Starting phenix.real_space_refine on Fri Jul 25 19:37:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwm_26836/07_2025/7uwm_26836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwm_26836/07_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_26836/07_2025/7uwm_26836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwm_26836/07_2025/7uwm_26836.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwm_26836/07_2025/7uwm_26836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwm_26836/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.01, per 1000 atoms: 0.75 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: 2.48 Conformation dependent library (CDL) restraints added in 1.9 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: 1.50 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: 3.30 Time building geometry restraints manager: 2.99 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 29.310 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- 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 8226 Z= 0.165 Angle : 0.599 6.733 11244 Z= 0.308 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 8) link_NAG-ASN : angle 1.55046 ( 24) link_BETA1-4 : bond 0.00083 ( 1) link_BETA1-4 : angle 0.95868 ( 3) hydrogen bonds : bond 0.15760 ( 246) hydrogen bonds : angle 7.08176 ( 732) SS BOND : bond 0.00226 ( 19) SS BOND : angle 1.55142 ( 38) covalent geometry : bond 0.00363 ( 8198) covalent geometry : angle 0.58933 (11179) *********************** 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 : 0.849 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: 1.2100 time to fit residues: 272.4020 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 : 0.842 ------------------------------------------------------------------------------- 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 8226 Z= 0.158 Angle : 0.578 7.278 11244 Z= 0.295 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 8) link_NAG-ASN : angle 1.88589 ( 24) link_BETA1-4 : bond 0.00039 ( 1) link_BETA1-4 : angle 1.14899 ( 3) hydrogen bonds : bond 0.04056 ( 246) hydrogen bonds : angle 5.74086 ( 732) SS BOND : bond 0.00302 ( 19) SS BOND : angle 1.30149 ( 38) covalent geometry : bond 0.00372 ( 8198) covalent geometry : angle 0.56719 (11179) *********************** 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 : 0.900 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: 1.3295 time to fit residues: 302.1555 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 : 0.905 ------------------------------------------------------------------------------- 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 8226 Z= 0.147 Angle : 0.568 6.695 11244 Z= 0.287 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 8) link_NAG-ASN : angle 1.98374 ( 24) link_BETA1-4 : bond 0.00203 ( 1) link_BETA1-4 : angle 1.19594 ( 3) hydrogen bonds : bond 0.03584 ( 246) hydrogen bonds : angle 5.51540 ( 732) SS BOND : bond 0.00272 ( 19) SS BOND : angle 1.34783 ( 38) covalent geometry : bond 0.00349 ( 8198) covalent geometry : angle 0.55598 (11179) *********************** 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 : 0.949 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: 1.2120 time to fit residues: 276.7614 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 : 0.914 ------------------------------------------------------------------------------- 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 8226 Z= 0.195 Angle : 0.600 6.716 11244 Z= 0.304 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 8) link_NAG-ASN : angle 2.09793 ( 24) link_BETA1-4 : bond 0.00069 ( 1) link_BETA1-4 : angle 1.29207 ( 3) hydrogen bonds : bond 0.03773 ( 246) hydrogen bonds : angle 5.61418 ( 732) SS BOND : bond 0.00394 ( 19) SS BOND : angle 1.49828 ( 38) covalent geometry : bond 0.00466 ( 8198) covalent geometry : angle 0.58703 (11179) *********************** 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 : 0.872 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: 1.1975 time to fit residues: 287.3206 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 : 0.920 ------------------------------------------------------------------------------- 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: 0.9980 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 8226 Z= 0.139 Angle : 0.568 6.643 11244 Z= 0.287 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 8) link_NAG-ASN : angle 2.06807 ( 24) link_BETA1-4 : bond 0.00089 ( 1) link_BETA1-4 : angle 1.22029 ( 3) hydrogen bonds : bond 0.03395 ( 246) hydrogen bonds : angle 5.44721 ( 732) SS BOND : bond 0.00267 ( 19) SS BOND : angle 1.46823 ( 38) covalent geometry : bond 0.00330 ( 8198) covalent geometry : angle 0.55500 (11179) *********************** 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 : 1.225 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: 1.3228 time to fit residues: 304.0509 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 : 0.839 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.3980 chunk 24 optimal weight: 0.6980 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.152682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133958 restraints weight = 10744.151| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.01 r_work: 0.3693 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8226 Z= 0.122 Angle : 0.553 6.626 11244 Z= 0.279 Chirality : 0.044 0.152 1253 Planarity : 0.004 0.043 1453 Dihedral : 5.621 51.558 1247 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.94 % Allowed : 23.60 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.26), residues: 947 helix: -1.62 (0.69), residues: 52 sheet: 0.09 (0.24), residues: 443 loop : -0.59 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 224 HIS 0.010 0.001 HIS C 187 PHE 0.014 0.001 PHE C 237 TYR 0.012 0.001 TYR E 85 ARG 0.005 0.000 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 8) link_NAG-ASN : angle 2.05899 ( 24) link_BETA1-4 : bond 0.00122 ( 1) link_BETA1-4 : angle 1.21049 ( 3) hydrogen bonds : bond 0.03227 ( 246) hydrogen bonds : angle 5.34468 ( 732) SS BOND : bond 0.00249 ( 19) SS BOND : angle 1.31497 ( 38) covalent geometry : bond 0.00288 ( 8198) covalent geometry : angle 0.54083 (11179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8585 (mt) REVERT: C 154 ASP cc_start: 0.7723 (t70) cc_final: 0.7444 (t70) REVERT: C 185 CYS cc_start: 0.7399 (m) cc_final: 0.7133 (m) REVERT: D 134 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7853 (ttt-90) REVERT: F 34 ARG cc_start: 0.8357 (ptt-90) cc_final: 0.7926 (ptt180) REVERT: F 87 GLN cc_start: 0.8136 (mp10) cc_final: 0.7598 (mp10) REVERT: F 156 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7491 (tp30) REVERT: F 174 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.6517 (p0) REVERT: F 181 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8303 (tt) outliers start: 45 outliers final: 26 residues processed: 216 average time/residue: 1.2593 time to fit residues: 288.2446 Evaluate side-chains 219 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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 290 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain 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 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 45 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.151084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132233 restraints weight = 10748.980| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.01 r_work: 0.3671 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8226 Z= 0.204 Angle : 0.614 8.859 11244 Z= 0.309 Chirality : 0.046 0.168 1253 Planarity : 0.005 0.043 1453 Dihedral : 5.747 50.511 1245 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.38 % Allowed : 23.60 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.26), residues: 947 helix: -1.70 (0.69), residues: 52 sheet: 0.08 (0.24), residues: 441 loop : -0.69 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 74 HIS 0.011 0.001 HIS C 187 PHE 0.022 0.002 PHE C 260 TYR 0.017 0.002 TYR C 230 ARG 0.006 0.000 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 8) link_NAG-ASN : angle 2.10686 ( 24) link_BETA1-4 : bond 0.00026 ( 1) link_BETA1-4 : angle 1.29845 ( 3) hydrogen bonds : bond 0.03666 ( 246) hydrogen bonds : angle 5.55398 ( 732) SS BOND : bond 0.00375 ( 19) SS BOND : angle 1.55607 ( 38) covalent geometry : bond 0.00487 ( 8198) covalent geometry : angle 0.60075 (11179) *********************** 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 239 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8563 (mt) REVERT: B 50 ASN cc_start: 0.7322 (m-40) cc_final: 0.6921 (m110) REVERT: B 97 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8332 (mp) REVERT: C 154 ASP cc_start: 0.7735 (t70) cc_final: 0.7436 (t70) REVERT: C 185 CYS cc_start: 0.7502 (m) cc_final: 0.7244 (m) REVERT: D 134 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7885 (ttt-90) REVERT: E 110 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.6938 (mmt) REVERT: F 34 ARG cc_start: 0.8441 (ptt-90) cc_final: 0.8046 (ptt180) REVERT: F 156 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: F 181 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8504 (tt) REVERT: F 207 ILE cc_start: 0.4920 (OUTLIER) cc_final: 0.4494 (pp) outliers start: 49 outliers final: 32 residues processed: 218 average time/residue: 1.6303 time to fit residues: 374.9618 Evaluate side-chains 229 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 77 HIS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 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 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 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 207 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.151758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133009 restraints weight = 10764.652| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.01 r_work: 0.3679 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8226 Z= 0.161 Angle : 0.588 7.143 11244 Z= 0.297 Chirality : 0.045 0.154 1253 Planarity : 0.005 0.043 1453 Dihedral : 5.695 49.583 1245 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.05 % Allowed : 24.26 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.26), residues: 947 helix: -1.64 (0.68), residues: 52 sheet: 0.02 (0.24), residues: 443 loop : -0.63 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 224 HIS 0.010 0.001 HIS C 187 PHE 0.021 0.001 PHE C 260 TYR 0.015 0.002 TYR C 230 ARG 0.006 0.000 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 8) link_NAG-ASN : angle 2.07480 ( 24) link_BETA1-4 : bond 0.00031 ( 1) link_BETA1-4 : angle 1.25045 ( 3) hydrogen bonds : bond 0.03409 ( 246) hydrogen bonds : angle 5.48590 ( 732) SS BOND : bond 0.00333 ( 19) SS BOND : angle 1.54512 ( 38) covalent geometry : bond 0.00386 ( 8198) covalent geometry : angle 0.57474 (11179) *********************** 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 232 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8525 (mt) REVERT: C 125 LEU cc_start: 0.8526 (tp) cc_final: 0.8239 (tt) REVERT: C 154 ASP cc_start: 0.7733 (t70) cc_final: 0.7439 (t70) REVERT: E 110 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.6800 (mmt) REVERT: F 34 ARG cc_start: 0.8410 (ptt-90) cc_final: 0.7986 (ptt180) REVERT: F 156 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7773 (tp30) REVERT: F 181 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8441 (tt) REVERT: F 207 ILE cc_start: 0.4955 (OUTLIER) cc_final: 0.4516 (pp) outliers start: 46 outliers final: 32 residues processed: 213 average time/residue: 1.2385 time to fit residues: 278.7540 Evaluate side-chains 225 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain 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 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 83 optimal weight: 0.0980 chunk 43 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.152001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133142 restraints weight = 10955.511| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.03 r_work: 0.3681 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8226 Z= 0.155 Angle : 0.579 6.661 11244 Z= 0.292 Chirality : 0.045 0.152 1253 Planarity : 0.005 0.043 1453 Dihedral : 5.644 49.867 1245 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.83 % Allowed : 24.15 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.26), residues: 947 helix: -1.58 (0.69), residues: 52 sheet: -0.03 (0.24), residues: 447 loop : -0.57 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 224 HIS 0.010 0.001 HIS C 187 PHE 0.021 0.001 PHE C 260 TYR 0.014 0.002 TYR C 230 ARG 0.006 0.000 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 8) link_NAG-ASN : angle 2.03685 ( 24) link_BETA1-4 : bond 0.00058 ( 1) link_BETA1-4 : angle 1.27360 ( 3) hydrogen bonds : bond 0.03359 ( 246) hydrogen bonds : angle 5.45001 ( 732) SS BOND : bond 0.00308 ( 19) SS BOND : angle 1.45018 ( 38) covalent geometry : bond 0.00369 ( 8198) covalent geometry : angle 0.56642 (11179) *********************** 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 232 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8526 (mt) REVERT: C 125 LEU cc_start: 0.8548 (tp) cc_final: 0.8259 (tt) REVERT: C 154 ASP cc_start: 0.7727 (t70) cc_final: 0.7438 (t70) REVERT: C 185 CYS cc_start: 0.7508 (m) cc_final: 0.7241 (m) REVERT: E 110 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.6777 (mmt) REVERT: F 34 ARG cc_start: 0.8403 (ptt-90) cc_final: 0.7976 (ptt180) REVERT: F 156 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: F 181 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8280 (tt) REVERT: F 207 ILE cc_start: 0.5065 (OUTLIER) cc_final: 0.4636 (pp) outliers start: 44 outliers final: 32 residues processed: 213 average time/residue: 1.3246 time to fit residues: 298.5323 Evaluate side-chains 226 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 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 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 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 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 138 HIS Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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 231 GLN C 250 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.153076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134462 restraints weight = 10752.038| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.00 r_work: 0.3699 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8226 Z= 0.119 Angle : 0.570 8.974 11244 Z= 0.285 Chirality : 0.044 0.141 1253 Planarity : 0.004 0.043 1453 Dihedral : 5.483 51.350 1245 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.17 % Allowed : 25.14 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.27), residues: 947 helix: -1.48 (0.69), residues: 52 sheet: -0.00 (0.24), residues: 447 loop : -0.52 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 224 HIS 0.011 0.001 HIS C 187 PHE 0.019 0.001 PHE C 260 TYR 0.011 0.001 TYR E 85 ARG 0.005 0.000 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 8) link_NAG-ASN : angle 1.95967 ( 24) link_BETA1-4 : bond 0.00177 ( 1) link_BETA1-4 : angle 1.21992 ( 3) hydrogen bonds : bond 0.03173 ( 246) hydrogen bonds : angle 5.29459 ( 732) SS BOND : bond 0.00250 ( 19) SS BOND : angle 1.26952 ( 38) covalent geometry : bond 0.00282 ( 8198) covalent geometry : angle 0.55909 (11179) ********************** 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 231 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 LEU cc_start: 0.8685 (tp) cc_final: 0.8450 (tp) REVERT: C 154 ASP cc_start: 0.7717 (t70) cc_final: 0.7437 (t70) REVERT: C 185 CYS cc_start: 0.7407 (m) cc_final: 0.7139 (m) REVERT: F 34 ARG cc_start: 0.8358 (ptt-90) cc_final: 0.7931 (ptt180) REVERT: F 156 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7506 (tp30) REVERT: F 174 ASN cc_start: 0.7074 (OUTLIER) cc_final: 0.6567 (t0) REVERT: F 181 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8216 (tt) REVERT: F 207 ILE cc_start: 0.4992 (OUTLIER) cc_final: 0.4556 (pp) outliers start: 38 outliers final: 26 residues processed: 213 average time/residue: 1.1884 time to fit residues: 267.6209 Evaluate side-chains 220 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 265 ASN 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 109 HIS 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 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 207 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 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 = 0.4018 r_free = 0.4018 target = 0.151903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133218 restraints weight = 10723.294| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.00 r_work: 0.3685 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8226 Z= 0.165 Angle : 0.599 9.863 11244 Z= 0.301 Chirality : 0.045 0.151 1253 Planarity : 0.005 0.043 1453 Dihedral : 5.542 50.363 1244 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.17 % Allowed : 25.03 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.27), residues: 947 helix: -1.47 (0.70), residues: 52 sheet: -0.02 (0.24), residues: 447 loop : -0.53 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 224 HIS 0.012 0.001 HIS C 187 PHE 0.028 0.002 PHE C 260 TYR 0.016 0.002 TYR C 230 ARG 0.006 0.000 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 8) link_NAG-ASN : angle 2.01462 ( 24) link_BETA1-4 : bond 0.00076 ( 1) link_BETA1-4 : angle 1.26996 ( 3) hydrogen bonds : bond 0.03387 ( 246) hydrogen bonds : angle 5.43899 ( 732) SS BOND : bond 0.00328 ( 19) SS BOND : angle 1.42389 ( 38) covalent geometry : bond 0.00396 ( 8198) covalent geometry : angle 0.58720 (11179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9193.46 seconds wall clock time: 160 minutes 46.08 seconds (9646.08 seconds total)