Starting phenix.real_space_refine on Mon Mar 11 10:12:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwm_26836/03_2024/7uwm_26836.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwm_26836/03_2024/7uwm_26836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwm_26836/03_2024/7uwm_26836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwm_26836/03_2024/7uwm_26836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwm_26836/03_2024/7uwm_26836.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwm_26836/03_2024/7uwm_26836.pdb" } resolution = 2.5 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= 0.021 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 58 5.16 5 C 4984 2.51 5 N 1460 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 83": "OE1" <-> "OE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7972 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 885 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 99} Chain breaks: 1 Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 885 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 99} Chain: "C" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2186 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 249} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 885 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 99} Chain breaks: 1 Chain: "E" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 881 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2124 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 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: 4.73, per 1000 atoms: 0.59 Number of scatterers: 7972 At special positions: 0 Unit cell: (94.874, 110.864, 125.788, 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 58 16.00 O 1470 8.00 N 1460 7.00 C 4984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 245 " - pdb=" SG CYS C 276 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 294 " distance=2.03 Simple disulfide: pdb=" SG CYS D 94 " - pdb=" SG CYS D 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 146 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 144 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 146 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 50 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 277 " - pdb=" SG CYS F 303 " distance=2.03 Simple disulfide: pdb=" SG CYS F 290 " - pdb=" SG CYS F 294 " 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 G 1 " - " NAG G 2 " NAG-ASN " NAG C 401 " - " ASN C 206 " " NAG C 402 " - " ASN C 225 " " NAG C 403 " - " ASN C 54 " " NAG C 404 " - " ASN C 265 " " NAG F 401 " - " ASN F 225 " " NAG F 402 " - " ASN F 54 " " NAG F 403 " - " ASN F 49 " " NAG G 1 " - " ASN C 49 " Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.3 seconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 19 sheets defined 7.4% alpha, 48.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 103 through 109 removed outlier: 3.536A pdb=" N ILE C 106 " --> pdb=" O ASP C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 removed outlier: 3.769A pdb=" N VAL C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'D' and resid 65 through 70 Processing helix chain 'F' and resid 59 through 64 Processing helix chain 'F' and resid 103 through 109 Processing helix chain 'F' and resid 189 through 192 Processing helix chain 'F' and resid 193 through 199 Processing helix chain 'F' and resid 256 through 260 removed outlier: 3.520A pdb=" N PHE F 260 " --> pdb=" O PRO F 257 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.687A pdb=" N GLN A 117 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER A 141 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE A 119 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU A 139 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 121 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LYS A 137 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG A 123 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU A 135 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASN B 50 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LYS A 137 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N HIS B 52 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU A 139 " --> pdb=" O HIS B 52 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE B 133 " --> pdb=" O MET A 46 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE B 115 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N CYS B 144 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 113 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 146 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN B 111 " --> pdb=" O CYS B 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 80 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 153 removed outlier: 5.916A pdb=" N LEU C 295 " --> pdb=" O PRO C 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 35 removed outlier: 4.499A pdb=" N ARG C 34 " --> pdb=" O VAL C 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 54 Processing sheet with id=AA9, first strand: chain 'C' and resid 74 through 83 removed outlier: 4.241A pdb=" N LEU C 76 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU C 97 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE C 78 " --> pdb=" O HIS C 95 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N HIS C 95 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU C 80 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 93 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE C 82 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE C 91 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 208 through 210 Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.381A pdb=" N ASN D 111 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS D 146 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL D 113 " --> pdb=" O CYS D 144 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N CYS D 144 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE D 115 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASN E 50 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS D 137 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS E 52 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU D 139 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE E 133 " --> pdb=" O MET D 46 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE E 115 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N CYS E 144 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL E 113 " --> pdb=" O CYS E 144 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS E 146 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASN E 111 " --> pdb=" O CYS E 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.381A pdb=" N ASN D 111 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS D 146 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL D 113 " --> pdb=" O CYS D 144 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N CYS D 144 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE D 115 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASN E 50 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS D 137 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS E 52 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU D 139 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE E 133 " --> pdb=" O MET D 46 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE E 115 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N CYS E 144 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL E 113 " --> pdb=" O CYS E 144 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS E 146 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASN E 111 " --> pdb=" O CYS E 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 74 through 80 Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AB6, first strand: chain 'D' and resid 150 through 153 removed outlier: 6.805A pdb=" N ILE D 150 " --> pdb=" O ARG F 296 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N SER F 298 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS D 152 " --> pdb=" O SER F 298 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR F 300 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU F 295 " --> pdb=" O PRO F 285 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 74 through 80 Processing sheet with id=AB8, first strand: chain 'F' and resid 34 through 35 removed outlier: 4.253A pdb=" N ARG F 34 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N HIS F 148 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA F 94 " --> pdb=" O HIS F 148 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL F 150 " --> pdb=" O PRO F 92 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE F 91 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE F 82 " --> pdb=" O PHE F 91 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL F 93 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU F 80 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N HIS F 95 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE F 78 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU F 97 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU F 76 " --> pdb=" O GLU F 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 50 through 55 removed outlier: 3.638A pdb=" N SER F 55 " --> pdb=" O CYS F 126 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS F 126 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 208 through 212 275 hydrogen bonds defined for protein. 732 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: 2.68 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2680 1.34 - 1.47: 1906 1.47 - 1.59: 3539 1.59 - 1.71: 0 1.71 - 1.84: 73 Bond restraints: 8198 Sorted by residual: bond pdb=" C PRO F 195 " pdb=" O PRO F 195 " ideal model delta sigma weight residual 1.237 1.217 0.020 1.26e-02 6.30e+03 2.59e+00 bond pdb=" C1 NAG F 402 " pdb=" O5 NAG F 402 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG F 403 " pdb=" O5 NAG F 403 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" C THR F 194 " pdb=" N PRO F 195 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.36e-02 5.41e+03 2.11e+00 bond pdb=" C1 NAG F 401 " pdb=" O5 NAG F 401 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 8193 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.59: 257 105.59 - 112.72: 4571 112.72 - 119.85: 2492 119.85 - 126.98: 3689 126.98 - 134.11: 170 Bond angle restraints: 11179 Sorted by residual: angle pdb=" CA ILE F 207 " pdb=" CB ILE F 207 " pdb=" CG1 ILE F 207 " ideal model delta sigma weight residual 110.40 114.97 -4.57 1.70e+00 3.46e-01 7.21e+00 angle pdb=" CA LYS D 39 " pdb=" CB LYS D 39 " pdb=" CG LYS D 39 " ideal model delta sigma weight residual 114.10 119.11 -5.01 2.00e+00 2.50e-01 6.27e+00 angle pdb=" CB ILE F 207 " pdb=" CG1 ILE F 207 " pdb=" CD1 ILE F 207 " ideal model delta sigma weight residual 113.80 118.93 -5.13 2.10e+00 2.27e-01 5.96e+00 angle pdb=" N THR C 56 " pdb=" CA THR C 56 " pdb=" C THR C 56 " ideal model delta sigma weight residual 110.50 107.18 3.32 1.41e+00 5.03e-01 5.54e+00 angle pdb=" CA ASN F 174 " pdb=" CB ASN F 174 " pdb=" CG ASN F 174 " ideal model delta sigma weight residual 112.60 114.86 -2.26 1.00e+00 1.00e+00 5.11e+00 ... (remaining 11174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4310 17.52 - 35.03: 581 35.03 - 52.55: 161 52.55 - 70.06: 42 70.06 - 87.58: 20 Dihedral angle restraints: 5114 sinusoidal: 2247 harmonic: 2867 Sorted by residual: dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 50 " pdb=" CB CYS C 50 " ideal model delta sinusoidal sigma weight residual 93.00 166.87 -73.87 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " pdb=" SG CYS A 144 " pdb=" CB CYS A 144 " ideal model delta sinusoidal sigma weight residual -86.00 -135.32 49.32 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS B 94 " pdb=" SG CYS B 94 " pdb=" SG CYS B 144 " pdb=" CB CYS B 144 " ideal model delta sinusoidal sigma weight residual -86.00 -130.31 44.31 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 5111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 747 0.032 - 0.064: 337 0.064 - 0.097: 101 0.097 - 0.129: 63 0.129 - 0.161: 5 Chirality restraints: 1253 Sorted by residual: chirality pdb=" CA ASN F 174 " pdb=" N ASN F 174 " pdb=" C ASN F 174 " pdb=" CB ASN F 174 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 265 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE F 252 " pdb=" N ILE F 252 " pdb=" C ILE F 252 " pdb=" CB ILE F 252 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1250 not shown) Planarity restraints: 1461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 81 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO E 82 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 82 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 82 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 45 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO F 46 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 46 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 46 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 256 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO F 257 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 257 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 257 " 0.025 5.00e-02 4.00e+02 ... (remaining 1458 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 132 2.67 - 3.22: 6645 3.22 - 3.78: 11870 3.78 - 4.34: 16607 4.34 - 4.90: 27536 Nonbonded interactions: 62790 Sorted by model distance: nonbonded pdb=" OG1 THR F 208 " pdb=" OG SER F 220 " model vdw 2.107 2.440 nonbonded pdb=" O VAL B 88 " pdb=" NH2 ARG C 124 " model vdw 2.159 2.520 nonbonded pdb=" OG1 THR F 99 " pdb=" O TRP F 142 " model vdw 2.196 2.440 nonbonded pdb=" OG1 THR C 121 " pdb=" OE1 GLU C 123 " model vdw 2.252 2.440 nonbonded pdb=" OE2 GLU F 156 " pdb=" ND2 ASN F 179 " model vdw 2.276 2.520 ... (remaining 62785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 42 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 150)) selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 33 through 190 or (resid 191 and (name N or name CA or nam \ e C or name O or name CB )) or resid 192 through 212 or (resid 213 and (name N o \ r name CA or name C or name O or name CB )) or resid 217 through 239 or (resid 2 \ 40 through 242 and (name N or name CA or name C or name O or name CB )) or resid \ 243 through 267 or resid 277 through 303 or resid 402 through 404)) selection = (chain 'F' and (resid 33 through 213 or resid 217 through 303 or resid 401 throu \ gh 403)) } 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: 1.160 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: 3.890 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.150 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.004 0.036 8198 Z= 0.245 Angle : 0.589 6.733 11179 Z= 0.304 Chirality : 0.044 0.161 1253 Planarity : 0.005 0.071 1453 Dihedral : 17.880 87.578 3169 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.96 % Allowed : 26.13 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -0.69 (0.27), residues: 947 helix: -1.94 (0.69), residues: 52 sheet: 0.01 (0.24), residues: 445 loop : -0.65 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 224 HIS 0.010 0.001 HIS C 187 PHE 0.017 0.001 PHE C 237 TYR 0.011 0.001 TYR B 85 ARG 0.004 0.000 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 192 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 34 ARG cc_start: 0.8201 (ptt-90) cc_final: 0.7884 (ptt180) outliers start: 27 outliers final: 22 residues processed: 213 average time/residue: 1.2428 time to fit residues: 279.3521 Evaluate side-chains 212 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.0050 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.0170 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 53 ASN B 55 ASN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 280 GLN F 45 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8198 Z= 0.215 Angle : 0.543 7.201 11179 Z= 0.277 Chirality : 0.044 0.166 1253 Planarity : 0.005 0.057 1453 Dihedral : 7.097 88.783 1270 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.16 % Allowed : 22.28 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -0.62 (0.27), residues: 947 helix: -1.88 (0.65), residues: 52 sheet: 0.11 (0.24), residues: 441 loop : -0.66 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 224 HIS 0.011 0.001 HIS C 187 PHE 0.017 0.001 PHE C 237 TYR 0.015 0.001 TYR E 85 ARG 0.003 0.000 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 189 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 110 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7115 (mmt) REVERT: F 34 ARG cc_start: 0.8244 (ptt-90) cc_final: 0.7876 (ptt180) REVERT: F 181 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8213 (tt) outliers start: 47 outliers final: 25 residues processed: 215 average time/residue: 1.2976 time to fit residues: 294.0544 Evaluate side-chains 213 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 290 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 55 ASN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 280 GLN F 45 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8198 Z= 0.289 Angle : 0.570 6.724 11179 Z= 0.290 Chirality : 0.045 0.174 1253 Planarity : 0.005 0.052 1453 Dihedral : 6.087 59.438 1246 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.71 % Allowed : 21.84 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -0.59 (0.26), residues: 947 helix: -1.85 (0.66), residues: 52 sheet: 0.19 (0.24), residues: 438 loop : -0.71 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 74 HIS 0.011 0.001 HIS C 187 PHE 0.017 0.002 PHE C 237 TYR 0.016 0.002 TYR E 85 ARG 0.003 0.000 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 154 ASP cc_start: 0.7337 (t70) cc_final: 0.7071 (t70) REVERT: D 134 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7881 (ttt-90) REVERT: E 110 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7170 (mmt) REVERT: F 34 ARG cc_start: 0.8278 (ptt-90) cc_final: 0.7834 (ptt180) REVERT: F 87 GLN cc_start: 0.8214 (mp10) cc_final: 0.7622 (mp10) REVERT: F 156 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: F 181 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8367 (tt) outliers start: 52 outliers final: 30 residues processed: 228 average time/residue: 1.2699 time to fit residues: 305.5682 Evaluate side-chains 232 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 198 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 211 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 53 ASN B 55 ASN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 280 GLN F 45 GLN F 118 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8198 Z= 0.259 Angle : 0.558 6.634 11179 Z= 0.283 Chirality : 0.045 0.166 1253 Planarity : 0.004 0.049 1453 Dihedral : 5.905 55.372 1246 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.49 % Allowed : 22.28 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -0.63 (0.26), residues: 947 helix: -1.85 (0.66), residues: 52 sheet: 0.17 (0.24), residues: 438 loop : -0.76 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 224 HIS 0.010 0.001 HIS C 187 PHE 0.016 0.002 PHE C 237 TYR 0.015 0.002 TYR E 85 ARG 0.003 0.000 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 198 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 VAL cc_start: 0.8838 (m) cc_final: 0.8572 (p) REVERT: C 154 ASP cc_start: 0.7317 (t70) cc_final: 0.7037 (t70) REVERT: E 110 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.6916 (mmt) REVERT: F 34 ARG cc_start: 0.8281 (ptt-90) cc_final: 0.7864 (ptt180) REVERT: F 156 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7558 (tp30) REVERT: F 181 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8376 (tt) outliers start: 50 outliers final: 32 residues processed: 227 average time/residue: 1.1968 time to fit residues: 287.3672 Evaluate side-chains 226 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.0060 chunk 36 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 79 ASN B 53 ASN B 117 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8198 Z= 0.217 Angle : 0.542 6.636 11179 Z= 0.275 Chirality : 0.045 0.252 1253 Planarity : 0.004 0.046 1453 Dihedral : 5.769 54.204 1246 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 6.04 % Allowed : 22.83 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -0.59 (0.26), residues: 947 helix: -1.73 (0.67), residues: 52 sheet: 0.19 (0.24), residues: 437 loop : -0.73 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 224 HIS 0.010 0.001 HIS C 187 PHE 0.015 0.001 PHE C 237 TYR 0.014 0.001 TYR E 85 ARG 0.003 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7867 (ttm-80) REVERT: C 154 ASP cc_start: 0.7318 (t70) cc_final: 0.7040 (t70) REVERT: C 185 CYS cc_start: 0.7322 (m) cc_final: 0.7063 (m) REVERT: E 110 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.6884 (mmt) REVERT: F 34 ARG cc_start: 0.8270 (ptt-90) cc_final: 0.7850 (ptt180) REVERT: F 156 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: F 181 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8335 (tt) outliers start: 55 outliers final: 36 residues processed: 221 average time/residue: 1.2400 time to fit residues: 289.4459 Evaluate side-chains 232 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 53 ASN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 261 HIS C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8198 Z= 0.398 Angle : 0.617 6.685 11179 Z= 0.314 Chirality : 0.047 0.198 1253 Planarity : 0.005 0.047 1453 Dihedral : 5.974 51.373 1246 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 7.24 % Allowed : 21.73 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -0.71 (0.26), residues: 947 helix: -1.86 (0.66), residues: 52 sheet: 0.11 (0.24), residues: 440 loop : -0.81 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 74 HIS 0.011 0.001 HIS C 187 PHE 0.016 0.002 PHE C 237 TYR 0.019 0.002 TYR E 85 ARG 0.004 0.000 ARG E 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 191 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.7513 (m-40) cc_final: 0.7161 (m110) REVERT: B 97 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8225 (mp) REVERT: C 154 ASP cc_start: 0.7350 (t70) cc_final: 0.7051 (t70) REVERT: E 110 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7170 (mmt) REVERT: F 34 ARG cc_start: 0.8419 (ptt-90) cc_final: 0.8059 (ptt180) REVERT: F 156 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: F 181 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8531 (tt) outliers start: 66 outliers final: 41 residues processed: 230 average time/residue: 1.2037 time to fit residues: 292.8015 Evaluate side-chains 236 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 191 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 53 ASN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 231 GLN C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8198 Z= 0.293 Angle : 0.585 8.389 11179 Z= 0.296 Chirality : 0.045 0.173 1253 Planarity : 0.005 0.046 1453 Dihedral : 5.893 50.052 1246 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.60 % Allowed : 23.27 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -0.72 (0.26), residues: 947 helix: -1.79 (0.67), residues: 52 sheet: 0.09 (0.24), residues: 439 loop : -0.81 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 74 HIS 0.010 0.001 HIS C 187 PHE 0.015 0.002 PHE C 237 TYR 0.017 0.002 TYR C 230 ARG 0.006 0.000 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 191 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8227 (mp) REVERT: C 154 ASP cc_start: 0.7337 (t70) cc_final: 0.7044 (t70) REVERT: E 110 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.6806 (mmt) REVERT: F 34 ARG cc_start: 0.8318 (ptt-90) cc_final: 0.7943 (ptt180) REVERT: F 156 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: F 181 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8448 (tt) REVERT: F 207 ILE cc_start: 0.4946 (OUTLIER) cc_final: 0.4480 (pp) outliers start: 51 outliers final: 34 residues processed: 220 average time/residue: 1.2462 time to fit residues: 289.3516 Evaluate side-chains 229 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 77 optimal weight: 0.0570 chunk 82 optimal weight: 1.9990 overall best weight: 0.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 79 ASN B 53 ASN B 117 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8198 Z= 0.287 Angle : 0.580 6.699 11179 Z= 0.294 Chirality : 0.045 0.171 1253 Planarity : 0.005 0.045 1453 Dihedral : 5.865 50.332 1246 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.49 % Allowed : 23.49 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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 (0.26), residues: 947 helix: -1.78 (0.67), residues: 52 sheet: 0.09 (0.24), residues: 439 loop : -0.78 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 74 HIS 0.010 0.001 HIS C 187 PHE 0.016 0.002 PHE C 237 TYR 0.017 0.002 TYR C 230 ARG 0.003 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 193 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8230 (mp) REVERT: C 154 ASP cc_start: 0.7325 (t70) cc_final: 0.7035 (t70) REVERT: E 110 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.6709 (mmt) REVERT: F 34 ARG cc_start: 0.8317 (ptt-90) cc_final: 0.7942 (ptt180) REVERT: F 156 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7568 (tp30) REVERT: F 181 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8480 (tt) REVERT: F 190 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7288 (tpt) REVERT: F 207 ILE cc_start: 0.4968 (OUTLIER) cc_final: 0.4496 (pp) outliers start: 50 outliers final: 35 residues processed: 220 average time/residue: 1.2205 time to fit residues: 283.6026 Evaluate side-chains 231 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 79 ASN B 53 ASN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8198 Z= 0.259 Angle : 0.569 6.686 11179 Z= 0.289 Chirality : 0.045 0.167 1253 Planarity : 0.005 0.045 1453 Dihedral : 5.814 50.516 1246 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.16 % Allowed : 24.15 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -0.66 (0.26), residues: 947 helix: -1.73 (0.67), residues: 52 sheet: 0.11 (0.24), residues: 439 loop : -0.75 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 224 HIS 0.010 0.001 HIS C 187 PHE 0.015 0.002 PHE C 237 TYR 0.015 0.002 TYR E 85 ARG 0.003 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 194 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8249 (mp) REVERT: C 154 ASP cc_start: 0.7321 (t70) cc_final: 0.7031 (t70) REVERT: C 185 CYS cc_start: 0.7395 (m) cc_final: 0.7132 (m) REVERT: E 110 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.6703 (mmt) REVERT: F 34 ARG cc_start: 0.8309 (ptt-90) cc_final: 0.7930 (ptt180) REVERT: F 156 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: F 181 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8427 (tt) REVERT: F 207 ILE cc_start: 0.4961 (OUTLIER) cc_final: 0.4487 (pp) outliers start: 47 outliers final: 32 residues processed: 219 average time/residue: 1.2796 time to fit residues: 295.9890 Evaluate side-chains 230 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 193 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 22 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: A 35 ASN A 79 ASN B 53 ASN B 55 ASN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8198 Z= 0.265 Angle : 0.580 7.903 11179 Z= 0.293 Chirality : 0.045 0.166 1253 Planarity : 0.005 0.045 1453 Dihedral : 5.788 50.944 1246 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.94 % Allowed : 24.48 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -0.65 (0.26), residues: 947 helix: -1.70 (0.67), residues: 52 sheet: 0.10 (0.24), residues: 440 loop : -0.73 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 224 HIS 0.010 0.001 HIS C 187 PHE 0.015 0.002 PHE C 237 TYR 0.016 0.002 TYR C 230 ARG 0.005 0.000 ARG F 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 193 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8247 (mp) REVERT: C 154 ASP cc_start: 0.7322 (t70) cc_final: 0.7039 (t70) REVERT: C 185 CYS cc_start: 0.7410 (m) cc_final: 0.7145 (m) REVERT: E 110 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.6708 (mmt) REVERT: F 34 ARG cc_start: 0.8314 (ptt-90) cc_final: 0.7936 (ptt180) REVERT: F 156 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7558 (tp30) REVERT: F 181 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8469 (tt) outliers start: 45 outliers final: 36 residues processed: 216 average time/residue: 1.2006 time to fit residues: 273.9011 Evaluate side-chains 231 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 53 ASN B 55 ASN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.151698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132976 restraints weight = 10654.984| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.99 r_work: 0.3675 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8198 Z= 0.265 Angle : 0.586 9.904 11179 Z= 0.295 Chirality : 0.045 0.165 1253 Planarity : 0.005 0.044 1453 Dihedral : 5.787 50.886 1246 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.16 % Allowed : 24.15 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % 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: -0.65 (0.26), residues: 947 helix: -1.66 (0.68), residues: 52 sheet: 0.11 (0.24), residues: 440 loop : -0.75 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 224 HIS 0.010 0.001 HIS C 187 PHE 0.015 0.002 PHE C 237 TYR 0.014 0.002 TYR C 230 ARG 0.006 0.000 ARG F 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4621.53 seconds wall clock time: 82 minutes 5.32 seconds (4925.32 seconds total)