Starting phenix.real_space_refine (version: dev) on Sat Feb 18 11:18:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwm_26836/02_2023/7uwm_26836.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwm_26836/02_2023/7uwm_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_26836/02_2023/7uwm_26836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwm_26836/02_2023/7uwm_26836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwm_26836/02_2023/7uwm_26836.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwm_26836/02_2023/7uwm_26836.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 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 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 chiralities: 3 Time building chain proxies: 5.41, per 1000 atoms: 0.68 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: 3.08 Conformation dependent library (CDL) restraints added in 1.1 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: 0.46 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: 2.10 Time building geometry restraints manager: 3.29 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=" 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=" CA PRO F 195 " pdb=" C PRO F 195 " ideal model delta sigma weight residual 1.517 1.536 -0.019 1.46e-02 4.69e+03 1.61e+00 bond pdb=" CB ASN F 174 " pdb=" CG ASN F 174 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.24e+00 bond pdb=" CA ASN F 174 " pdb=" CB ASN F 174 " ideal model delta sigma weight residual 1.532 1.547 -0.015 1.43e-02 4.89e+03 1.10e+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: 4191 17.52 - 35.03: 569 35.03 - 52.55: 159 52.55 - 70.06: 40 70.06 - 87.58: 20 Dihedral angle restraints: 4979 sinusoidal: 2112 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 4976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 765 0.032 - 0.064: 328 0.064 - 0.097: 93 0.097 - 0.129: 62 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 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. 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: 0.820 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: 4.070 Check model and map are aligned: 0.120 Process input model: 24.090 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.003 0.036 8198 Z= 0.218 Angle : 0.565 6.733 11179 Z= 0.299 Chirality : 0.044 0.161 1253 Planarity : 0.005 0.071 1453 Dihedral : 18.135 87.578 3034 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 % 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 *********************** 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 : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 22 residues processed: 213 average time/residue: 1.2395 time to fit residues: 279.2789 Evaluate side-chains 212 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 1.2206 time to fit residues: 6.5528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.0670 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: 0.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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: 0.7935 moved from start: 0.0445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8198 Z= 0.218 Angle : 0.543 7.075 11179 Z= 0.278 Chirality : 0.044 0.172 1253 Planarity : 0.005 0.057 1453 Dihedral : 4.930 24.761 1100 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 6.37 % 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: -0.61 (0.27), residues: 947 helix: -1.91 (0.65), residues: 52 sheet: 0.11 (0.24), residues: 441 loop : -0.65 (0.28), residues: 454 *********************** 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 247 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 36 residues processed: 225 average time/residue: 1.2422 time to fit residues: 296.1655 Evaluate side-chains 222 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 22 residues processed: 14 average time/residue: 0.5504 time to fit residues: 9.8753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 90 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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: 0.7938 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 8198 Z= 0.239 Angle : 0.546 6.696 11179 Z= 0.277 Chirality : 0.044 0.170 1253 Planarity : 0.004 0.051 1453 Dihedral : 4.989 25.178 1100 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 6.04 % 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: -0.55 (0.27), residues: 947 helix: -1.81 (0.66), residues: 52 sheet: 0.19 (0.24), residues: 440 loop : -0.66 (0.28), residues: 455 *********************** 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 248 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 32 residues processed: 230 average time/residue: 1.2821 time to fit residues: 311.0686 Evaluate side-chains 226 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 8 average time/residue: 0.5821 time to fit residues: 6.5433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 B 117 GLN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0766 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= 0.272 Angle : 0.565 6.915 11179 Z= 0.287 Chirality : 0.045 0.171 1253 Planarity : 0.004 0.049 1453 Dihedral : 5.047 25.466 1100 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 6.04 % 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: -0.60 (0.26), residues: 947 helix: -1.84 (0.65), residues: 52 sheet: 0.16 (0.24), residues: 440 loop : -0.71 (0.28), residues: 455 *********************** 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 253 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 198 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 39 residues processed: 233 average time/residue: 1.1912 time to fit residues: 293.7946 Evaluate side-chains 229 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 27 residues processed: 12 average time/residue: 0.6719 time to fit residues: 10.1601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0849 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= 0.256 Angle : 0.562 6.632 11179 Z= 0.285 Chirality : 0.045 0.234 1253 Planarity : 0.004 0.046 1453 Dihedral : 5.050 25.726 1100 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 6.15 % 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: -0.61 (0.26), residues: 947 helix: -1.80 (0.66), residues: 52 sheet: 0.17 (0.24), residues: 438 loop : -0.72 (0.28), residues: 457 *********************** 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 247 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 191 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 36 residues processed: 231 average time/residue: 1.2054 time to fit residues: 294.5918 Evaluate side-chains 222 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 8 average time/residue: 0.4698 time to fit residues: 5.5442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 chunk 52 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 117 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 280 GLN E 131 ASN 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: 0.7942 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 8198 Z= 0.234 Angle : 0.549 6.655 11179 Z= 0.280 Chirality : 0.044 0.177 1253 Planarity : 0.004 0.045 1453 Dihedral : 5.016 26.094 1100 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 5.49 % 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: -0.56 (0.26), residues: 947 helix: -1.70 (0.68), residues: 52 sheet: 0.20 (0.24), residues: 437 loop : -0.70 (0.28), residues: 458 *********************** 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 244 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 194 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 41 residues processed: 227 average time/residue: 1.2379 time to fit residues: 296.6967 Evaluate side-chains 231 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 30 residues processed: 11 average time/residue: 0.5979 time to fit residues: 8.5993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0990 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= 0.279 Angle : 0.576 9.270 11179 Z= 0.291 Chirality : 0.045 0.181 1253 Planarity : 0.005 0.045 1453 Dihedral : 5.078 26.444 1100 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 5.71 % 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: -0.60 (0.26), residues: 947 helix: -1.78 (0.67), residues: 52 sheet: 0.17 (0.24), residues: 437 loop : -0.72 (0.28), residues: 458 *********************** 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 246 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 194 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 38 residues processed: 234 average time/residue: 1.1699 time to fit residues: 289.9501 Evaluate side-chains 231 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 30 residues processed: 8 average time/residue: 0.4910 time to fit residues: 5.8224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 261 HIS C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN F 250 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 8198 Z= 0.388 Angle : 0.628 10.507 11179 Z= 0.320 Chirality : 0.047 0.190 1253 Planarity : 0.005 0.045 1453 Dihedral : 5.330 27.483 1100 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 5.82 % 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: -1.91 (0.66), residues: 52 sheet: 0.12 (0.24), residues: 439 loop : -0.79 (0.28), residues: 456 *********************** 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 235 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 182 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 40 residues processed: 221 average time/residue: 1.2173 time to fit residues: 284.5551 Evaluate side-chains 220 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 31 residues processed: 9 average time/residue: 0.4727 time to fit residues: 6.0621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.0870 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 53 ASN B 117 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 280 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8198 Z= 0.213 Angle : 0.556 8.291 11179 Z= 0.282 Chirality : 0.044 0.163 1253 Planarity : 0.004 0.045 1453 Dihedral : 5.070 26.962 1100 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 5.38 % 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: -1.72 (0.68), residues: 52 sheet: 0.16 (0.24), residues: 439 loop : -0.71 (0.28), residues: 456 *********************** 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 236 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 39 residues processed: 224 average time/residue: 1.2369 time to fit residues: 293.1121 Evaluate side-chains 223 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 31 residues processed: 8 average time/residue: 0.5156 time to fit residues: 6.0109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1153 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= 0.263 Angle : 0.574 10.266 11179 Z= 0.292 Chirality : 0.045 0.175 1253 Planarity : 0.005 0.045 1453 Dihedral : 5.111 27.692 1100 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 3.73 % 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 (0.68), residues: 52 sheet: 0.16 (0.24), residues: 439 loop : -0.70 (0.28), residues: 456 ********************** 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 217 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 31 residues processed: 216 average time/residue: 1.2757 time to fit residues: 290.9155 Evaluate side-chains 215 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 1.2771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 73 optimal weight: 0.0770 chunk 30 optimal weight: 0.0970 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 64 optimal weight: 0.0020 chunk 4 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 overall best weight: 0.1482 ------------------------------------------------------------------------------- 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 B 68 ASN B 117 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 280 GLN D 117 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.154689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136029 restraints weight = 10723.952| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.00 r_work: 0.3720 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 8198 Z= 0.154 Angle : 0.527 9.334 11179 Z= 0.266 Chirality : 0.043 0.164 1253 Planarity : 0.004 0.044 1453 Dihedral : 4.773 26.224 1100 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 4.50 % 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: -0.44 (0.27), residues: 947 helix: -1.59 (0.69), residues: 52 sheet: 0.24 (0.24), residues: 439 loop : -0.58 (0.29), residues: 456 =============================================================================== Job complete usr+sys time: 4638.43 seconds wall clock time: 82 minutes 27.39 seconds (4947.39 seconds total)