue 1194 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** 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: 0.7759 moved from start: 0.9047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8925 Z= 0.230 Angle : 0.720 11.235 12105 Z= 0.344 Chirality : 0.044 0.360 1584 Planarity : 0.003 0.029 1479 Dihedral : 10.320 101.870 2247 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 3.04 % Allowed : 21.72 % Favored : 75.24 % 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: 1.14 (0.26), residues: 1008 helix: 2.27 (0.22), residues: 480 sheet: 0.41 (0.46), residues: 109 loop : -0.99 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1099 HIS 0.005 0.001 HIS A1045 PHE 0.015 0.002 PHE B 924 TYR 0.010 0.001 TYR C1064 ARG 0.005 0.000 ARG B1182 ********************** 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 fitting. rotamer outliers: 28 poor density : 38 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1047 MET cc_start: 0.8109 (tpp) cc_final: 0.7895 (tpp) outliers start: 28 outliers final: 25 residues processed: 63 average time/residue: 0.2017 time to fit residues: 18.6684 Evaluate side-chains 62 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 37 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 914 TYR Chi-restraints excluded: chain C residue 959 LEU 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 914 TYR Chi-restraints excluded: chain A residue 979 SER 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 B residue 735 CYS Chi-restraints excluded: chain B residue 740 CYS Chi-restraints excluded: chain B residue 1015 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.0070 chunk 4 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** 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 = 0.3686 r_free = 0.3686 target = 0.071032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.054121 restraints weight = 41587.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.055839 restraints weight = 22039.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.056952 restraints weight = 15120.778| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.9142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8925 Z= 0.191 Angle : 0.698 10.170 12105 Z= 0.331 Chirality : 0.043 0.345 1584 Planarity : 0.003 0.031 1479 Dihedral : 9.884 101.569 2247 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.63 % Rotamer: Outliers : 2.61 % Allowed : 22.26 % Favored : 75.14 % 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: 1.19 (0.26), residues: 1008 helix: 2.53 (0.23), residues: 468 sheet: -0.10 (0.42), residues: 139 loop : -1.04 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1099 HIS 0.002 0.001 HIS A1098 PHE 0.010 0.001 PHE B 924 TYR 0.010 0.001 TYR B1004 ARG 0.002 0.000 ARG A 762 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1991.37 seconds wall clock time: 36 minutes 49.21 seconds (2209.21 seconds total)