Starting phenix.real_space_refine on Wed Mar 12 14:31:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwm_26836/03_2025/7uwm_26836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwm_26836/03_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_26836/03_2025/7uwm_26836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwm_26836/03_2025/7uwm_26836.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwm_26836/03_2025/7uwm_26836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwm_26836/03_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-5624/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: 5.17, 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: 1.75 Conformation dependent library (CDL) restraints added in 1.2 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: 0.95 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: 2.01 Time building geometry restraints manager: 2.07 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: 1.040 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.350 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- 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 : 0.909 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: 1.2157 time to fit residues: 273.6294 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 : 0.816 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133783 restraints weight = 10657.154| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.00 r_work: 0.3689 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 110 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7167 (mmt) REVERT: F 34 ARG cc_start: 0.8344 (ptt-90) cc_final: 0.7983 (ptt180) REVERT: F 181 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8279 (tt) outliers start: 40 outliers final: 22 residues processed: 215 average time/residue: 1.2775 time to fit residues: 290.4286 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 : 0.829 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 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: 0.7980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133536 restraints weight = 10814.211| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.02 r_work: 0.3688 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8198 Z= 0.233 Angle : 0.556 6.695 11179 Z= 0.283 Chirality : 0.044 0.186 1253 Planarity : 0.005 0.050 1453 Dihedral : 6.028 59.490 1248 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.27 % Allowed : 22.06 % 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: -0.49 (0.26), residues: 947 helix: -1.84 (0.66), residues: 52 sheet: 0.20 (0.24), residues: 440 loop : -0.57 (0.28), residues: 455 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 0.016 0.001 PHE C 237 TYR 0.014 0.001 TYR E 85 ARG 0.004 0.000 ARG F 66 *********************** 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 239 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7993 (mtt-85) REVERT: C 154 ASP cc_start: 0.7688 (t70) cc_final: 0.7432 (t70) REVERT: D 134 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7922 (ttt-90) REVERT: E 110 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.6939 (mmt) REVERT: F 34 ARG cc_start: 0.8342 (ptt-90) cc_final: 0.7875 (ptt180) REVERT: F 87 GLN cc_start: 0.8119 (mp10) cc_final: 0.7565 (mp10) REVERT: F 156 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: F 181 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8364 (tt) outliers start: 48 outliers final: 23 residues processed: 216 average time/residue: 1.2012 time to fit residues: 274.5033 Evaluate side-chains 219 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 44 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 124 ARG 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 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 E residue 110 MET Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 290 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN F 179 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.151076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.132234 restraints weight = 10752.039| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.01 r_work: 0.3668 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8198 Z= 0.310 Angle : 0.587 6.716 11179 Z= 0.300 Chirality : 0.046 0.184 1253 Planarity : 0.005 0.048 1453 Dihedral : 5.957 57.879 1247 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.38 % Allowed : 22.06 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.26), residues: 947 helix: -1.84 (0.67), residues: 52 sheet: 0.13 (0.24), residues: 438 loop : -0.66 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 224 HIS 0.011 0.001 HIS C 187 PHE 0.017 0.002 PHE C 237 TYR 0.017 0.002 TYR E 85 ARG 0.005 0.000 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 249 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.7376 (m-40) cc_final: 0.6996 (m110) REVERT: C 154 ASP cc_start: 0.7725 (t70) cc_final: 0.7437 (t70) REVERT: D 134 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7896 (ttt-90) REVERT: E 110 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7222 (mmt) REVERT: F 34 ARG cc_start: 0.8403 (ptt-90) cc_final: 0.7972 (ptt180) REVERT: F 87 GLN cc_start: 0.8113 (mp10) cc_final: 0.7584 (mp10) REVERT: F 181 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8441 (tt) outliers start: 49 outliers final: 28 residues processed: 227 average time/residue: 1.2256 time to fit residues: 294.3298 Evaluate side-chains 224 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 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 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 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: 0.5980 chunk 74 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 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 = 0.4018 r_free = 0.4018 target = 0.152117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133348 restraints weight = 10647.406| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.00 r_work: 0.3686 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1070 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= 0.221 Angle : 0.555 6.643 11179 Z= 0.283 Chirality : 0.044 0.162 1253 Planarity : 0.005 0.045 1453 Dihedral : 5.776 55.956 1247 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.38 % Allowed : 22.94 % 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: -0.61 (0.26), residues: 947 helix: -1.68 (0.69), residues: 52 sheet: 0.08 (0.24), residues: 443 loop : -0.64 (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 0.015 0.001 PHE C 237 TYR 0.013 0.001 TYR C 230 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 241 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8603 (mt) REVERT: C 154 ASP cc_start: 0.7725 (t70) cc_final: 0.7438 (t70) REVERT: D 134 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7863 (ttt-90) REVERT: E 110 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.6767 (mmt) REVERT: F 34 ARG cc_start: 0.8360 (ptt-90) cc_final: 0.7939 (ptt180) REVERT: F 87 GLN cc_start: 0.8135 (mp10) cc_final: 0.7591 (mp10) REVERT: F 181 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8389 (tt) outliers start: 49 outliers final: 27 residues processed: 218 average time/residue: 1.2220 time to fit residues: 281.2176 Evaluate side-chains 220 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 53 LYS 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 235 THR 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 E residue 110 MET Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 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: 0.0870 chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 37 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 overall best weight: 0.1834 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.154099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.135430 restraints weight = 10767.452| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.01 r_work: 0.3713 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8198 Z= 0.154 Angle : 0.521 6.592 11179 Z= 0.265 Chirality : 0.043 0.136 1253 Planarity : 0.004 0.043 1453 Dihedral : 5.481 51.715 1247 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.28 % Allowed : 24.15 % Favored : 71.57 % 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: -0.51 (0.26), residues: 947 helix: -1.57 (0.69), residues: 52 sheet: 0.12 (0.24), residues: 444 loop : -0.55 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 98 HIS 0.010 0.000 HIS C 187 PHE 0.014 0.001 PHE C 237 TYR 0.009 0.001 TYR B 85 ARG 0.004 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 234 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 LEU cc_start: 0.8670 (tp) cc_final: 0.8438 (tp) REVERT: C 154 ASP cc_start: 0.7696 (t70) cc_final: 0.7439 (t70) REVERT: C 185 CYS cc_start: 0.7342 (m) cc_final: 0.7077 (m) REVERT: D 133 PHE cc_start: 0.7456 (m-80) cc_final: 0.7236 (m-80) REVERT: D 134 ARG cc_start: 0.8293 (tpt-90) cc_final: 0.7831 (ttt-90) REVERT: F 34 ARG cc_start: 0.8318 (ptt-90) cc_final: 0.7950 (ptt180) REVERT: F 59 ASP cc_start: 0.7590 (t70) cc_final: 0.7195 (m-30) REVERT: F 156 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7341 (tp30) REVERT: F 174 ASN cc_start: 0.7102 (OUTLIER) cc_final: 0.6330 (p0) REVERT: F 181 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8114 (tt) REVERT: F 190 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6863 (tpp) outliers start: 39 outliers final: 21 residues processed: 216 average time/residue: 1.4483 time to fit residues: 331.8041 Evaluate side-chains 213 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 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 290 CYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain F residue 36 LEU 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 190 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 290 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 45 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 chunk 20 optimal weight: 0.0570 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 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 = 0.4027 r_free = 0.4027 target = 0.152809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134089 restraints weight = 10780.553| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.01 r_work: 0.3696 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1252 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= 0.216 Angle : 0.544 6.629 11179 Z= 0.276 Chirality : 0.044 0.146 1253 Planarity : 0.004 0.043 1453 Dihedral : 5.470 51.283 1245 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.83 % Allowed : 23.38 % Favored : 71.79 % 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: -0.50 (0.26), residues: 947 helix: -1.56 (0.69), residues: 52 sheet: 0.13 (0.24), residues: 443 loop : -0.56 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 224 HIS 0.011 0.001 HIS C 187 PHE 0.018 0.001 PHE C 260 TYR 0.013 0.001 TYR E 85 ARG 0.005 0.000 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 236 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8578 (mt) REVERT: C 154 ASP cc_start: 0.7720 (t70) cc_final: 0.7444 (t70) REVERT: C 185 CYS cc_start: 0.7402 (m) cc_final: 0.7148 (m) REVERT: D 134 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7857 (ttt-90) REVERT: F 34 ARG cc_start: 0.8368 (ptt-90) cc_final: 0.7909 (ptt180) REVERT: F 156 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7362 (tp30) REVERT: F 174 ASN cc_start: 0.7210 (OUTLIER) cc_final: 0.6660 (t0) REVERT: F 181 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8197 (tt) REVERT: F 190 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7049 (tpp) outliers start: 44 outliers final: 29 residues processed: 215 average time/residue: 1.2689 time to fit residues: 289.3853 Evaluate side-chains 226 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 128 ARG 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 116 GLN Chi-restraints excluded: chain D residue 134 ARG 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 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 102 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 138 HIS 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 190 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 290 CYS 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: 0.7980 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 174 ASN C 187 HIS C 231 GLN C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.151420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132649 restraints weight = 10759.878| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.01 r_work: 0.3675 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.005 0.042 8198 Z= 0.323 Angle : 0.605 8.363 11179 Z= 0.308 Chirality : 0.046 0.170 1253 Planarity : 0.005 0.042 1453 Dihedral : 5.651 49.994 1245 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.39 % Allowed : 24.04 % Favored : 71.57 % 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: -1.63 (0.69), 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 0.011 0.002 TRP F 224 HIS 0.012 0.001 HIS C 187 PHE 0.021 0.002 PHE C 260 TYR 0.018 0.002 TYR E 85 ARG 0.006 0.001 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 227 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8551 (mt) REVERT: C 154 ASP cc_start: 0.7758 (t70) cc_final: 0.7469 (t70) REVERT: C 185 CYS cc_start: 0.7475 (m) cc_final: 0.7213 (m) REVERT: D 134 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7878 (ttt-90) REVERT: E 110 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.6853 (mmt) REVERT: F 34 ARG cc_start: 0.8440 (ptt-90) cc_final: 0.8063 (ptt180) REVERT: F 156 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7790 (tp30) REVERT: F 181 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8504 (tt) outliers start: 40 outliers final: 26 residues processed: 207 average time/residue: 1.2244 time to fit residues: 268.1837 Evaluate side-chains 217 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU 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 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 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 D residue 137 LYS 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 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 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: 0.9990 chunk 87 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 41 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 79 ASN B 53 ASN B 117 GLN C 67 ASN C 187 HIS C 231 GLN C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.151574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.132784 restraints weight = 10952.000| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.03 r_work: 0.3674 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8198 Z= 0.280 Angle : 0.579 6.687 11179 Z= 0.296 Chirality : 0.045 0.157 1253 Planarity : 0.005 0.043 1453 Dihedral : 5.485 49.681 1243 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.17 % Allowed : 24.59 % Favored : 71.24 % 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: -1.59 (0.69), residues: 52 sheet: 0.05 (0.24), residues: 443 loop : -0.58 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 224 HIS 0.011 0.001 HIS C 187 PHE 0.022 0.002 PHE C 260 TYR 0.016 0.002 TYR C 230 ARG 0.006 0.001 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 223 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8531 (mt) REVERT: C 154 ASP cc_start: 0.7763 (t70) cc_final: 0.7477 (t70) REVERT: C 185 CYS cc_start: 0.7496 (m) cc_final: 0.7238 (m) REVERT: D 134 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7888 (ttt-90) REVERT: E 110 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.6687 (mmt) REVERT: F 34 ARG cc_start: 0.8419 (ptt-90) cc_final: 0.8046 (ptt180) REVERT: F 156 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: F 181 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8496 (tt) outliers start: 38 outliers final: 26 residues processed: 205 average time/residue: 1.4620 time to fit residues: 316.0565 Evaluate side-chains 221 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU 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 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 260 PHE Chi-restraints excluded: chain D residue 134 ARG 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 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 290 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 52 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 B 117 GLN C 67 ASN C 187 HIS C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.151937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133353 restraints weight = 10721.696| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.99 r_work: 0.3683 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8198 Z= 0.249 Angle : 0.569 7.407 11179 Z= 0.291 Chirality : 0.045 0.152 1253 Planarity : 0.005 0.043 1453 Dihedral : 5.436 49.993 1243 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.17 % Allowed : 24.26 % Favored : 71.57 % 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 (0.27), residues: 947 helix: -1.52 (0.69), residues: 52 sheet: -0.01 (0.24), residues: 447 loop : -0.51 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 224 HIS 0.011 0.001 HIS C 187 PHE 0.021 0.002 PHE C 260 TYR 0.014 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 223 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8521 (mt) REVERT: C 154 ASP cc_start: 0.7748 (t70) cc_final: 0.7462 (t70) REVERT: C 185 CYS cc_start: 0.7486 (m) cc_final: 0.7223 (m) REVERT: D 134 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7874 (ttt-90) REVERT: E 110 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.6674 (mmt) REVERT: F 34 ARG cc_start: 0.8405 (ptt-90) cc_final: 0.8035 (ptt180) REVERT: F 156 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: F 181 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8490 (tt) outliers start: 38 outliers final: 29 residues processed: 205 average time/residue: 1.2431 time to fit residues: 269.0430 Evaluate side-chains 222 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU 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 145 THR 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 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 137 LYS 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 102 THR 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 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: 0.6980 chunk 78 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.151929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133246 restraints weight = 10728.518| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.01 r_work: 0.3683 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8198 Z= 0.253 Angle : 0.585 9.377 11179 Z= 0.297 Chirality : 0.045 0.152 1253 Planarity : 0.005 0.043 1453 Dihedral : 5.435 50.067 1243 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.28 % Allowed : 24.37 % 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: -0.58 (0.27), residues: 947 helix: -1.49 (0.70), residues: 52 sheet: -0.03 (0.24), residues: 447 loop : -0.49 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 224 HIS 0.011 0.001 HIS C 187 PHE 0.021 0.001 PHE C 260 TYR 0.015 0.002 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: 8391.93 seconds wall clock time: 145 minutes 3.97 seconds (8703.97 seconds total)