Starting phenix.real_space_refine on Sun Aug 4 03:38:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vq9_43435/08_2024/8vq9_43435.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vq9_43435/08_2024/8vq9_43435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vq9_43435/08_2024/8vq9_43435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vq9_43435/08_2024/8vq9_43435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vq9_43435/08_2024/8vq9_43435.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vq9_43435/08_2024/8vq9_43435.cif" } resolution = 2.7 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= 0.105 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 63 5.16 5 C 6090 2.51 5 N 1614 2.21 5 O 1746 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 TYR 789": "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 PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 1103": "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 TYR 789": "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 PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 1103": "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 TYR 789": "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 PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 1103": "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: 9513 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3045 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 4 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3045 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 4 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3045 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 4 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 114 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 6.08, per 1000 atoms: 0.64 Number of scatterers: 9513 At special positions: 0 Unit cell: (88, 91, 136, 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 63 16.00 O 1746 8.00 N 1614 7.00 C 6090 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 C 883 " distance=2.20 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.10 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 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 B 707 " distance=2.20 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=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.10 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 883 " - pdb=" SG CYS C 707 " distance=2.20 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=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.10 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 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=2.02 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 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-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A1134 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1098 " Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.6 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 50.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.115A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.949A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.216A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.396A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.841A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.674A 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 1145 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.114A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.949A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.216A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.396A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.841A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.674A 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 1145 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.114A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.949A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 834 through 841 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.216A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.395A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.841A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.674A 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 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AA2, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.134A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.227A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) 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 715 Processing sheet with id=AA6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.134A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.227A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) 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 715 Processing sheet with id=AB1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.134A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.227A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1120 through 1122 567 hydrogen bonds defined for protein. 1647 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: 2.63 Time building geometry restraints manager: 3.98 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: 2535 1.33 - 1.45: 1860 1.45 - 1.58: 5217 1.58 - 1.70: 0 1.70 - 1.83: 84 Bond restraints: 9696 Sorted by residual: bond pdb=" C5 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C5 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C5 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C5 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.413 1.471 -0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 8.19e+00 ... (remaining 9691 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.78: 285 106.78 - 113.51: 5412 113.51 - 120.24: 3218 120.24 - 126.97: 4282 126.97 - 133.70: 51 Bond angle restraints: 13248 Sorted by residual: angle pdb=" C ALA C1078 " pdb=" N PRO C1079 " pdb=" CA PRO C1079 " ideal model delta sigma weight residual 119.24 127.43 -8.19 1.04e+00 9.25e-01 6.20e+01 angle pdb=" C ALA B1078 " pdb=" N PRO B1079 " pdb=" CA PRO B1079 " ideal model delta sigma weight residual 119.24 127.38 -8.14 1.04e+00 9.25e-01 6.12e+01 angle pdb=" C ALA A1078 " pdb=" N PRO A1079 " pdb=" CA PRO A1079 " ideal model delta sigma weight residual 119.24 127.38 -8.14 1.04e+00 9.25e-01 6.12e+01 angle pdb=" C PRO C 862 " pdb=" N PRO C 863 " pdb=" CA PRO C 863 " ideal model delta sigma weight residual 120.03 127.68 -7.65 9.90e-01 1.02e+00 5.97e+01 angle pdb=" C PRO A 862 " pdb=" N PRO A 863 " pdb=" CA PRO A 863 " ideal model delta sigma weight residual 120.03 127.66 -7.63 9.90e-01 1.02e+00 5.95e+01 ... (remaining 13243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5868 17.95 - 35.91: 201 35.91 - 53.86: 39 53.86 - 71.82: 6 71.82 - 89.77: 9 Dihedral angle restraints: 6123 sinusoidal: 2418 harmonic: 3705 Sorted by residual: dihedral pdb=" CB CYS B 883 " pdb=" SG CYS B 883 " pdb=" SG CYS C 707 " pdb=" CB CYS C 707 " ideal model delta sinusoidal sigma weight residual -86.00 -37.56 -48.44 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS A 883 " pdb=" SG CYS A 883 " pdb=" SG CYS B 707 " pdb=" CB CYS B 707 " ideal model delta sinusoidal sigma weight residual -86.00 -37.57 -48.43 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS A 707 " pdb=" SG CYS A 707 " pdb=" SG CYS C 883 " pdb=" CB CYS C 883 " ideal model delta sinusoidal sigma weight residual -86.00 -37.59 -48.41 1 1.00e+01 1.00e-02 3.23e+01 ... (remaining 6120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1230 0.078 - 0.156: 318 0.156 - 0.234: 63 0.234 - 0.312: 27 0.312 - 0.390: 12 Chirality restraints: 1650 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.27e+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 -2.55 0.15 2.00e-02 2.50e+03 5.26e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.24e+01 ... (remaining 1647 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " 0.052 2.00e-02 2.50e+03 2.75e-02 1.51e+01 pdb=" CG TYR B 904 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 904 " -0.051 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR C 904 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 904 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 904 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR C 904 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR C 904 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR C 904 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 904 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " -0.051 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR A 904 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " -0.040 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4997 2.99 - 3.47: 9255 3.47 - 3.94: 15145 3.94 - 4.42: 17532 4.42 - 4.90: 27446 Nonbonded interactions: 74375 Sorted by model distance: nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.511 3.120 nonbonded pdb=" NZ LYS C1028 " pdb=" O PHE C1042 " model vdw 2.511 3.120 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.511 3.120 nonbonded pdb=" OE1 GLN B1011 " pdb=" NH1 ARG B1014 " model vdw 2.582 3.120 nonbonded pdb=" OE1 GLN A1011 " pdb=" NH1 ARG A1014 " model vdw 2.582 3.120 ... (remaining 74370 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' } 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 individual isotropic 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: 3.480 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.800 Find NCS groups from input model: 0.360 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:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.010 0.063 9696 Z= 0.693 Angle : 1.197 8.186 13248 Z= 0.810 Chirality : 0.082 0.390 1650 Planarity : 0.004 0.028 1698 Dihedral : 9.901 89.774 3654 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.54 (0.21), residues: 1248 helix: 1.19 (0.20), residues: 570 sheet: 1.57 (0.43), residues: 120 loop : -0.78 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP C 886 HIS 0.002 0.001 HIS B1048 PHE 0.017 0.003 PHE C 833 TYR 0.052 0.005 TYR B 904 ARG 0.003 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.055 Fit side-chains REVERT: A 725 GLU cc_start: 0.7970 (tt0) cc_final: 0.7712 (tt0) REVERT: A 855 PHE cc_start: 0.7618 (m-80) cc_final: 0.7404 (m-80) REVERT: A 935 GLN cc_start: 0.7494 (mt0) cc_final: 0.7268 (mt0) REVERT: B 1029 MET cc_start: 0.8402 (tpp) cc_final: 0.8088 (tpp) REVERT: C 725 GLU cc_start: 0.8028 (tt0) cc_final: 0.7764 (tt0) REVERT: C 752 LEU cc_start: 0.8316 (mt) cc_final: 0.8089 (mt) REVERT: C 803 SER cc_start: 0.8512 (p) cc_final: 0.8217 (p) REVERT: C 1138 TYR cc_start: 0.7781 (t80) cc_final: 0.7420 (t80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.3193 time to fit residues: 247.1204 Evaluate side-chains 117 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 907 ASN A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1005 GLN B 755 GLN B 907 ASN B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 907 ASN C 913 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9696 Z= 0.243 Angle : 0.595 8.654 13248 Z= 0.315 Chirality : 0.042 0.144 1650 Planarity : 0.005 0.040 1698 Dihedral : 4.109 15.120 1893 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.50 % Allowed : 9.17 % Favored : 88.33 % 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: 1.67 (0.23), residues: 1248 helix: 2.55 (0.21), residues: 573 sheet: 1.19 (0.38), residues: 153 loop : -0.60 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 886 HIS 0.003 0.001 HIS C1101 PHE 0.022 0.002 PHE C 906 TYR 0.017 0.002 TYR C1067 ARG 0.004 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.035 Fit side-chains REVERT: A 725 GLU cc_start: 0.8003 (tt0) cc_final: 0.7725 (tt0) REVERT: A 752 LEU cc_start: 0.8644 (mt) cc_final: 0.8328 (mt) REVERT: A 855 PHE cc_start: 0.7696 (m-80) cc_final: 0.7475 (m-80) REVERT: A 935 GLN cc_start: 0.6946 (mt0) cc_final: 0.6612 (mt0) REVERT: B 804 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7353 (mt0) REVERT: B 904 TYR cc_start: 0.7204 (m-10) cc_final: 0.6122 (m-10) REVERT: B 1028 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8198 (mttm) REVERT: B 1029 MET cc_start: 0.8243 (tpp) cc_final: 0.8040 (tpp) REVERT: C 725 GLU cc_start: 0.8045 (tt0) cc_final: 0.7729 (tt0) REVERT: C 752 LEU cc_start: 0.8565 (mt) cc_final: 0.8355 (mt) outliers start: 21 outliers final: 5 residues processed: 131 average time/residue: 1.2030 time to fit residues: 169.1556 Evaluate side-chains 115 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 91 optimal weight: 1.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1054 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9696 Z= 0.277 Angle : 0.564 5.135 13248 Z= 0.299 Chirality : 0.042 0.132 1650 Planarity : 0.005 0.042 1698 Dihedral : 3.792 16.613 1893 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.26 % Allowed : 10.36 % Favored : 87.38 % 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: 1.60 (0.23), residues: 1248 helix: 2.51 (0.21), residues: 585 sheet: 1.10 (0.37), residues: 153 loop : -0.73 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 886 HIS 0.004 0.001 HIS A1083 PHE 0.022 0.002 PHE C 906 TYR 0.021 0.002 TYR C1067 ARG 0.005 0.001 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.993 Fit side-chains REVERT: A 725 GLU cc_start: 0.8089 (tt0) cc_final: 0.7734 (tt0) REVERT: A 752 LEU cc_start: 0.8671 (mt) cc_final: 0.8366 (mt) REVERT: A 855 PHE cc_start: 0.7872 (m-80) cc_final: 0.7581 (m-80) REVERT: B 904 TYR cc_start: 0.7109 (m-10) cc_final: 0.6225 (m-10) REVERT: C 725 GLU cc_start: 0.8084 (tt0) cc_final: 0.7810 (tt0) REVERT: C 752 LEU cc_start: 0.8585 (mt) cc_final: 0.8380 (mt) REVERT: C 900 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8059 (mtp) REVERT: C 904 TYR cc_start: 0.7190 (m-10) cc_final: 0.6893 (m-10) REVERT: C 1050 MET cc_start: 0.8318 (ptm) cc_final: 0.8048 (ptp) outliers start: 19 outliers final: 7 residues processed: 122 average time/residue: 1.2587 time to fit residues: 164.4112 Evaluate side-chains 115 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN B 955 ASN B1119 ASN C 764 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9696 Z= 0.201 Angle : 0.500 5.024 13248 Z= 0.264 Chirality : 0.040 0.127 1650 Planarity : 0.004 0.040 1698 Dihedral : 3.577 14.962 1893 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.19 % Allowed : 11.67 % Favored : 87.14 % 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: 1.70 (0.23), residues: 1248 helix: 2.62 (0.21), residues: 597 sheet: 0.99 (0.37), residues: 153 loop : -0.74 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 886 HIS 0.003 0.001 HIS B1101 PHE 0.012 0.001 PHE A 906 TYR 0.017 0.002 TYR C1067 ARG 0.003 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.142 Fit side-chains REVERT: A 725 GLU cc_start: 0.8033 (tt0) cc_final: 0.7718 (tt0) REVERT: A 731 MET cc_start: 0.8666 (ptt) cc_final: 0.8448 (ptt) REVERT: A 752 LEU cc_start: 0.8650 (mt) cc_final: 0.8376 (mt) REVERT: A 855 PHE cc_start: 0.7908 (m-80) cc_final: 0.7581 (m-80) REVERT: B 731 MET cc_start: 0.8687 (ptt) cc_final: 0.8278 (ptp) REVERT: B 904 TYR cc_start: 0.7032 (m-10) cc_final: 0.6200 (m-10) REVERT: C 725 GLU cc_start: 0.8087 (tt0) cc_final: 0.7808 (tt0) REVERT: C 752 LEU cc_start: 0.8621 (mt) cc_final: 0.8421 (mt) REVERT: C 904 TYR cc_start: 0.7123 (m-10) cc_final: 0.6808 (m-10) REVERT: C 935 GLN cc_start: 0.6971 (mt0) cc_final: 0.6646 (mt0) outliers start: 10 outliers final: 4 residues processed: 113 average time/residue: 1.3157 time to fit residues: 159.0947 Evaluate side-chains 107 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9696 Z= 0.225 Angle : 0.518 9.623 13248 Z= 0.270 Chirality : 0.041 0.131 1650 Planarity : 0.004 0.040 1698 Dihedral : 3.683 15.537 1893 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.79 % Allowed : 11.90 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.23), residues: 1248 helix: 2.60 (0.21), residues: 600 sheet: 0.93 (0.37), residues: 153 loop : -0.78 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 886 HIS 0.003 0.001 HIS B1101 PHE 0.013 0.001 PHE C 906 TYR 0.018 0.002 TYR C1067 ARG 0.002 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.050 Fit side-chains REVERT: A 725 GLU cc_start: 0.8049 (tt0) cc_final: 0.7733 (tt0) REVERT: A 731 MET cc_start: 0.8729 (ptt) cc_final: 0.8434 (ptt) REVERT: A 752 LEU cc_start: 0.8665 (mt) cc_final: 0.8383 (mt) REVERT: A 855 PHE cc_start: 0.7938 (m-80) cc_final: 0.7655 (m-80) REVERT: B 731 MET cc_start: 0.8698 (ptt) cc_final: 0.8256 (ptp) REVERT: B 904 TYR cc_start: 0.7009 (m-10) cc_final: 0.6167 (m-10) REVERT: C 725 GLU cc_start: 0.8130 (tt0) cc_final: 0.7866 (tt0) REVERT: C 752 LEU cc_start: 0.8619 (mt) cc_final: 0.8399 (mt) REVERT: C 755 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7769 (pt0) REVERT: C 904 TYR cc_start: 0.7190 (m-10) cc_final: 0.6856 (m-10) REVERT: C 935 GLN cc_start: 0.7039 (mt0) cc_final: 0.6806 (mt0) outliers start: 15 outliers final: 6 residues processed: 114 average time/residue: 1.2774 time to fit residues: 155.9190 Evaluate side-chains 109 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9696 Z= 0.226 Angle : 0.512 7.582 13248 Z= 0.268 Chirality : 0.041 0.134 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.723 15.801 1893 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.26 % Allowed : 12.02 % Favored : 85.71 % 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: 1.69 (0.23), residues: 1248 helix: 2.60 (0.21), residues: 600 sheet: 0.95 (0.37), residues: 153 loop : -0.75 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.011 0.001 PHE C 898 TYR 0.018 0.002 TYR C1067 ARG 0.002 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.000 Fit side-chains REVERT: A 725 GLU cc_start: 0.8067 (tt0) cc_final: 0.7752 (tt0) REVERT: A 731 MET cc_start: 0.8735 (ptt) cc_final: 0.8396 (ptt) REVERT: A 752 LEU cc_start: 0.8674 (mt) cc_final: 0.8405 (mt) REVERT: A 855 PHE cc_start: 0.7947 (m-80) cc_final: 0.7638 (m-80) REVERT: B 731 MET cc_start: 0.8721 (ptt) cc_final: 0.8296 (ptp) REVERT: B 904 TYR cc_start: 0.7026 (m-10) cc_final: 0.6177 (m-10) REVERT: C 725 GLU cc_start: 0.8080 (tt0) cc_final: 0.7829 (tt0) REVERT: C 752 LEU cc_start: 0.8625 (mt) cc_final: 0.8421 (mt) REVERT: C 904 TYR cc_start: 0.7173 (m-10) cc_final: 0.6851 (m-10) REVERT: C 935 GLN cc_start: 0.7061 (mt0) cc_final: 0.6811 (mt0) REVERT: C 1050 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7998 (ptp) outliers start: 19 outliers final: 9 residues processed: 111 average time/residue: 1.2683 time to fit residues: 150.6402 Evaluate side-chains 112 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 999 CYS Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9696 Z= 0.216 Angle : 0.521 10.484 13248 Z= 0.271 Chirality : 0.041 0.131 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.727 15.862 1893 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.14 % Allowed : 12.26 % Favored : 85.60 % 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: 1.67 (0.23), residues: 1248 helix: 2.60 (0.21), residues: 600 sheet: 1.00 (0.37), residues: 153 loop : -0.79 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.011 0.001 PHE B1121 TYR 0.017 0.002 TYR C1067 ARG 0.002 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.965 Fit side-chains REVERT: A 725 GLU cc_start: 0.8067 (tt0) cc_final: 0.7752 (tt0) REVERT: A 731 MET cc_start: 0.8728 (ptt) cc_final: 0.8384 (ptt) REVERT: A 855 PHE cc_start: 0.7972 (m-80) cc_final: 0.7696 (m-80) REVERT: B 731 MET cc_start: 0.8727 (ptt) cc_final: 0.8319 (ptp) REVERT: B 904 TYR cc_start: 0.7004 (m-10) cc_final: 0.6167 (m-10) REVERT: C 725 GLU cc_start: 0.8082 (tt0) cc_final: 0.7843 (tt0) REVERT: C 904 TYR cc_start: 0.7209 (m-10) cc_final: 0.6888 (m-10) REVERT: C 935 GLN cc_start: 0.7132 (mt0) cc_final: 0.6883 (mt0) REVERT: C 1050 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7991 (ptp) outliers start: 18 outliers final: 8 residues processed: 107 average time/residue: 1.3770 time to fit residues: 157.4808 Evaluate side-chains 108 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 999 CYS Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 0.0470 chunk 106 optimal weight: 4.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9696 Z= 0.217 Angle : 0.519 9.108 13248 Z= 0.270 Chirality : 0.040 0.125 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.741 16.319 1893 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.90 % Allowed : 12.62 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.23), residues: 1248 helix: 2.60 (0.21), residues: 600 sheet: 1.00 (0.37), residues: 153 loop : -0.78 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.011 0.001 PHE B1121 TYR 0.017 0.002 TYR C1067 ARG 0.002 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 1.071 Fit side-chains REVERT: A 725 GLU cc_start: 0.8071 (tt0) cc_final: 0.7767 (tt0) REVERT: A 731 MET cc_start: 0.8730 (ptt) cc_final: 0.8381 (ptt) REVERT: A 935 GLN cc_start: 0.6974 (mt0) cc_final: 0.6760 (tt0) REVERT: B 731 MET cc_start: 0.8725 (ptt) cc_final: 0.8333 (ptp) REVERT: B 904 TYR cc_start: 0.6998 (m-10) cc_final: 0.6164 (m-10) REVERT: C 725 GLU cc_start: 0.8083 (tt0) cc_final: 0.7846 (tt0) REVERT: C 765 ARG cc_start: 0.7368 (mtp-110) cc_final: 0.7092 (mtp85) REVERT: C 904 TYR cc_start: 0.7258 (m-10) cc_final: 0.6874 (m-10) REVERT: C 935 GLN cc_start: 0.7114 (mt0) cc_final: 0.6689 (mt0) REVERT: C 1050 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8007 (ptp) outliers start: 16 outliers final: 9 residues processed: 109 average time/residue: 1.4495 time to fit residues: 168.3950 Evaluate side-chains 111 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 999 CYS Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 116 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9696 Z= 0.193 Angle : 0.503 9.225 13248 Z= 0.261 Chirality : 0.040 0.129 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.676 17.111 1893 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.43 % Allowed : 12.98 % Favored : 85.60 % 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: 1.77 (0.23), residues: 1248 helix: 2.68 (0.21), residues: 600 sheet: 1.03 (0.37), residues: 153 loop : -0.74 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.011 0.001 PHE B1121 TYR 0.016 0.001 TYR C1067 ARG 0.002 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.251 Fit side-chains REVERT: A 725 GLU cc_start: 0.8055 (tt0) cc_final: 0.7746 (tt0) REVERT: A 731 MET cc_start: 0.8707 (ptt) cc_final: 0.8390 (ptt) REVERT: B 731 MET cc_start: 0.8697 (ptt) cc_final: 0.8316 (ptp) REVERT: B 904 TYR cc_start: 0.6956 (m-10) cc_final: 0.6118 (m-10) REVERT: C 765 ARG cc_start: 0.7321 (mtp-110) cc_final: 0.7031 (mtp85) REVERT: C 904 TYR cc_start: 0.7182 (m-10) cc_final: 0.6916 (m-10) REVERT: C 935 GLN cc_start: 0.7030 (mt0) cc_final: 0.6825 (mt0) REVERT: C 1050 MET cc_start: 0.8312 (ptm) cc_final: 0.7982 (ptp) outliers start: 12 outliers final: 8 residues processed: 109 average time/residue: 1.3559 time to fit residues: 157.7217 Evaluate side-chains 114 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 115 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 0.0770 chunk 79 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 969 ASN B1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9696 Z= 0.141 Angle : 0.467 9.231 13248 Z= 0.242 Chirality : 0.039 0.125 1650 Planarity : 0.004 0.037 1698 Dihedral : 3.454 17.404 1893 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.83 % Allowed : 14.05 % Favored : 85.12 % 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: 1.98 (0.24), residues: 1248 helix: 2.85 (0.22), residues: 603 sheet: 1.07 (0.38), residues: 153 loop : -0.62 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 886 HIS 0.002 0.001 HIS C1048 PHE 0.010 0.001 PHE B1121 TYR 0.015 0.001 TYR A1067 ARG 0.001 0.000 ARG C 995 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 1.045 Fit side-chains REVERT: A 725 GLU cc_start: 0.8049 (tt0) cc_final: 0.7730 (tt0) REVERT: A 731 MET cc_start: 0.8621 (ptt) cc_final: 0.8242 (ptm) REVERT: B 731 MET cc_start: 0.8693 (ptt) cc_final: 0.8300 (ptp) REVERT: B 904 TYR cc_start: 0.6907 (m-10) cc_final: 0.6290 (m-10) REVERT: C 765 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.6977 (mtp85) REVERT: C 935 GLN cc_start: 0.6972 (mt0) cc_final: 0.6755 (mt0) REVERT: C 1050 MET cc_start: 0.8258 (ptm) cc_final: 0.7970 (ptp) outliers start: 7 outliers final: 3 residues processed: 116 average time/residue: 1.3821 time to fit residues: 170.5150 Evaluate side-chains 110 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.5980 chunk 92 optimal weight: 0.1980 chunk 14 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.146654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114366 restraints weight = 9630.811| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.75 r_work: 0.3145 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9696 Z= 0.178 Angle : 0.488 8.963 13248 Z= 0.253 Chirality : 0.040 0.125 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.521 16.769 1893 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.07 % Allowed : 14.29 % Favored : 84.64 % 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: 2.02 (0.24), residues: 1248 helix: 2.81 (0.21), residues: 603 sheet: 1.53 (0.41), residues: 123 loop : -0.53 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.011 0.001 PHE B1121 TYR 0.017 0.001 TYR C1067 ARG 0.001 0.000 ARG A 995 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3410.05 seconds wall clock time: 60 minutes 32.59 seconds (3632.59 seconds total)