Starting phenix.real_space_refine on Thu Jul 2 08:53:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uwm_26836/07_2026/7uwm_26836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwm_26836/07_2026/7uwm_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 { model { file = "/net/cci-nas-00/data/ceres_data/7uwm_26836/07_2026/7uwm_26836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwm_26836/07_2026/7uwm_26836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uwm_26836/07_2026/7uwm_26836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwm_26836/07_2026/7uwm_26836.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uwm_26836/07_2026/7uwm_26836.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uwm_26836/07_2026/7uwm_26836.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7972 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 885 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 99} Chain breaks: 1 Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 885 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 99} Chain: "C" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2186 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 249} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 885 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 99} Chain breaks: 1 Chain: "E" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 881 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2124 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.95, per 1000 atoms: 0.24 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: 0.64 Conformation dependent library (CDL) restraints added in 415.0 milliseconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 19 sheets defined 7.4% alpha, 48.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 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: 1.18 Time building geometry restraints manager: 0.86 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: 4137 17.52 - 35.03: 569 35.03 - 52.55: 159 52.55 - 70.06: 40 70.06 - 87.58: 20 Dihedral angle restraints: 4925 sinusoidal: 2058 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 4922 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 403)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.020 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.500 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:9.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 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 : 18.271 87.578 2980 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG D 134 TYR 0.011 0.001 TYR B 85 PHE 0.017 0.001 PHE C 237 TRP 0.019 0.002 TRP F 224 HIS 0.010 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 8198) covalent geometry : angle 0.58933 / 0.30 (11179) SS BOND : bond 0.00226 / 0.15 ( 19) SS BOND : angle 1.55142 / 1.06 ( 38) hydrogen bonds : bond 0.15760 / 9.41 ( 246) hydrogen bonds : angle 7.08176 / 4.68 ( 732) link_BETA1-4 : bond 0.00083 / 0.06 ( 1) link_BETA1-4 : angle 0.95868 / 0.68 ( 3) link_NAG-ASN : bond 0.00173 / 0.07 ( 8) link_NAG-ASN : angle 1.55046 / 0.99 ( 24) *********************** 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 : 0.348 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: 0.5456 time to fit residues: 122.7079 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 : 0.309 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN B 55 ASN C 174 ASN C 187 HIS C 261 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.150057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131045 restraints weight = 10717.620| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.01 r_work: 0.3651 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 8226 Z= 0.299 Angle : 0.689 7.592 11244 Z= 0.353 Chirality : 0.049 0.237 1253 Planarity : 0.006 0.061 1453 Dihedral : 7.486 88.858 1081 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.04 % Allowed : 20.86 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.26), residues: 947 helix: -2.07 (0.64), residues: 52 sheet: 0.08 (0.24), residues: 439 loop : -0.74 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 296 TYR 0.022 0.002 TYR E 85 PHE 0.020 0.002 PHE C 237 TRP 0.015 0.002 TRP A 74 HIS 0.012 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.30 ( 8198) covalent geometry : angle 0.67476 / 0.35 (11179) SS BOND : bond 0.00610 / 0.42 ( 19) SS BOND : angle 1.88203 / 1.20 ( 38) hydrogen bonds : bond 0.04677 / 2.96 ( 246) hydrogen bonds : angle 6.09947 / 4.03 ( 732) link_BETA1-4 : bond 0.00260 / 0.17 ( 1) link_BETA1-4 : angle 1.10039 / 0.80 ( 3) link_NAG-ASN : bond 0.00445 / 0.25 ( 8) link_NAG-ASN : angle 2.12236 / 1.44 ( 24) *********************** 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 246 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.7503 (m-40) cc_final: 0.7089 (m110) REVERT: C 154 ASP cc_start: 0.7689 (t70) cc_final: 0.7399 (t70) REVERT: F 34 ARG cc_start: 0.8512 (ptt-90) cc_final: 0.8062 (ptt180) REVERT: F 87 GLN cc_start: 0.8155 (mp10) cc_final: 0.7577 (mp10) REVERT: F 181 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8550 (tt) outliers start: 55 outliers final: 33 residues processed: 223 average time/residue: 0.5195 time to fit residues: 122.8416 Evaluate side-chains 220 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 121 VAL 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 127 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 TRP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 140 VAL 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 59 ASP Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 68 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 44 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN C 187 HIS C 261 HIS C 280 GLN F 118 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.151231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132375 restraints weight = 10638.186| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.00 r_work: 0.3670 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8226 Z= 0.173 Angle : 0.596 7.025 11244 Z= 0.304 Chirality : 0.045 0.185 1253 Planarity : 0.005 0.053 1453 Dihedral : 6.282 58.916 1062 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.49 % Allowed : 22.06 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.26), residues: 947 helix: -2.02 (0.64), residues: 52 sheet: 0.05 (0.24), residues: 442 loop : -0.69 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 124 TYR 0.016 0.002 TYR E 85 PHE 0.017 0.002 PHE C 237 TRP 0.010 0.002 TRP A 74 HIS 0.010 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 8198) covalent geometry : angle 0.58457 / 0.30 (11179) SS BOND : bond 0.00330 / 0.22 ( 19) SS BOND : angle 1.43521 / 0.95 ( 38) hydrogen bonds : bond 0.03843 / 2.41 ( 246) hydrogen bonds : angle 5.73029 / 3.78 ( 732) link_BETA1-4 : bond 0.00106 / 0.07 ( 1) link_BETA1-4 : angle 1.08419 / 0.76 ( 3) link_NAG-ASN : bond 0.00304 / 0.16 ( 8) link_NAG-ASN : angle 2.01906 / 1.42 ( 24) *********************** 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 247 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.7406 (m-40) cc_final: 0.7027 (m110) REVERT: C 154 ASP cc_start: 0.7687 (t70) cc_final: 0.7399 (t70) REVERT: D 134 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7932 (ttt-90) REVERT: E 110 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.6889 (mmt) REVERT: F 34 ARG cc_start: 0.8377 (ptt-90) cc_final: 0.7936 (ptt180) REVERT: F 87 GLN cc_start: 0.8136 (mp10) cc_final: 0.7610 (mp10) REVERT: F 181 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8425 (tt) outliers start: 50 outliers final: 27 residues processed: 226 average time/residue: 0.5474 time to fit residues: 131.0622 Evaluate side-chains 229 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 134 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 74 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN B 117 GLN C 174 ASN C 187 HIS C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.150745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131829 restraints weight = 10825.309| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.02 r_work: 0.3663 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8226 Z= 0.196 Angle : 0.611 6.704 11244 Z= 0.310 Chirality : 0.046 0.187 1253 Planarity : 0.005 0.049 1453 Dihedral : 6.161 56.905 1059 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.15 % Allowed : 22.72 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.26), residues: 947 helix: -1.96 (0.65), residues: 52 sheet: 0.04 (0.24), residues: 444 loop : -0.77 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 66 TYR 0.017 0.002 TYR E 85 PHE 0.017 0.002 PHE C 237 TRP 0.010 0.002 TRP A 74 HIS 0.010 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 8198) covalent geometry : angle 0.59825 / 0.31 (11179) SS BOND : bond 0.00370 / 0.24 ( 19) SS BOND : angle 1.58099 / 1.06 ( 38) hydrogen bonds : bond 0.03856 / 2.44 ( 246) hydrogen bonds : angle 5.70566 / 3.77 ( 732) link_BETA1-4 : bond 0.00044 / 0.03 ( 1) link_BETA1-4 : angle 1.12594 / 0.82 ( 3) link_NAG-ASN : bond 0.00348 / 0.20 ( 8) link_NAG-ASN : angle 2.05479 / 1.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.7424 (m-40) cc_final: 0.7049 (m110) REVERT: B 97 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8343 (mp) REVERT: C 154 ASP cc_start: 0.7733 (t70) cc_final: 0.7433 (t70) REVERT: D 124 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7861 (mtt90) REVERT: D 134 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7901 (ttt-90) REVERT: E 110 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7089 (mmt) REVERT: F 34 ARG cc_start: 0.8411 (ptt-90) cc_final: 0.8003 (ptt180) REVERT: F 87 GLN cc_start: 0.8174 (mp10) cc_final: 0.7590 (mp10) REVERT: F 181 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8479 (tt) outliers start: 56 outliers final: 32 residues processed: 222 average time/residue: 0.5710 time to fit residues: 134.0579 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 : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 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 217 LEU 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 112 SER Chi-restraints excluded: chain D residue 124 ARG 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 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 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 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN B 55 ASN B 117 GLN C 187 HIS C 250 HIS C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.151248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132399 restraints weight = 10782.244| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.02 r_work: 0.3676 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1096 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= 0.150 Angle : 0.573 6.657 11244 Z= 0.291 Chirality : 0.044 0.167 1253 Planarity : 0.005 0.046 1453 Dihedral : 6.041 55.050 1059 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.16 % Allowed : 24.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.26), residues: 947 helix: -1.79 (0.67), residues: 52 sheet: 0.04 (0.24), residues: 443 loop : -0.75 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 66 TYR 0.014 0.001 TYR C 230 PHE 0.016 0.001 PHE C 237 TRP 0.010 0.001 TRP C 224 HIS 0.010 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 8198) covalent geometry : angle 0.56130 / 0.29 (11179) SS BOND : bond 0.00315 / 0.20 ( 19) SS BOND : angle 1.39986 / 0.95 ( 38) hydrogen bonds : bond 0.03514 / 2.23 ( 246) hydrogen bonds : angle 5.55721 / 3.67 ( 732) link_BETA1-4 : bond 0.00100 / 0.07 ( 1) link_BETA1-4 : angle 1.06340 / 0.76 ( 3) link_NAG-ASN : bond 0.00286 / 0.16 ( 8) link_NAG-ASN : angle 2.01339 / 1.43 ( 24) *********************** 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 245 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.7378 (m-40) cc_final: 0.6975 (m110) REVERT: B 97 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8334 (mp) REVERT: C 154 ASP cc_start: 0.7722 (t70) cc_final: 0.7439 (t70) REVERT: C 185 CYS cc_start: 0.7473 (m) cc_final: 0.7205 (m) REVERT: D 134 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7869 (ttt-90) REVERT: E 110 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.6660 (mmt) REVERT: F 34 ARG cc_start: 0.8381 (ptt-90) cc_final: 0.7935 (ptt180) REVERT: F 87 GLN cc_start: 0.8163 (mp10) cc_final: 0.7593 (mp10) REVERT: F 181 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8442 (tt) REVERT: F 190 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6880 (tpp) REVERT: F 207 ILE cc_start: 0.5133 (OUTLIER) cc_final: 0.4785 (pp) outliers start: 47 outliers final: 28 residues processed: 223 average time/residue: 0.5290 time to fit residues: 124.7265 Evaluate side-chains 232 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 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 134 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 207 ILE 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 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 78 optimal weight: 0.0070 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 46 optimal weight: 4.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4013 r_free = 0.4013 target = 0.151491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.132625 restraints weight = 10739.449| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.02 r_work: 0.3678 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8226 Z= 0.154 Angle : 0.578 6.644 11244 Z= 0.292 Chirality : 0.044 0.166 1253 Planarity : 0.005 0.045 1453 Dihedral : 5.976 49.852 1059 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.05 % Allowed : 24.70 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.26), residues: 947 helix: -1.70 (0.68), residues: 52 sheet: 0.02 (0.24), residues: 443 loop : -0.70 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 66 TYR 0.015 0.001 TYR C 230 PHE 0.017 0.001 PHE C 237 TRP 0.010 0.001 TRP C 224 HIS 0.010 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 8198) covalent geometry : angle 0.56496 / 0.29 (11179) SS BOND : bond 0.00308 / 0.20 ( 19) SS BOND : angle 1.53087 / 1.04 ( 38) hydrogen bonds : bond 0.03457 / 2.18 ( 246) hydrogen bonds : angle 5.52332 / 3.64 ( 732) link_BETA1-4 : bond 0.00078 / 0.05 ( 1) link_BETA1-4 : angle 1.10127 / 0.81 ( 3) link_NAG-ASN : bond 0.00294 / 0.16 ( 8) link_NAG-ASN : angle 2.02048 / 1.45 ( 24) *********************** 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 238 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.7363 (m-40) cc_final: 0.6951 (m110) REVERT: B 97 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8354 (mp) REVERT: C 154 ASP cc_start: 0.7727 (t70) cc_final: 0.7437 (t70) REVERT: C 185 CYS cc_start: 0.7493 (m) cc_final: 0.7221 (m) REVERT: D 134 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7863 (ttt-90) REVERT: E 110 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.6756 (mmt) REVERT: F 34 ARG cc_start: 0.8391 (ptt-90) cc_final: 0.7987 (ptt180) REVERT: F 87 GLN cc_start: 0.8156 (mp10) cc_final: 0.7558 (mp10) REVERT: F 181 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8456 (tt) REVERT: F 190 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6857 (tpp) REVERT: F 207 ILE cc_start: 0.5112 (OUTLIER) cc_final: 0.4756 (pp) outliers start: 46 outliers final: 29 residues processed: 217 average time/residue: 0.4996 time to fit residues: 114.7881 Evaluate side-chains 228 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 217 LEU 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 D residue 112 SER Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 0.3980 chunk 20 optimal weight: 0.0060 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN B 55 ASN B 117 GLN C 187 HIS C 280 GLN ** F 148 HIS ** 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 = 0.4015 r_free = 0.4015 target = 0.151649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132787 restraints weight = 10751.380| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.02 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: 0.7968 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8226 Z= 0.147 Angle : 0.569 6.675 11244 Z= 0.287 Chirality : 0.044 0.157 1253 Planarity : 0.005 0.043 1453 Dihedral : 5.897 49.666 1057 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.49 % Allowed : 24.15 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.26), residues: 947 helix: -1.58 (0.70), residues: 52 sheet: -0.03 (0.24), residues: 447 loop : -0.66 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 66 TYR 0.014 0.001 TYR E 85 PHE 0.015 0.001 PHE C 237 TRP 0.010 0.001 TRP C 224 HIS 0.010 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 8198) covalent geometry : angle 0.55653 / 0.28 (11179) SS BOND : bond 0.00299 / 0.19 ( 19) SS BOND : angle 1.41324 / 0.97 ( 38) hydrogen bonds : bond 0.03391 / 2.15 ( 246) hydrogen bonds : angle 5.47412 / 3.61 ( 732) link_BETA1-4 : bond 0.00098 / 0.07 ( 1) link_BETA1-4 : angle 1.09671 / 0.80 ( 3) link_NAG-ASN : bond 0.00266 / 0.14 ( 8) link_NAG-ASN : angle 1.96011 / 1.40 ( 24) *********************** 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 243 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.7351 (m-40) cc_final: 0.6953 (m110) REVERT: C 154 ASP cc_start: 0.7739 (t70) cc_final: 0.7451 (t70) REVERT: C 185 CYS cc_start: 0.7488 (m) cc_final: 0.7215 (m) REVERT: D 134 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7856 (ttt-90) REVERT: E 110 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.6739 (mmt) REVERT: F 34 ARG cc_start: 0.8396 (ptt-90) cc_final: 0.7980 (ptt180) REVERT: F 156 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7512 (tp30) REVERT: F 181 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8298 (tt) REVERT: F 190 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6880 (tpp) REVERT: F 207 ILE cc_start: 0.5093 (OUTLIER) cc_final: 0.4753 (pp) outliers start: 50 outliers final: 33 residues processed: 221 average time/residue: 0.4991 time to fit residues: 116.8809 Evaluate side-chains 231 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 217 LEU 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 112 SER Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 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 190 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN B 55 ASN C 187 HIS C 261 HIS C 280 GLN C 284 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.150373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131529 restraints weight = 10730.499| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.01 r_work: 0.3660 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8226 Z= 0.234 Angle : 0.641 6.971 11244 Z= 0.325 Chirality : 0.047 0.184 1253 Planarity : 0.005 0.044 1453 Dihedral : 6.176 49.469 1057 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.49 % Allowed : 24.15 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.26), residues: 947 helix: -1.67 (0.70), residues: 52 sheet: -0.05 (0.24), residues: 447 loop : -0.74 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 66 TYR 0.019 0.002 TYR E 85 PHE 0.017 0.002 PHE C 237 TRP 0.010 0.002 TRP F 224 HIS 0.011 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 ( 8198) covalent geometry : angle 0.62704 / 0.32 (11179) SS BOND : bond 0.00429 / 0.28 ( 19) SS BOND : angle 1.81099 / 1.18 ( 38) hydrogen bonds : bond 0.03836 / 2.44 ( 246) hydrogen bonds : angle 5.74186 / 3.78 ( 732) link_BETA1-4 : bond 0.00020 / 0.01 ( 1) link_BETA1-4 : angle 1.22793 / 0.94 ( 3) link_NAG-ASN : bond 0.00342 / 0.18 ( 8) link_NAG-ASN : angle 2.05503 / 1.43 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.7472 (m-40) cc_final: 0.7085 (m110) REVERT: C 154 ASP cc_start: 0.7768 (t70) cc_final: 0.7464 (t70) REVERT: D 134 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7877 (ttt-90) REVERT: E 110 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7075 (mmt) REVERT: F 34 ARG cc_start: 0.8529 (ptt-90) cc_final: 0.8167 (ptt180) REVERT: F 156 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7801 (tp30) REVERT: F 181 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8549 (tt) REVERT: F 207 ILE cc_start: 0.5250 (OUTLIER) cc_final: 0.4914 (pp) outliers start: 50 outliers final: 34 residues processed: 216 average time/residue: 0.5203 time to fit residues: 119.2772 Evaluate side-chains 230 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 208 THR 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 112 SER Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 79 optimal weight: 0.0980 chunk 80 optimal weight: 0.1980 chunk 68 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN B 117 GLN C 187 HIS C 280 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.151470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.132701 restraints weight = 10722.589| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.01 r_work: 0.3677 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8226 Z= 0.149 Angle : 0.581 6.819 11244 Z= 0.294 Chirality : 0.045 0.156 1253 Planarity : 0.005 0.044 1453 Dihedral : 5.965 49.344 1057 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.94 % Allowed : 24.70 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.26), residues: 947 helix: -1.57 (0.70), residues: 52 sheet: -0.08 (0.24), residues: 449 loop : -0.65 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 66 TYR 0.014 0.001 TYR C 230 PHE 0.015 0.001 PHE C 237 TRP 0.017 0.002 TRP F 224 HIS 0.011 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 8198) covalent geometry : angle 0.56857 / 0.29 (11179) SS BOND : bond 0.00307 / 0.20 ( 19) SS BOND : angle 1.50787 / 1.02 ( 38) hydrogen bonds : bond 0.03391 / 2.16 ( 246) hydrogen bonds : angle 5.52178 / 3.64 ( 732) link_BETA1-4 : bond 0.00095 / 0.06 ( 1) link_BETA1-4 : angle 1.12131 / 0.82 ( 3) link_NAG-ASN : bond 0.00290 / 0.14 ( 8) link_NAG-ASN : angle 1.93850 / 1.37 ( 24) *********************** 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 240 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.7377 (m-40) cc_final: 0.6978 (m110) REVERT: C 125 LEU cc_start: 0.8538 (tp) cc_final: 0.8333 (tt) REVERT: C 154 ASP cc_start: 0.7752 (t70) cc_final: 0.7455 (t70) REVERT: C 185 CYS cc_start: 0.7514 (m) cc_final: 0.7236 (m) REVERT: E 110 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.6600 (mmt) REVERT: F 34 ARG cc_start: 0.8404 (ptt-90) cc_final: 0.7991 (ptt180) REVERT: F 156 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7522 (tp30) REVERT: F 181 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8288 (tt) REVERT: F 190 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6865 (tpp) outliers start: 45 outliers final: 35 residues processed: 219 average time/residue: 0.5448 time to fit residues: 126.2075 Evaluate side-chains 235 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 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 112 SER Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 chunk 85 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN B 53 ASN B 55 ASN C 187 HIS C 280 GLN C 284 GLN F 45 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133523 restraints weight = 10753.370| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.02 r_work: 0.3688 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1352 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= 0.129 Angle : 0.568 7.049 11244 Z= 0.287 Chirality : 0.044 0.145 1253 Planarity : 0.005 0.045 1453 Dihedral : 5.868 50.591 1057 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.06 % Allowed : 25.58 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.26), residues: 947 helix: -1.48 (0.71), residues: 52 sheet: -0.06 (0.24), residues: 449 loop : -0.58 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 66 TYR 0.011 0.001 TYR E 85 PHE 0.015 0.001 PHE C 237 TRP 0.023 0.002 TRP F 224 HIS 0.011 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 8198) covalent geometry : angle 0.55682 / 0.28 (11179) SS BOND : bond 0.00267 / 0.17 ( 19) SS BOND : angle 1.35474 / 0.93 ( 38) hydrogen bonds : bond 0.03224 / 2.07 ( 246) hydrogen bonds : angle 5.39542 / 3.55 ( 732) link_BETA1-4 : bond 0.00199 / 0.13 ( 1) link_BETA1-4 : angle 1.12400 / 0.83 ( 3) link_NAG-ASN : bond 0.00275 / 0.13 ( 8) link_NAG-ASN : angle 1.86918 / 1.32 ( 24) ********************** 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 232 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 ASP cc_start: 0.7725 (t70) cc_final: 0.7440 (t70) REVERT: C 185 CYS cc_start: 0.7415 (m) cc_final: 0.7140 (m) REVERT: E 110 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.6497 (mmt) REVERT: F 34 ARG cc_start: 0.8375 (ptt-90) cc_final: 0.7959 (ptt180) REVERT: F 156 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: F 181 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8258 (tt) outliers start: 37 outliers final: 30 residues processed: 214 average time/residue: 0.5409 time to fit residues: 122.2529 Evaluate side-chains 229 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 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 112 SER Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN B 55 ASN C 67 ASN C 174 ASN C 187 HIS C 280 GLN C 284 GLN ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.151080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132298 restraints weight = 10713.046| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.01 r_work: 0.3673 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8226 Z= 0.195 Angle : 0.613 6.744 11244 Z= 0.310 Chirality : 0.046 0.163 1253 Planarity : 0.005 0.045 1453 Dihedral : 5.888 49.904 1055 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.17 % Allowed : 25.58 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.26), residues: 947 helix: -1.49 (0.71), residues: 52 sheet: -0.09 (0.24), residues: 447 loop : -0.61 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 66 TYR 0.017 0.002 TYR C 230 PHE 0.016 0.002 PHE C 237 TRP 0.029 0.002 TRP F 224 HIS 0.012 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 ( 8198) covalent geometry : angle 0.60086 / 0.31 (11179) SS BOND : bond 0.00377 / 0.25 ( 19) SS BOND : angle 1.57436 / 1.04 ( 38) hydrogen bonds : bond 0.03555 / 2.26 ( 246) hydrogen bonds : angle 5.53814 / 3.65 ( 732) link_BETA1-4 : bond 0.00006 / 0.00 ( 1) link_BETA1-4 : angle 1.18261 / 0.90 ( 3) link_NAG-ASN : bond 0.00297 / 0.15 ( 8) link_NAG-ASN : angle 1.92455 / 1.34 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3831.47 seconds wall clock time: 65 minutes 43.98 seconds (3943.98 seconds total)