Starting phenix.real_space_refine on Wed Feb 12 14:02:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwm_26836/02_2025/7uwm_26836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwm_26836/02_2025/7uwm_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/cci-nas-00/data/ceres_data/7uwm_26836/02_2025/7uwm_26836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwm_26836/02_2025/7uwm_26836.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwm_26836/02_2025/7uwm_26836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwm_26836/02_2025/7uwm_26836.cif" } 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. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.16, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 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: 1.92 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: 0.98 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: 2.23 Time building geometry restraints manager: 2.27 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: 0.00 - 1.35: 10748 1.35 - 2.69: 347 2.69 - 4.04: 66 4.04 - 5.39: 15 5.39 - 6.73: 3 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 3.040 nonbonded pdb=" O VAL B 88 " pdb=" NH2 ARG C 124 " model vdw 2.159 3.120 nonbonded pdb=" OG1 THR F 99 " pdb=" O TRP F 142 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR C 121 " pdb=" OE1 GLU C 123 " model vdw 2.252 3.040 nonbonded pdb=" OE2 GLU F 156 " pdb=" ND2 ASN F 179 " model vdw 2.276 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 1.190 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.220 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.855 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: 1.2636 time to fit residues: 284.3227 Evaluate side-chains 212 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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: 0.0770 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.152722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133795 restraints weight = 10657.154| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.00 r_work: 0.3686 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.0562 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= 0.247 Angle : 0.567 7.278 11179 Z= 0.292 Chirality : 0.044 0.209 1253 Planarity : 0.005 0.058 1453 Dihedral : 7.112 89.863 1270 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.39 % Allowed : 22.61 % Favored : 73.00 % 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: -0.54 (0.26), residues: 947 helix: -1.87 (0.65), residues: 52 sheet: 0.16 (0.24), residues: 440 loop : -0.60 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.006 0.000 ARG F 296 *********************** 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 230 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 110 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7168 (mmt) REVERT: F 34 ARG cc_start: 0.8345 (ptt-90) cc_final: 0.7985 (ptt180) REVERT: F 181 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8282 (tt) outliers start: 40 outliers final: 22 residues processed: 215 average time/residue: 1.2827 time to fit residues: 291.6472 Evaluate side-chains 211 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 145 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 THR 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 61 optimal weight: 0.0030 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.2848 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.153317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134504 restraints weight = 10831.992| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.02 r_work: 0.3701 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0827 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= 0.177 Angle : 0.534 6.681 11179 Z= 0.272 Chirality : 0.043 0.177 1253 Planarity : 0.004 0.049 1453 Dihedral : 5.947 59.044 1248 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.61 % Allowed : 22.72 % Favored : 72.67 % 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: -0.45 (0.26), residues: 947 helix: -1.79 (0.66), residues: 52 sheet: 0.22 (0.24), residues: 441 loop : -0.54 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 98 HIS 0.010 0.001 HIS C 187 PHE 0.015 0.001 PHE C 237 TYR 0.011 0.001 TYR E 85 ARG 0.004 0.000 ARG F 296 *********************** 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 236 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 LEU cc_start: 0.8691 (tp) cc_final: 0.8435 (tp) REVERT: C 124 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8044 (mtt-85) REVERT: C 154 ASP cc_start: 0.7686 (t70) cc_final: 0.7441 (t70) REVERT: D 134 ARG cc_start: 0.8351 (tpt-90) cc_final: 0.7889 (ttt-90) REVERT: E 83 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7153 (mm-30) REVERT: E 110 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.6689 (mmt) REVERT: F 34 ARG cc_start: 0.8286 (ptt-90) cc_final: 0.7803 (ptt180) REVERT: F 87 GLN cc_start: 0.8112 (mp10) cc_final: 0.7572 (mp10) REVERT: F 156 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: F 174 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.6699 (p0) REVERT: F 181 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8275 (tt) outliers start: 42 outliers final: 20 residues processed: 213 average time/residue: 1.2876 time to fit residues: 289.6593 Evaluate side-chains 218 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 C residue 56 THR Chi-restraints excluded: chain C residue 124 ARG 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 265 ASN Chi-restraints excluded: chain D residue 136 GLU 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 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 290 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 B 111 ASN C 174 ASN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.150641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131800 restraints weight = 10739.299| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.01 r_work: 0.3661 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.0997 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= 0.375 Angle : 0.616 6.797 11179 Z= 0.314 Chirality : 0.047 0.197 1253 Planarity : 0.005 0.048 1453 Dihedral : 6.070 58.758 1247 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.38 % Allowed : 21.95 % Favored : 72.67 % 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: -1.89 (0.66), residues: 52 sheet: 0.13 (0.24), residues: 440 loop : -0.68 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 74 HIS 0.011 0.001 HIS C 187 PHE 0.017 0.002 PHE C 237 TYR 0.018 0.002 TYR E 85 ARG 0.005 0.001 ARG F 66 *********************** 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 247 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 VAL cc_start: 0.8863 (m) cc_final: 0.8624 (p) REVERT: B 50 ASN cc_start: 0.7407 (m-40) cc_final: 0.7007 (m110) REVERT: C 154 ASP cc_start: 0.7738 (t70) cc_final: 0.7443 (t70) REVERT: F 34 ARG cc_start: 0.8433 (ptt-90) cc_final: 0.8012 (ptt180) REVERT: F 87 GLN cc_start: 0.8118 (mp10) cc_final: 0.7612 (mp10) REVERT: F 181 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8483 (tt) outliers start: 49 outliers final: 32 residues processed: 225 average time/residue: 1.1933 time to fit residues: 284.6235 Evaluate side-chains 227 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 135 LEU 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 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 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 140 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 110 MET 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 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 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 82 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 0.0270 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 64 optimal weight: 0.0020 overall best weight: 0.3446 ------------------------------------------------------------------------------- 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 187 HIS C 280 GLN C 284 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133814 restraints weight = 10657.804| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.00 r_work: 0.3693 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1032 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= 0.188 Angle : 0.543 6.640 11179 Z= 0.277 Chirality : 0.044 0.158 1253 Planarity : 0.004 0.045 1453 Dihedral : 5.755 56.662 1247 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.72 % Allowed : 23.16 % Favored : 72.12 % 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: -1.68 (0.68), residues: 52 sheet: 0.08 (0.24), residues: 443 loop : -0.61 (0.28), residues: 452 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 0.014 0.001 PHE C 237 TYR 0.011 0.001 TYR E 85 ARG 0.004 0.000 ARG F 66 *********************** 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 240 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 ASP cc_start: 0.7711 (t70) cc_final: 0.7437 (t70) REVERT: C 185 CYS cc_start: 0.7408 (m) cc_final: 0.7151 (m) REVERT: D 134 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7879 (ttt-90) REVERT: E 83 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7122 (mm-30) REVERT: F 34 ARG cc_start: 0.8339 (ptt-90) cc_final: 0.7916 (ptt180) REVERT: F 87 GLN cc_start: 0.8129 (mp10) cc_final: 0.7593 (mp10) REVERT: F 174 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6603 (p0) REVERT: F 181 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8356 (tt) outliers start: 43 outliers final: 22 residues processed: 220 average time/residue: 1.2723 time to fit residues: 295.4099 Evaluate side-chains 218 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 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 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 44 THR 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 190 MET Chi-restraints excluded: chain F residue 192 VAL 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 51 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 117 GLN C 174 ASN C 187 HIS C 280 GLN F 45 GLN F 101 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133948 restraints weight = 10732.880| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.01 r_work: 0.3691 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1104 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= 0.209 Angle : 0.545 6.628 11179 Z= 0.277 Chirality : 0.044 0.153 1253 Planarity : 0.004 0.044 1453 Dihedral : 5.639 52.069 1247 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.83 % Allowed : 23.49 % Favored : 71.68 % 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: -0.58 (0.26), residues: 947 helix: -1.63 (0.69), residues: 52 sheet: 0.07 (0.24), residues: 443 loop : -0.58 (0.28), residues: 452 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 0.014 0.001 PHE C 237 TYR 0.012 0.001 TYR E 85 ARG 0.005 0.000 ARG F 66 *********************** 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 236 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 ASP cc_start: 0.7707 (t70) cc_final: 0.7424 (t70) REVERT: C 185 CYS cc_start: 0.7410 (m) cc_final: 0.7155 (m) REVERT: D 134 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7869 (ttt-90) REVERT: E 110 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.6739 (mmt) REVERT: F 34 ARG cc_start: 0.8366 (ptt-90) cc_final: 0.7939 (ptt180) REVERT: F 87 GLN cc_start: 0.8121 (mp10) cc_final: 0.7592 (mp10) REVERT: F 156 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7750 (tp30) REVERT: F 174 ASN cc_start: 0.7237 (OUTLIER) cc_final: 0.6536 (p0) REVERT: F 181 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8397 (tt) outliers start: 44 outliers final: 28 residues processed: 213 average time/residue: 1.2495 time to fit residues: 281.4070 Evaluate side-chains 223 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 145 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 119 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 217 LEU Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain D residue 134 ARG 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 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 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 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 45 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 HIS B 53 ASN B 117 GLN C 67 ASN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.151002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132199 restraints weight = 10738.627| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.01 r_work: 0.3669 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8198 Z= 0.335 Angle : 0.601 6.817 11179 Z= 0.306 Chirality : 0.046 0.170 1253 Planarity : 0.005 0.043 1453 Dihedral : 5.824 50.909 1247 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.16 % Allowed : 23.49 % Favored : 71.35 % 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: -1.71 (0.69), residues: 52 sheet: 0.05 (0.24), residues: 441 loop : -0.68 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 74 HIS 0.011 0.001 HIS C 187 PHE 0.016 0.002 PHE C 237 TYR 0.017 0.002 TYR E 85 ARG 0.006 0.001 ARG F 66 *********************** 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 237 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.7357 (m-40) cc_final: 0.6952 (m110) REVERT: B 97 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8340 (mp) REVERT: C 154 ASP cc_start: 0.7764 (t70) cc_final: 0.7465 (t70) REVERT: C 185 CYS cc_start: 0.7505 (m) cc_final: 0.7253 (m) REVERT: E 110 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.6975 (mmt) REVERT: F 34 ARG cc_start: 0.8444 (ptt-90) cc_final: 0.8046 (ptt180) REVERT: F 156 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7808 (tp30) REVERT: F 181 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8525 (tt) REVERT: F 207 ILE cc_start: 0.4955 (OUTLIER) cc_final: 0.4511 (pp) outliers start: 47 outliers final: 31 residues processed: 215 average time/residue: 1.2266 time to fit residues: 279.2405 Evaluate side-chains 226 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 53 LYS Chi-restraints excluded: chain C residue 56 THR 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 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 C residue 290 CYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 137 LYS 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 59 ASP 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 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 79 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 57 optimal weight: 0.0020 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 0.0570 chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 overall best weight: 0.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 117 GLN C 67 ASN 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 = 0.4037 r_free = 0.4037 target = 0.153509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.134917 restraints weight = 10795.269| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.01 r_work: 0.3703 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8198 Z= 0.165 Angle : 0.533 6.658 11179 Z= 0.271 Chirality : 0.043 0.136 1253 Planarity : 0.004 0.044 1453 Dihedral : 5.529 51.433 1247 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.28 % Allowed : 24.92 % Favored : 70.80 % 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: -1.56 (0.69), residues: 52 sheet: -0.00 (0.24), residues: 447 loop : -0.53 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 98 HIS 0.011 0.001 HIS C 187 PHE 0.014 0.001 PHE C 260 TYR 0.009 0.001 TYR B 85 ARG 0.005 0.000 ARG F 66 *********************** 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 237 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8450 (tpt-90) cc_final: 0.8176 (ttt-90) REVERT: B 139 LEU cc_start: 0.8659 (tp) cc_final: 0.8437 (tp) REVERT: C 154 ASP cc_start: 0.7705 (t70) cc_final: 0.7437 (t70) REVERT: D 134 ARG cc_start: 0.8109 (tpt-90) cc_final: 0.7750 (ttt-90) REVERT: F 34 ARG cc_start: 0.8336 (ptt-90) cc_final: 0.7906 (ptt180) REVERT: F 156 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: F 174 ASN cc_start: 0.7065 (OUTLIER) cc_final: 0.6508 (t0) REVERT: F 181 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8181 (tt) REVERT: F 207 ILE cc_start: 0.4847 (OUTLIER) cc_final: 0.4378 (pp) outliers start: 39 outliers final: 22 residues processed: 220 average time/residue: 1.2682 time to fit residues: 295.0455 Evaluate side-chains 220 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 260 PHE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain F residue 36 LEU 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 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 207 ILE Chi-restraints excluded: chain F residue 290 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 83 optimal weight: 0.0670 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 117 GLN C 67 ASN C 174 ASN C 187 HIS C 280 GLN C 284 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.153020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134233 restraints weight = 10987.734| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.04 r_work: 0.3698 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8198 Z= 0.199 Angle : 0.561 9.258 11179 Z= 0.282 Chirality : 0.044 0.141 1253 Planarity : 0.004 0.044 1453 Dihedral : 5.427 51.591 1244 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.84 % Allowed : 25.25 % 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: -0.55 (0.27), residues: 947 helix: -1.53 (0.69), residues: 52 sheet: -0.00 (0.24), residues: 447 loop : -0.47 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 224 HIS 0.012 0.001 HIS C 187 PHE 0.013 0.001 PHE C 237 TYR 0.011 0.001 TYR E 85 ARG 0.005 0.000 ARG F 66 *********************** 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 230 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 154 ASP cc_start: 0.7736 (t70) cc_final: 0.7462 (t70) REVERT: C 185 CYS cc_start: 0.7385 (m) cc_final: 0.7126 (m) REVERT: D 134 ARG cc_start: 0.8153 (tpt-90) cc_final: 0.7774 (ttt-90) REVERT: F 34 ARG cc_start: 0.8366 (ptt-90) cc_final: 0.7913 (ptt180) REVERT: F 156 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7498 (tp30) REVERT: F 174 ASN cc_start: 0.7084 (OUTLIER) cc_final: 0.6560 (t0) REVERT: F 181 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8189 (tt) REVERT: F 207 ILE cc_start: 0.4920 (OUTLIER) cc_final: 0.4488 (pp) outliers start: 35 outliers final: 23 residues processed: 213 average time/residue: 1.2548 time to fit residues: 282.3065 Evaluate side-chains 219 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 145 THR 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 260 PHE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 36 LEU 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 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 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 27 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 55 ASN B 117 GLN C 67 ASN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.151827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133101 restraints weight = 10704.802| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.00 r_work: 0.3683 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1297 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= 0.293 Angle : 0.594 6.856 11179 Z= 0.303 Chirality : 0.045 0.157 1253 Planarity : 0.005 0.044 1453 Dihedral : 5.443 50.084 1242 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.73 % Allowed : 25.69 % 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: -0.60 (0.27), residues: 947 helix: -1.56 (0.68), residues: 52 sheet: -0.05 (0.24), residues: 447 loop : -0.49 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 224 HIS 0.012 0.001 HIS C 187 PHE 0.015 0.002 PHE C 237 TYR 0.016 0.002 TYR E 85 ARG 0.006 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 224 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 154 ASP cc_start: 0.7727 (t70) cc_final: 0.7438 (t70) REVERT: C 185 CYS cc_start: 0.7493 (m) cc_final: 0.7233 (m) REVERT: D 134 ARG cc_start: 0.8212 (tpt-90) cc_final: 0.7886 (ttt-90) REVERT: E 110 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.6657 (mmt) REVERT: F 34 ARG cc_start: 0.8429 (ptt-90) cc_final: 0.8052 (ptt180) REVERT: F 156 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: F 181 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8446 (tt) REVERT: F 207 ILE cc_start: 0.5005 (OUTLIER) cc_final: 0.4583 (pp) outliers start: 34 outliers final: 24 residues processed: 207 average time/residue: 1.2433 time to fit residues: 271.9908 Evaluate side-chains 220 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 145 THR 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 260 PHE Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 141 SER 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 59 ASP 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 207 ILE Chi-restraints excluded: chain F residue 290 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.0570 chunk 72 optimal weight: 0.7980 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 55 ASN C 67 ASN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.133924 restraints weight = 10747.092| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.01 r_work: 0.3690 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1339 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= 0.222 Angle : 0.580 9.993 11179 Z= 0.292 Chirality : 0.044 0.146 1253 Planarity : 0.004 0.043 1453 Dihedral : 5.354 50.387 1242 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.29 % Allowed : 26.34 % Favored : 70.36 % 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 (0.27), residues: 947 helix: -1.48 (0.69), residues: 52 sheet: -0.07 (0.24), residues: 447 loop : -0.47 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 224 HIS 0.012 0.001 HIS C 187 PHE 0.014 0.001 PHE C 260 TYR 0.013 0.001 TYR E 85 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: 8602.98 seconds wall clock time: 151 minutes 36.96 seconds (9096.96 seconds total)