Starting phenix.real_space_refine on Sun Aug 4 03:25:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vqa_43436/08_2024/8vqa_43436.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vqa_43436/08_2024/8vqa_43436.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/8vqa_43436/08_2024/8vqa_43436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vqa_43436/08_2024/8vqa_43436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vqa_43436/08_2024/8vqa_43436.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vqa_43436/08_2024/8vqa_43436.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= -0.001 sd= 0.080 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 69 5.16 5 C 6093 2.51 5 N 1620 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9495 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3025 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 23, 'TRANS': 406} Chain breaks: 3 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'ASN:plan1': 7, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 144 Chain: "B" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3025 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 23, 'TRANS': 406} Chain breaks: 3 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'ASN:plan1': 7, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 144 Chain: "C" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3025 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 23, 'TRANS': 406} Chain breaks: 3 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'ASN:plan1': 7, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 144 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: 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: "F" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: 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: "K" 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 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: 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 Time building chain proxies: 6.18, per 1000 atoms: 0.65 Number of scatterers: 9495 At special positions: 0 Unit cell: (90, 90, 134, 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 69 16.00 O 1713 8.00 N 1620 7.00 C 6093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 707 " - pdb=" SG CYS B 883 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS C 707 " distance=2.02 Simple disulfide: pdb=" SG CYS A 970 " - pdb=" SG CYS A 999 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 707 " - pdb=" SG CYS C 883 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 970 " - pdb=" SG CYS B 999 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 970 " - pdb=" SG CYS C 999 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 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-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 3.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 47.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.846A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 879 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 938 Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.173A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.846A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 879 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.173A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.846A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 834 through 841 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 879 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.173A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AA5, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AA8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AA9, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB3, first strand: chain 'C' and resid 1120 through 1122 561 hydrogen bonds defined for protein. 1665 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: 2.75 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2783 1.33 - 1.46: 2271 1.46 - 1.58: 4537 1.58 - 1.71: 0 1.71 - 1.84: 96 Bond restraints: 9687 Sorted by residual: bond pdb=" NE ARG A 847 " pdb=" CZ ARG A 847 " ideal model delta sigma weight residual 1.326 1.371 -0.045 1.10e-02 8.26e+03 1.65e+01 bond pdb=" NE ARG C 847 " pdb=" CZ ARG C 847 " ideal model delta sigma weight residual 1.326 1.370 -0.044 1.10e-02 8.26e+03 1.61e+01 bond pdb=" NE ARG B 847 " pdb=" CZ ARG B 847 " ideal model delta sigma weight residual 1.326 1.370 -0.044 1.10e-02 8.26e+03 1.59e+01 bond pdb=" C5 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.413 1.477 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.477 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 9682 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.08: 269 105.08 - 112.25: 4981 112.25 - 119.41: 2704 119.41 - 126.57: 5207 126.57 - 133.73: 75 Bond angle restraints: 13236 Sorted by residual: angle pdb=" C LEU C 861 " pdb=" N PRO C 862 " pdb=" CA PRO C 862 " ideal model delta sigma weight residual 119.66 126.03 -6.37 7.20e-01 1.93e+00 7.84e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.02 -6.36 7.20e-01 1.93e+00 7.80e+01 angle pdb=" C LEU B 861 " pdb=" N PRO B 862 " pdb=" CA PRO B 862 " ideal model delta sigma weight residual 119.66 126.00 -6.34 7.20e-01 1.93e+00 7.75e+01 angle pdb=" C ALA C1078 " pdb=" N PRO C1079 " pdb=" CA PRO C1079 " ideal model delta sigma weight residual 119.24 127.76 -8.52 1.04e+00 9.25e-01 6.71e+01 angle pdb=" C ALA B1078 " pdb=" N PRO B1079 " pdb=" CA PRO B1079 " ideal model delta sigma weight residual 119.24 127.73 -8.49 1.04e+00 9.25e-01 6.67e+01 ... (remaining 13231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 5940 16.88 - 33.76: 162 33.76 - 50.63: 48 50.63 - 67.51: 24 67.51 - 84.39: 6 Dihedral angle restraints: 6180 sinusoidal: 2439 harmonic: 3741 Sorted by residual: dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual 93.00 135.86 -42.86 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual 93.00 135.85 -42.85 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 135.83 -42.83 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 6177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1316 0.099 - 0.199: 255 0.199 - 0.298: 46 0.298 - 0.397: 21 0.397 - 0.496: 3 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.51e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.41e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.39e+01 ... (remaining 1638 not shown) Planarity restraints: 1713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " -0.033 2.00e-02 2.50e+03 3.35e-02 1.41e+01 pdb=" CG ASN C1134 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " 0.052 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1134 " 0.032 2.00e-02 2.50e+03 3.34e-02 1.40e+01 pdb=" CG ASN B1134 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B1134 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B1134 " -0.052 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.032 2.00e-02 2.50e+03 3.34e-02 1.39e+01 pdb=" CG ASN A1134 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.051 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.040 2.00e-02 2.50e+03 ... (remaining 1710 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 4194 2.93 - 3.43: 8891 3.43 - 3.92: 15011 3.92 - 4.41: 16898 4.41 - 4.90: 27061 Nonbonded interactions: 72055 Sorted by model distance: nonbonded pdb=" OD1 ASN B 709 " pdb=" O5 NAG B1301 " model vdw 2.443 3.040 nonbonded pdb=" OD1 ASN A 709 " pdb=" O5 NAG A1301 " model vdw 2.443 3.040 nonbonded pdb=" OD1 ASN C 709 " pdb=" O5 NAG C1301 " model vdw 2.443 3.040 nonbonded pdb=" O ASN C 969 " pdb=" N GLY C 971 " model vdw 2.547 3.120 nonbonded pdb=" O ASN B 969 " pdb=" N GLY B 971 " model vdw 2.547 3.120 ... (remaining 72050 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 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.960 Find NCS groups from input model: 0.400 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 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 : 0.011 0.064 9687 Z= 0.712 Angle : 1.337 17.624 13236 Z= 0.886 Chirality : 0.089 0.496 1641 Planarity : 0.005 0.019 1695 Dihedral : 9.894 84.391 3693 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.71 % Allowed : 2.61 % Favored : 96.68 % Rotamer: Outliers : 0.77 % Allowed : 0.77 % Favored : 98.46 % 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: 0.07 (0.22), residues: 1266 helix: 0.94 (0.19), residues: 585 sheet: 1.14 (0.47), residues: 120 loop : -1.15 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 886 HIS 0.002 0.001 HIS C1088 PHE 0.018 0.003 PHE C 833 TYR 0.018 0.003 TYR B 789 ARG 0.002 0.000 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1011 MET cc_start: 0.7020 (mmp) cc_final: 0.6789 (mmt) REVERT: A 1014 ARG cc_start: 0.6479 (ttm170) cc_final: 0.6219 (ttm170) REVERT: B 752 LEU cc_start: 0.8281 (mt) cc_final: 0.8060 (mt) REVERT: B 854 LYS cc_start: 0.6885 (ttmt) cc_final: 0.6582 (ttpp) REVERT: B 1011 MET cc_start: 0.7021 (mmp) cc_final: 0.6800 (mmt) REVERT: B 1019 ARG cc_start: 0.7963 (tpt170) cc_final: 0.7709 (tpt170) REVERT: C 1011 MET cc_start: 0.6987 (mmp) cc_final: 0.6757 (mmt) REVERT: C 1019 ARG cc_start: 0.8009 (tpt170) cc_final: 0.7726 (tpt170) outliers start: 6 outliers final: 3 residues processed: 143 average time/residue: 0.3601 time to fit residues: 63.6666 Evaluate side-chains 71 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.0670 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 61 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A1101 HIS B 935 GLN C 935 GLN C1113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9687 Z= 0.216 Angle : 0.598 6.972 13236 Z= 0.322 Chirality : 0.044 0.234 1641 Planarity : 0.005 0.046 1695 Dihedral : 4.740 44.150 1986 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.51 % Allowed : 5.66 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1266 helix: 2.10 (0.20), residues: 594 sheet: 0.60 (0.40), residues: 156 loop : -1.22 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS A1064 PHE 0.013 0.001 PHE B1121 TYR 0.019 0.002 TYR A1067 ARG 0.003 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 720 ILE cc_start: 0.7919 (mm) cc_final: 0.7578 (mm) REVERT: B 752 LEU cc_start: 0.8367 (mt) cc_final: 0.8110 (mt) REVERT: C 752 LEU cc_start: 0.8244 (mt) cc_final: 0.7753 (mp) REVERT: C 1019 ARG cc_start: 0.8179 (tpt170) cc_final: 0.7965 (tpt170) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 0.2903 time to fit residues: 31.8652 Evaluate side-chains 75 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS B1088 HIS C1088 HIS C1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9687 Z= 0.259 Angle : 0.585 6.230 13236 Z= 0.303 Chirality : 0.045 0.270 1641 Planarity : 0.005 0.052 1695 Dihedral : 4.406 39.131 1986 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.29 % Allowed : 7.34 % Favored : 91.38 % 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: 0.90 (0.23), residues: 1266 helix: 2.30 (0.21), residues: 594 sheet: 0.03 (0.37), residues: 165 loop : -1.35 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C1102 HIS 0.006 0.002 HIS A1064 PHE 0.013 0.002 PHE C1042 TYR 0.020 0.002 TYR A1067 ARG 0.003 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6508 (mtt90) cc_final: 0.5189 (mtt180) REVERT: B 752 LEU cc_start: 0.8428 (mt) cc_final: 0.8116 (mt) REVERT: B 895 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6752 (mt0) REVERT: C 752 LEU cc_start: 0.8295 (mt) cc_final: 0.8011 (mt) REVERT: C 815 ARG cc_start: 0.6738 (mtt90) cc_final: 0.5501 (mtt180) outliers start: 10 outliers final: 4 residues processed: 104 average time/residue: 0.3229 time to fit residues: 42.7419 Evaluate side-chains 74 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 9687 Z= 0.285 Angle : 0.574 7.653 13236 Z= 0.298 Chirality : 0.045 0.277 1641 Planarity : 0.005 0.054 1695 Dihedral : 4.322 35.845 1986 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.67 % Allowed : 7.46 % Favored : 90.86 % 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: 0.61 (0.23), residues: 1266 helix: 2.09 (0.21), residues: 597 sheet: -0.06 (0.33), residues: 195 loop : -1.67 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C1102 HIS 0.004 0.001 HIS A1064 PHE 0.013 0.002 PHE C1121 TYR 0.021 0.002 TYR C1067 ARG 0.002 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.5196 (mtt180) REVERT: A 1111 GLU cc_start: 0.7789 (pp20) cc_final: 0.7025 (mm-30) REVERT: B 752 LEU cc_start: 0.8462 (mt) cc_final: 0.8158 (mt) REVERT: B 815 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.5134 (mtt180) REVERT: B 1011 MET cc_start: 0.6470 (mmt) cc_final: 0.6216 (mmt) REVERT: C 752 LEU cc_start: 0.8339 (mt) cc_final: 0.8061 (mt) outliers start: 13 outliers final: 11 residues processed: 90 average time/residue: 0.2408 time to fit residues: 30.1942 Evaluate side-chains 87 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.0870 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 106 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 779 GLN C1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9687 Z= 0.209 Angle : 0.518 5.478 13236 Z= 0.266 Chirality : 0.044 0.276 1641 Planarity : 0.004 0.049 1695 Dihedral : 4.154 34.270 1986 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.06 % Allowed : 8.75 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1266 helix: 2.28 (0.21), residues: 597 sheet: -0.22 (0.37), residues: 165 loop : -1.50 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 PHE 0.014 0.001 PHE C1121 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8018 (m-80) cc_final: 0.7678 (m-80) REVERT: A 815 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.5207 (mtt180) REVERT: A 854 LYS cc_start: 0.7020 (ttmt) cc_final: 0.6807 (tppt) REVERT: A 1091 ARG cc_start: 0.8595 (tpp-160) cc_final: 0.8228 (tpp80) REVERT: A 1111 GLU cc_start: 0.7740 (pp20) cc_final: 0.7049 (mm-30) REVERT: B 752 LEU cc_start: 0.8371 (mt) cc_final: 0.8070 (mt) REVERT: B 815 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5126 (mtt180) REVERT: C 752 LEU cc_start: 0.8253 (mt) cc_final: 0.7903 (mt) REVERT: C 815 ARG cc_start: 0.6694 (mtt90) cc_final: 0.5512 (mtt180) outliers start: 16 outliers final: 9 residues processed: 95 average time/residue: 0.2438 time to fit residues: 31.5522 Evaluate side-chains 85 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9687 Z= 0.304 Angle : 0.571 6.777 13236 Z= 0.295 Chirality : 0.045 0.271 1641 Planarity : 0.005 0.045 1695 Dihedral : 4.257 31.205 1986 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.32 % Allowed : 9.78 % Favored : 87.90 % 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: 0.53 (0.23), residues: 1266 helix: 2.09 (0.21), residues: 594 sheet: -0.30 (0.38), residues: 165 loop : -1.61 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 886 HIS 0.005 0.001 HIS A1064 PHE 0.014 0.002 PHE C1121 TYR 0.021 0.002 TYR C1067 ARG 0.002 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8008 (m-80) cc_final: 0.7641 (m-80) REVERT: A 815 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.5254 (mtt180) REVERT: A 854 LYS cc_start: 0.7049 (ttmt) cc_final: 0.6837 (tppt) REVERT: A 934 ILE cc_start: 0.7876 (tp) cc_final: 0.7614 (tp) REVERT: A 1091 ARG cc_start: 0.8619 (tpp-160) cc_final: 0.8217 (tpp80) REVERT: A 1111 GLU cc_start: 0.7805 (pp20) cc_final: 0.7120 (mm-30) REVERT: B 752 LEU cc_start: 0.8452 (mt) cc_final: 0.8174 (mt) REVERT: B 815 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.5153 (mtt180) REVERT: B 1011 MET cc_start: 0.6536 (mmt) cc_final: 0.6224 (mmt) REVERT: B 1111 GLU cc_start: 0.7854 (pp20) cc_final: 0.7211 (mm-30) REVERT: C 752 LEU cc_start: 0.8354 (mt) cc_final: 0.8051 (mt) outliers start: 18 outliers final: 12 residues processed: 99 average time/residue: 0.2523 time to fit residues: 34.1048 Evaluate side-chains 91 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.0070 chunk 71 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9687 Z= 0.195 Angle : 0.508 5.080 13236 Z= 0.262 Chirality : 0.043 0.271 1641 Planarity : 0.004 0.042 1695 Dihedral : 4.011 30.937 1986 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.29 % Allowed : 10.17 % Favored : 88.55 % 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: 0.68 (0.23), residues: 1266 helix: 2.28 (0.21), residues: 594 sheet: -0.37 (0.39), residues: 165 loop : -1.57 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 886 HIS 0.003 0.001 HIS C1101 PHE 0.014 0.001 PHE C1121 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8008 (m-80) cc_final: 0.7578 (m-80) REVERT: A 815 ARG cc_start: 0.6521 (OUTLIER) cc_final: 0.5269 (mtt180) REVERT: A 854 LYS cc_start: 0.6982 (ttmt) cc_final: 0.6771 (tppt) REVERT: A 934 ILE cc_start: 0.7747 (tp) cc_final: 0.7515 (tp) REVERT: A 1091 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8287 (ttm-80) REVERT: A 1111 GLU cc_start: 0.7696 (pp20) cc_final: 0.7095 (mm-30) REVERT: B 752 LEU cc_start: 0.8302 (mt) cc_final: 0.8034 (mt) REVERT: B 756 TYR cc_start: 0.8002 (m-80) cc_final: 0.7544 (m-80) REVERT: B 789 TYR cc_start: 0.5708 (t80) cc_final: 0.5357 (t80) REVERT: B 815 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.5187 (mtt180) REVERT: B 1111 GLU cc_start: 0.7709 (pp20) cc_final: 0.7485 (mt-10) REVERT: C 752 LEU cc_start: 0.8218 (mt) cc_final: 0.7914 (mt) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.2347 time to fit residues: 30.5279 Evaluate side-chains 89 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS C1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9687 Z= 0.246 Angle : 0.530 5.316 13236 Z= 0.273 Chirality : 0.044 0.260 1641 Planarity : 0.004 0.041 1695 Dihedral : 4.028 27.956 1986 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.42 % Allowed : 10.68 % Favored : 87.90 % 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: 0.60 (0.23), residues: 1266 helix: 2.21 (0.21), residues: 597 sheet: -0.25 (0.35), residues: 195 loop : -1.78 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 PHE 0.015 0.001 PHE C1121 TYR 0.020 0.002 TYR A1067 ARG 0.002 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8044 (m-80) cc_final: 0.7579 (m-80) REVERT: A 815 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.5198 (mtt180) REVERT: A 854 LYS cc_start: 0.6929 (ttmt) cc_final: 0.6699 (tppt) REVERT: A 934 ILE cc_start: 0.7789 (tp) cc_final: 0.7550 (tp) REVERT: A 1091 ARG cc_start: 0.8619 (tpp-160) cc_final: 0.8294 (ttm-80) REVERT: A 1111 GLU cc_start: 0.7701 (pp20) cc_final: 0.7128 (mm-30) REVERT: B 752 LEU cc_start: 0.8466 (mt) cc_final: 0.8219 (mt) REVERT: B 756 TYR cc_start: 0.8067 (m-80) cc_final: 0.7601 (m-80) REVERT: B 815 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.5284 (mtt180) REVERT: C 752 LEU cc_start: 0.8355 (mt) cc_final: 0.8025 (mt) outliers start: 11 outliers final: 6 residues processed: 93 average time/residue: 0.2254 time to fit residues: 29.3914 Evaluate side-chains 89 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 0.0170 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.0570 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9687 Z= 0.175 Angle : 0.493 5.096 13236 Z= 0.254 Chirality : 0.043 0.262 1641 Planarity : 0.004 0.051 1695 Dihedral : 3.720 28.236 1982 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.03 % Allowed : 11.20 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1266 helix: 2.34 (0.21), residues: 597 sheet: -0.23 (0.35), residues: 195 loop : -1.68 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.003 0.001 HIS C1101 PHE 0.014 0.001 PHE C1121 TYR 0.020 0.001 TYR A1067 ARG 0.002 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8007 (m-80) cc_final: 0.7527 (m-80) REVERT: A 779 GLN cc_start: 0.7569 (tp40) cc_final: 0.6996 (mt0) REVERT: A 934 ILE cc_start: 0.7679 (tp) cc_final: 0.7421 (tp) REVERT: A 1091 ARG cc_start: 0.8624 (tpp-160) cc_final: 0.8314 (ttm-80) REVERT: A 1111 GLU cc_start: 0.7677 (pp20) cc_final: 0.7433 (mt-10) REVERT: B 815 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5267 (mtt180) REVERT: B 992 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7221 (mm110) REVERT: C 720 ILE cc_start: 0.8037 (mm) cc_final: 0.7739 (mm) REVERT: C 752 LEU cc_start: 0.8284 (mt) cc_final: 0.7963 (mt) REVERT: C 789 TYR cc_start: 0.5645 (t80) cc_final: 0.5376 (t80) REVERT: C 1014 ARG cc_start: 0.5482 (OUTLIER) cc_final: 0.4640 (mtm180) outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 0.2311 time to fit residues: 29.6405 Evaluate side-chains 87 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 chunk 128 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9687 Z= 0.243 Angle : 0.522 5.097 13236 Z= 0.268 Chirality : 0.044 0.260 1641 Planarity : 0.005 0.056 1695 Dihedral : 3.819 26.272 1982 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.90 % Allowed : 11.33 % Favored : 87.77 % 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: 0.67 (0.23), residues: 1266 helix: 2.30 (0.21), residues: 597 sheet: -0.29 (0.35), residues: 195 loop : -1.76 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 PHE 0.015 0.001 PHE B1121 TYR 0.020 0.002 TYR C1067 ARG 0.002 0.000 ARG A1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8061 (m-80) cc_final: 0.7594 (m-80) REVERT: A 779 GLN cc_start: 0.7606 (tp40) cc_final: 0.7023 (mt0) REVERT: A 934 ILE cc_start: 0.7754 (tp) cc_final: 0.7478 (tp) REVERT: A 1014 ARG cc_start: 0.6267 (ttm170) cc_final: 0.5940 (ttm170) REVERT: A 1091 ARG cc_start: 0.8621 (tpp-160) cc_final: 0.8304 (ttm-80) REVERT: A 1111 GLU cc_start: 0.7691 (pp20) cc_final: 0.7427 (mt-10) REVERT: B 752 LEU cc_start: 0.8212 (mt) cc_final: 0.8007 (mp) REVERT: B 815 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.5302 (mtt180) REVERT: B 992 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7228 (mm-40) REVERT: C 752 LEU cc_start: 0.8315 (mt) cc_final: 0.8008 (mt) REVERT: C 1014 ARG cc_start: 0.5565 (OUTLIER) cc_final: 0.4717 (mtm180) outliers start: 7 outliers final: 5 residues processed: 87 average time/residue: 0.2367 time to fit residues: 28.6501 Evaluate side-chains 91 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.170994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141485 restraints weight = 10384.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144972 restraints weight = 7056.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147396 restraints weight = 5480.662| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9687 Z= 0.204 Angle : 0.503 5.102 13236 Z= 0.258 Chirality : 0.043 0.260 1641 Planarity : 0.005 0.052 1695 Dihedral : 3.684 23.553 1980 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.64 % Allowed : 11.71 % Favored : 87.64 % 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: 0.70 (0.24), residues: 1266 helix: 2.33 (0.21), residues: 597 sheet: -0.29 (0.35), residues: 195 loop : -1.75 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 PHE 0.014 0.001 PHE C1121 TYR 0.020 0.001 TYR A1067 ARG 0.002 0.000 ARG A1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.76 seconds wall clock time: 32 minutes 53.35 seconds (1973.35 seconds total)