Starting phenix.real_space_refine on Fri Oct 30 07:15:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7boi_12244/10_2026/7boi_12244.cif Found real_map, /net/cci-nas-00/data/ceres_data/7boi_12244/10_2026/7boi_12244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7boi_12244/10_2026/7boi_12244.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7boi_12244/10_2026/7boi_12244.cif" model { file = "/net/cci-nas-00/data/ceres_data/7boi_12244/10_2026/7boi_12244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7boi_12244/10_2026/7boi_12244.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7boi_12244/10_2026/7boi_12244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7boi_12244/10_2026/7boi_12244.map" } resolution = 2.98 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= -0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1081 5.49 5 Mg 72 5.21 5 S 51 5.16 5 C 18274 2.51 5 N 6688 2.21 5 O 9803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35970 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 23172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 23172 Classifications: {'RNA': 7, 'RNAv2': 1071} Modifications used: {'rna2p': 1, 'rna2p_pur': 79, 'rna2p_pyr': 52, 'rna3p': 7, 'rna3p_pur': 542, 'rna3p_pyr': 397} Link IDs: {'rna2p': 131, 'rna3p': 946} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 551 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "W" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2456 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Unusual residues: {' MG': 70} Classifications: {'undetermined': 70} Link IDs: {None: 69} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'GNP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35454 SG CYS W 297 103.267 175.784 111.924 1.00138.41 S ATOM 35500 SG CYS W 302 100.646 176.420 109.591 1.00139.90 S ATOM 35559 SG CYS W 310 104.236 175.553 107.507 1.00143.63 S Time building chain proxies: 6.92, per 1000 atoms: 0.19 Number of scatterers: 35970 At special positions: 0 Unit cell: (137.795, 218.085, 147.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 51 16.00 P 1081 15.00 Mg 72 11.99 O 9803 8.00 N 6688 7.00 C 18274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 732.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN W 401 " pdb="ZN ZN W 401 " - pdb=" ND1 HIS W 304 " pdb="ZN ZN W 401 " - pdb=" SG CYS W 297 " pdb="ZN ZN W 401 " - pdb=" SG CYS W 310 " pdb="ZN ZN W 401 " - pdb=" SG CYS W 302 " Number of angles added : 3 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2992 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 15 sheets defined 40.6% alpha, 21.6% beta 371 base pairs and 591 stacking pairs defined. Time for finding SS restraints: 5.81 Creating SS restraints... Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.533A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.573A pdb=" N TYR D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 96 removed outlier: 3.650A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.287A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 162 removed outlier: 3.862A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.606A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D 202 " --> pdb=" O HIS D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 146 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'F' and resid 12 through 15 Processing helix chain 'F' and resid 17 through 31 Processing helix chain 'F' and resid 67 through 80 removed outlier: 3.724A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 94 through 99 removed outlier: 3.782A pdb=" N ALA H 97 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 53 through 57 Processing helix chain 'K' and resid 59 through 72 removed outlier: 3.766A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 92 through 102 removed outlier: 3.942A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.640A pdb=" N GLY L 118 " --> pdb=" O SER L 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 4.092A pdb=" N VAL O 29 " --> pdb=" O THR O 25 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.328A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.908A pdb=" N ARG O 84 " --> pdb=" O GLN O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 removed outlier: 3.596A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'Q' and resid 48 through 52 removed outlier: 3.589A pdb=" N ASN Q 51 " --> pdb=" O ASP Q 48 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU Q 52 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 48 through 52' Processing helix chain 'R' and resid 11 through 16 Processing helix chain 'R' and resid 28 through 33 removed outlier: 3.752A pdb=" N ILE R 33 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 Processing helix chain 'U' and resid 11 through 26 Processing helix chain 'U' and resid 27 through 35 Processing helix chain 'U' and resid 40 through 65 removed outlier: 3.781A pdb=" N GLU U 63 " --> pdb=" O LYS U 59 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA U 65 " --> pdb=" O ALA U 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 137 through 151 removed outlier: 3.507A pdb=" N ASP W 142 " --> pdb=" O LEU W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 166 through 182 removed outlier: 3.945A pdb=" N GLU W 175 " --> pdb=" O ALA W 171 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLN W 176 " --> pdb=" O PHE W 172 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE W 179 " --> pdb=" O GLU W 175 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR W 180 " --> pdb=" O GLN W 176 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG W 181 " --> pdb=" O MET W 177 " (cutoff:3.500A) Processing helix chain 'W' and resid 197 through 206 removed outlier: 4.341A pdb=" N LEU W 201 " --> pdb=" O GLY W 197 " (cutoff:3.500A) Processing helix chain 'W' and resid 219 through 229 Processing helix chain 'W' and resid 279 through 287 removed outlier: 3.521A pdb=" N ILE W 283 " --> pdb=" O GLU W 279 " (cutoff:3.500A) Processing helix chain 'W' and resid 288 through 294 removed outlier: 3.741A pdb=" N HIS W 291 " --> pdb=" O VAL W 288 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP W 292 " --> pdb=" O GLU W 289 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU W 294 " --> pdb=" O HIS W 291 " (cutoff:3.500A) Processing helix chain 'W' and resid 310 through 318 removed outlier: 3.524A pdb=" N GLU W 314 " --> pdb=" O CYS W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 322 through 339 Processing sheet with id=AA1, first strand: chain 'D' and resid 128 through 129 removed outlier: 4.002A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 12 through 24 removed outlier: 6.636A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL E 18 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR E 34 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG E 20 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER E 32 " --> pdb=" O ARG E 20 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER E 22 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE E 30 " --> pdb=" O SER E 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 88 through 89 removed outlier: 6.566A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 35 through 40 removed outlier: 6.246A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 35 through 40 removed outlier: 6.246A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR F 92 " --> pdb=" O HIS F 3 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.981A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AA8, first strand: chain 'H' and resid 74 through 77 removed outlier: 5.737A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 41 through 46 removed outlier: 3.562A pdb=" N GLY K 19 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS K 87 " --> pdb=" O ILE K 23 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU K 82 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE K 110 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL K 84 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP K 112 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL K 86 " --> pdb=" O ASP K 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 29 through 40 removed outlier: 5.466A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER L 78 " --> pdb=" O CYS L 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 50 through 52 removed outlier: 5.637A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 8 through 14 removed outlier: 7.889A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG Q 11 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS Q 71 " --> pdb=" O PRO Q 66 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TRP Q 73 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N CYS Q 64 " --> pdb=" O TRP Q 73 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU Q 75 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ARG Q 62 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 40 through 48 removed outlier: 5.569A pdb=" N VAL W 44 " --> pdb=" O GLU W 55 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU W 55 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL W 97 " --> pdb=" O ARG W 82 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG W 82 " --> pdb=" O VAL W 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'W' and resid 106 through 111 removed outlier: 6.837A pdb=" N LEU W 107 " --> pdb=" O ILE W 119 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'W' and resid 187 through 189 removed outlier: 9.324A pdb=" N LEU W 188 " --> pdb=" O PRO W 155 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE W 157 " --> pdb=" O LEU W 188 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE W 126 " --> pdb=" O ILE W 156 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL W 158 " --> pdb=" O ILE W 126 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE W 128 " --> pdb=" O VAL W 158 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASN W 160 " --> pdb=" O ILE W 128 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER W 130 " --> pdb=" O ASN W 160 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 912 hydrogen bonds 1360 hydrogen bond angles 0 basepair planarities 371 basepair parallelities 591 stacking parallelities Total time for adding SS restraints: 13.62 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6295 1.33 - 1.45: 15483 1.45 - 1.58: 14844 1.58 - 1.70: 2159 1.70 - 1.82: 85 Bond restraints: 38866 Sorted by residual: bond pdb=" N3B GNP W 402 " pdb=" PG GNP W 402 " ideal model delta sigma weight residual 1.801 1.630 0.171 2.00e-02 2.50e+03 7.33e+01 bond pdb=" C4 PSU A 516 " pdb=" C5 PSU A 516 " ideal model delta sigma weight residual 1.390 1.475 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" O3A GNP W 402 " pdb=" PB GNP W 402 " ideal model delta sigma weight residual 1.687 1.604 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" N LEU W 133 " pdb=" CA LEU W 133 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.63e+01 bond pdb=" C5 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.382 1.462 -0.080 2.00e-02 2.50e+03 1.60e+01 ... (remaining 38861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 55530 2.74 - 5.48: 2214 5.48 - 8.23: 59 8.23 - 10.97: 13 10.97 - 13.71: 2 Bond angle restraints: 57818 Sorted by residual: angle pdb=" N LEU R 67 " pdb=" CA LEU R 67 " pdb=" C LEU R 67 " ideal model delta sigma weight residual 112.90 104.38 8.52 1.31e+00 5.83e-01 4.23e+01 angle pdb=" C3' G7M A 527 " pdb=" C2' G7M A 527 " pdb=" C1' G7M A 527 " ideal model delta sigma weight residual 101.30 95.75 5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" N GLY H 68 " pdb=" CA GLY H 68 " pdb=" C GLY H 68 " ideal model delta sigma weight residual 114.67 107.28 7.39 1.41e+00 5.03e-01 2.75e+01 angle pdb=" CA ARG P 14 " pdb=" C ARG P 14 " pdb=" N PRO P 15 " ideal model delta sigma weight residual 117.44 122.18 -4.74 9.20e-01 1.18e+00 2.65e+01 angle pdb=" N ILE R 26 " pdb=" CA ILE R 26 " pdb=" C ILE R 26 " ideal model delta sigma weight residual 113.10 108.30 4.80 9.70e-01 1.06e+00 2.45e+01 ... (remaining 57813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 17970 24.80 - 49.60: 1945 49.60 - 74.40: 999 74.40 - 99.20: 23 99.20 - 124.00: 2 Dihedral angle restraints: 20939 sinusoidal: 16302 harmonic: 4637 Sorted by residual: dihedral pdb=" C4' G A 818 " pdb=" C3' G A 818 " pdb=" C2' G A 818 " pdb=" C1' G A 818 " ideal model delta sinusoidal sigma weight residual 36.34 -38.63 74.97 1 3.10e+00 1.04e-01 7.40e+02 dihedral pdb=" C4' A A 913 " pdb=" C3' A A 913 " pdb=" C2' A A 913 " pdb=" C1' A A 913 " ideal model delta sinusoidal sigma weight residual 36.34 -38.23 74.57 1 3.10e+00 1.04e-01 7.33e+02 dihedral pdb=" C4' A A 495 " pdb=" C3' A A 495 " pdb=" C2' A A 495 " pdb=" C1' A A 495 " ideal model delta sinusoidal sigma weight residual 36.34 -38.03 74.37 1 3.10e+00 1.04e-01 7.30e+02 ... (remaining 20936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5494 0.086 - 0.172: 434 0.172 - 0.258: 1206 0.258 - 0.343: 186 0.343 - 0.429: 2 Chirality restraints: 7322 Sorted by residual: chirality pdb=" CA GLU F 33 " pdb=" N GLU F 33 " pdb=" C GLU F 33 " pdb=" CB GLU F 33 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA LYS Q 19 " pdb=" N LYS Q 19 " pdb=" C LYS Q 19 " pdb=" CB LYS Q 19 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ASN U 9 " pdb=" N ASN U 9 " pdb=" C ASN U 9 " pdb=" CB ASN U 9 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 7319 not shown) Planarity restraints: 3334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " 0.121 2.00e-02 2.50e+03 2.01e-01 4.03e+02 pdb=" N6 MA6 A1518 " -0.348 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " 0.115 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " 0.118 2.00e-02 2.50e+03 1.96e-01 3.84e+02 pdb=" N6 MA6 A1519 " -0.339 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " 0.112 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 4OC A1402 " -0.075 2.00e-02 2.50e+03 8.88e-02 1.97e+02 pdb=" N1 4OC A1402 " -0.032 2.00e-02 2.50e+03 pdb=" C2 4OC A1402 " 0.029 2.00e-02 2.50e+03 pdb=" O2 4OC A1402 " 0.040 2.00e-02 2.50e+03 pdb=" N3 4OC A1402 " 0.081 2.00e-02 2.50e+03 pdb=" C4 4OC A1402 " 0.071 2.00e-02 2.50e+03 pdb=" N4 4OC A1402 " 0.119 2.00e-02 2.50e+03 pdb=" C5 4OC A1402 " 0.012 2.00e-02 2.50e+03 pdb=" C6 4OC A1402 " -0.040 2.00e-02 2.50e+03 pdb=" CM4 4OC A1402 " -0.205 2.00e-02 2.50e+03 ... (remaining 3331 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 378 2.53 - 3.12: 26629 3.12 - 3.71: 74098 3.71 - 4.31: 101766 4.31 - 4.90: 135864 Nonbonded interactions: 338735 Sorted by model distance: nonbonded pdb=" OP2 G A 289 " pdb="MG MG A1667 " model vdw 1.934 2.170 nonbonded pdb=" OP2 A A 441 " pdb="MG MG A1627 " model vdw 1.962 2.170 nonbonded pdb=" OP2 C A 175 " pdb="MG MG A1642 " model vdw 1.963 2.170 nonbonded pdb=" OP2 A A 608 " pdb="MG MG A1622 " model vdw 1.964 2.170 nonbonded pdb=" OP2 A A 116 " pdb="MG MG A1667 " model vdw 1.976 2.170 ... (remaining 338730 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.670 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: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 48.280 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 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 : 0.007 0.171 38870 Z= 0.423 Angle : 1.023 28.562 57821 Z= 0.517 Chirality : 0.105 0.429 7322 Planarity : 0.006 0.201 3334 Dihedral : 20.190 123.998 17947 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 16.58 % Favored : 83.42 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % 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: -1.74 (0.20), residues: 1588 helix: -0.78 (0.20), residues: 588 sheet: -1.49 (0.29), residues: 279 loop : -1.17 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 54 TYR 0.012 0.001 TYR L 38 PHE 0.016 0.001 PHE W 172 TRP 0.007 0.001 TRP P 60 HIS 0.004 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.42 (38866) covalent geometry : angle 1.01333 / 0.52 (57818) hydrogen bonds : bond 0.11738 / 6.23 ( 1497) hydrogen bonds : angle 5.42161 / 2.25 ( 3007) metal coordination : bond 0.10171 / 5.09 ( 4) metal coordination : angle 19.66437 / 6.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 GLU cc_start: 0.8236 (mp0) cc_final: 0.7880 (mp0) REVERT: E 23 LYS cc_start: 0.9087 (ttpt) cc_final: 0.7887 (mmtt) REVERT: E 31 PHE cc_start: 0.8973 (m-80) cc_final: 0.8715 (m-80) REVERT: E 50 TYR cc_start: 0.9078 (t80) cc_final: 0.8757 (t80) REVERT: E 61 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8885 (tp40) REVERT: F 59 TYR cc_start: 0.8137 (m-80) cc_final: 0.7783 (m-80) REVERT: H 50 LYS cc_start: 0.8551 (pttp) cc_final: 0.8321 (pttp) REVERT: H 52 GLU cc_start: 0.8506 (mp0) cc_final: 0.7571 (mp0) REVERT: H 59 LEU cc_start: 0.9661 (tp) cc_final: 0.9323 (tp) REVERT: H 61 LEU cc_start: 0.9620 (mp) cc_final: 0.9085 (mt) REVERT: H 64 LYS cc_start: 0.9036 (mtpp) cc_final: 0.8664 (mtpt) REVERT: H 73 GLU cc_start: 0.8473 (pp20) cc_final: 0.8166 (pp20) REVERT: H 111 MET cc_start: 0.8605 (ptp) cc_final: 0.8396 (ptp) REVERT: K 64 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8538 (tm-30) REVERT: K 68 GLU cc_start: 0.9273 (mp0) cc_final: 0.8748 (pm20) REVERT: K 83 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8243 (mp0) REVERT: K 87 LYS cc_start: 0.9346 (ptmm) cc_final: 0.8998 (pttm) REVERT: K 126 LYS cc_start: 0.9108 (tppt) cc_final: 0.8870 (tppt) REVERT: L 47 SER cc_start: 0.8796 (m) cc_final: 0.8420 (p) REVERT: L 73 ASN cc_start: 0.9067 (p0) cc_final: 0.8729 (p0) REVERT: O 64 ARG cc_start: 0.8350 (tpm170) cc_final: 0.8051 (tpp-160) REVERT: O 68 ASP cc_start: 0.8174 (m-30) cc_final: 0.7879 (m-30) REVERT: O 80 GLN cc_start: 0.8525 (pp30) cc_final: 0.8052 (pp30) REVERT: P 12 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8966 (ttpp) REVERT: P 18 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7880 (mm-40) REVERT: P 44 SER cc_start: 0.8221 (p) cc_final: 0.6359 (t) REVERT: P 76 LYS cc_start: 0.9020 (tttt) cc_final: 0.8423 (tttt) REVERT: Q 8 LEU cc_start: 0.9518 (mt) cc_final: 0.8777 (mp) REVERT: Q 16 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8713 (mtmt) REVERT: Q 61 ILE cc_start: 0.9613 (pt) cc_final: 0.9362 (pp) REVERT: R 18 VAL cc_start: 0.8579 (t) cc_final: 0.8369 (p) REVERT: R 22 ASP cc_start: 0.7950 (t0) cc_final: 0.7513 (t70) REVERT: R 32 TYR cc_start: 0.9239 (m-80) cc_final: 0.8980 (m-80) REVERT: R 51 TYR cc_start: 0.9092 (m-80) cc_final: 0.8788 (m-10) REVERT: U 20 LYS cc_start: 0.9203 (ttpt) cc_final: 0.8987 (tmmt) REVERT: U 31 GLU cc_start: 0.8641 (tp30) cc_final: 0.8173 (tp30) REVERT: U 39 GLU cc_start: 0.8385 (tt0) cc_final: 0.8123 (tt0) REVERT: U 58 LYS cc_start: 0.9442 (mtpt) cc_final: 0.9191 (tmmt) REVERT: W 152 GLN cc_start: 0.9411 (mm110) cc_final: 0.9131 (mp10) REVERT: W 180 TYR cc_start: 0.9270 (m-80) cc_final: 0.9037 (m-80) REVERT: W 282 GLN cc_start: 0.9317 (mt0) cc_final: 0.8819 (mt0) outliers start: 0 outliers final: 3 residues processed: 504 average time/residue: 0.8006 time to fit residues: 474.1219 Evaluate side-chains 373 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 370 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain T residue 39 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 GLN F 55 HIS H 21 ASN H 67 GLN H 118 GLN K 38 GLN Q 9 GLN T 52 ASN W 338 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.037085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.029953 restraints weight = 215898.903| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 1.73 r_work: 0.2483 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2397 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 38870 Z= 0.264 Angle : 1.209 19.515 57821 Z= 0.491 Chirality : 0.101 1.433 7322 Planarity : 0.005 0.045 3334 Dihedral : 18.736 167.912 14782 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.68 % Allowed : 24.50 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.90 (0.20), residues: 1588 helix: 0.12 (0.21), residues: 598 sheet: -1.11 (0.30), residues: 281 loop : -0.88 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 43 TYR 0.015 0.002 TYR K 77 PHE 0.030 0.002 PHE F 80 TRP 0.018 0.001 TRP F 42 HIS 0.007 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.26 (38866) covalent geometry : angle 1.20862 / 0.49 (57818) hydrogen bonds : bond 0.08160 / 4.29 ( 1497) hydrogen bonds : angle 4.08135 / 1.66 ( 3007) metal coordination : bond 0.02201 / 1.10 ( 4) metal coordination : angle 5.46627 / 1.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 409 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 ASN cc_start: 0.9522 (m110) cc_final: 0.9056 (m-40) REVERT: D 198 HIS cc_start: 0.9214 (p90) cc_final: 0.8847 (p-80) REVERT: E 20 ARG cc_start: 0.9355 (ttp-170) cc_final: 0.9137 (ttp80) REVERT: E 23 LYS cc_start: 0.9282 (ttpt) cc_final: 0.8078 (mmtt) REVERT: E 31 PHE cc_start: 0.9272 (m-80) cc_final: 0.9041 (m-80) REVERT: E 50 TYR cc_start: 0.9258 (t80) cc_final: 0.9005 (t80) REVERT: E 60 ILE cc_start: 0.9543 (pp) cc_final: 0.9162 (mt) REVERT: E 61 GLN cc_start: 0.9410 (tp-100) cc_final: 0.9098 (tp-100) REVERT: E 65 GLU cc_start: 0.9114 (tp30) cc_final: 0.8649 (tp30) REVERT: E 69 ARG cc_start: 0.8991 (mtm-85) cc_final: 0.8505 (mtm-85) REVERT: F 59 TYR cc_start: 0.8447 (m-80) cc_final: 0.8213 (m-80) REVERT: F 65 GLU cc_start: 0.7945 (pp20) cc_final: 0.7680 (pp20) REVERT: F 72 ASP cc_start: 0.9006 (m-30) cc_final: 0.8727 (m-30) REVERT: H 9 ASP cc_start: 0.8916 (t70) cc_final: 0.8536 (t0) REVERT: H 42 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8642 (tm-30) REVERT: H 43 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8883 (mm-30) REVERT: H 61 LEU cc_start: 0.9570 (mp) cc_final: 0.9369 (mt) REVERT: K 64 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8802 (tm-30) REVERT: K 68 GLU cc_start: 0.9316 (mp0) cc_final: 0.8791 (pm20) REVERT: K 83 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8663 (mp0) REVERT: K 87 LYS cc_start: 0.9326 (ptmm) cc_final: 0.8933 (pttm) REVERT: K 126 LYS cc_start: 0.9190 (tppt) cc_final: 0.8944 (tppt) REVERT: L 62 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8447 (mm-30) REVERT: L 88 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7882 (tmtm) REVERT: O 64 ARG cc_start: 0.8990 (tpm170) cc_final: 0.8779 (tpp-160) REVERT: O 68 ASP cc_start: 0.8935 (m-30) cc_final: 0.8602 (m-30) REVERT: P 12 LYS cc_start: 0.9530 (ttmt) cc_final: 0.9252 (ttpp) REVERT: P 76 LYS cc_start: 0.9242 (tttt) cc_final: 0.8802 (tttt) REVERT: Q 11 ARG cc_start: 0.9070 (ptm160) cc_final: 0.8862 (ttm110) REVERT: Q 27 ARG cc_start: 0.9034 (ptt90) cc_final: 0.8815 (ptt90) REVERT: Q 60 GLU cc_start: 0.8194 (tp30) cc_final: 0.7930 (tp30) REVERT: R 16 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8648 (mp0) REVERT: R 18 VAL cc_start: 0.8765 (t) cc_final: 0.8341 (p) REVERT: R 33 ILE cc_start: 0.9632 (pt) cc_final: 0.9306 (pp) REVERT: R 51 TYR cc_start: 0.9399 (m-80) cc_final: 0.9097 (m-10) REVERT: T 40 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9128 (pt0) REVERT: U 24 GLU cc_start: 0.8780 (pp20) cc_final: 0.8394 (pp20) REVERT: U 25 LYS cc_start: 0.9473 (mmtt) cc_final: 0.9110 (mttm) REVERT: U 31 GLU cc_start: 0.8872 (tp30) cc_final: 0.8486 (tp30) REVERT: U 39 GLU cc_start: 0.9119 (tt0) cc_final: 0.8809 (tt0) REVERT: U 56 HIS cc_start: 0.9379 (t70) cc_final: 0.9135 (t70) REVERT: U 58 LYS cc_start: 0.9441 (mtpt) cc_final: 0.9161 (tmmt) REVERT: W 282 GLN cc_start: 0.9370 (mt0) cc_final: 0.9147 (mt0) outliers start: 76 outliers final: 32 residues processed: 446 average time/residue: 0.7325 time to fit residues: 388.5303 Evaluate side-chains 398 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain W residue 345 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: [46, 55, 0, 117, 83, 259, 174, 34, 68, 105, 28] chunk 46 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN D 196 ASN E 70 ASN E 146 ASN H 21 ASN H 118 GLN K 38 GLN Q 9 GLN W 62 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.035775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.028588 restraints weight = 219313.265| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 1.76 r_work: 0.2427 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2340 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9217 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 38870 Z= 0.407 Angle : 1.178 16.953 57821 Z= 0.483 Chirality : 0.091 1.081 7322 Planarity : 0.005 0.062 3334 Dihedral : 18.768 169.299 14778 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 7.24 % Allowed : 25.54 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1588 helix: 0.29 (0.21), residues: 604 sheet: -1.06 (0.29), residues: 297 loop : -0.74 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 93 TYR 0.030 0.002 TYR W 299 PHE 0.027 0.002 PHE W 172 TRP 0.013 0.002 TRP F 42 HIS 0.007 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00827 / 0.41 (38866) covalent geometry : angle 1.17715 / 0.48 (57818) hydrogen bonds : bond 0.08589 / 4.50 ( 1497) hydrogen bonds : angle 4.09388 / 1.65 ( 3007) metal coordination : bond 0.02260 / 1.13 ( 4) metal coordination : angle 6.25204 / 2.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 388 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8578 (tptp) REVERT: E 23 LYS cc_start: 0.9386 (ttpt) cc_final: 0.8185 (mmtt) REVERT: E 50 TYR cc_start: 0.9246 (t80) cc_final: 0.8894 (t80) REVERT: E 60 ILE cc_start: 0.9558 (pp) cc_final: 0.9249 (mt) REVERT: E 61 GLN cc_start: 0.9422 (tp-100) cc_final: 0.8243 (tp-100) REVERT: E 71 MET cc_start: 0.8685 (mmm) cc_final: 0.8409 (mmm) REVERT: E 152 MET cc_start: 0.9066 (mtp) cc_final: 0.8805 (ptp) REVERT: E 156 LYS cc_start: 0.9623 (OUTLIER) cc_final: 0.9396 (ptpp) REVERT: F 9 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8378 (mtm) REVERT: F 13 ASP cc_start: 0.8943 (m-30) cc_final: 0.8732 (t0) REVERT: F 72 ASP cc_start: 0.8877 (m-30) cc_final: 0.8650 (m-30) REVERT: H 47 GLU cc_start: 0.8126 (mp0) cc_final: 0.7910 (mp0) REVERT: H 92 LEU cc_start: 0.9397 (mt) cc_final: 0.9194 (mp) REVERT: K 14 LYS cc_start: 0.8750 (tmmm) cc_final: 0.7701 (mptt) REVERT: K 64 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8807 (tm-30) REVERT: K 68 GLU cc_start: 0.9306 (mp0) cc_final: 0.8849 (pm20) REVERT: K 83 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8748 (mp0) REVERT: K 126 LYS cc_start: 0.9202 (tppt) cc_final: 0.8937 (tppt) REVERT: O 64 ARG cc_start: 0.9011 (tpm170) cc_final: 0.8657 (tpp-160) REVERT: O 68 ASP cc_start: 0.9004 (m-30) cc_final: 0.8717 (m-30) REVERT: P 48 GLU cc_start: 0.7717 (tt0) cc_final: 0.7499 (pt0) REVERT: P 76 LYS cc_start: 0.9307 (tttt) cc_final: 0.8787 (tttt) REVERT: Q 8 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9246 (mt) REVERT: Q 27 ARG cc_start: 0.9108 (ptt90) cc_final: 0.8817 (ptt90) REVERT: R 18 VAL cc_start: 0.8740 (t) cc_final: 0.8293 (p) REVERT: R 33 ILE cc_start: 0.9635 (pt) cc_final: 0.9295 (pp) REVERT: R 51 TYR cc_start: 0.9437 (m-80) cc_final: 0.9124 (m-10) REVERT: T 40 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9178 (pt0) REVERT: U 24 GLU cc_start: 0.8832 (pp20) cc_final: 0.8557 (pp20) REVERT: U 25 LYS cc_start: 0.9476 (mmtt) cc_final: 0.9149 (mttm) REVERT: U 31 GLU cc_start: 0.8912 (tp30) cc_final: 0.8501 (tp30) REVERT: U 39 GLU cc_start: 0.9065 (tt0) cc_final: 0.8760 (tt0) REVERT: U 58 LYS cc_start: 0.9435 (mtpt) cc_final: 0.9148 (tmmt) REVERT: W 310 CYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7416 (t) REVERT: W 340 LYS cc_start: 0.8923 (ptpt) cc_final: 0.8276 (tptp) outliers start: 97 outliers final: 41 residues processed: 437 average time/residue: 0.7322 time to fit residues: 380.9189 Evaluate side-chains 413 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 367 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 211 ILE Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain W residue 310 CYS Chi-restraints excluded: chain W residue 345 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: [205, 190, 13, 213, 186, 55, 177, 18, 133, 82, 178] chunk 205 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 196 ASN H 21 ASN H 118 GLN K 38 GLN T 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.037414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.030257 restraints weight = 214298.141| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 1.75 r_work: 0.2493 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 38870 Z= 0.236 Angle : 1.050 14.978 57821 Z= 0.431 Chirality : 0.081 0.891 7322 Planarity : 0.004 0.049 3334 Dihedral : 18.634 173.219 14778 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.65 % Allowed : 27.41 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.21), residues: 1588 helix: 0.60 (0.21), residues: 595 sheet: -0.92 (0.30), residues: 283 loop : -0.63 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 24 TYR 0.016 0.002 TYR F 59 PHE 0.025 0.002 PHE F 80 TRP 0.008 0.001 TRP F 42 HIS 0.006 0.001 HIS L 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.24 (38866) covalent geometry : angle 1.04978 / 0.43 (57818) hydrogen bonds : bond 0.07880 / 4.13 ( 1497) hydrogen bonds : angle 3.87880 / 1.56 ( 3007) metal coordination : bond 0.01913 / 0.96 ( 4) metal coordination : angle 4.71836 / 1.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 408 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 ASN cc_start: 0.9542 (m110) cc_final: 0.9178 (m-40) REVERT: E 23 LYS cc_start: 0.9415 (ttpt) cc_final: 0.8227 (mmtt) REVERT: E 32 SER cc_start: 0.9478 (m) cc_final: 0.9240 (t) REVERT: E 50 TYR cc_start: 0.9278 (t80) cc_final: 0.8986 (t80) REVERT: E 60 ILE cc_start: 0.9574 (pp) cc_final: 0.9249 (mt) REVERT: E 61 GLN cc_start: 0.9308 (tp-100) cc_final: 0.8352 (tp40) REVERT: E 65 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8951 (mm-30) REVERT: F 1 MET cc_start: 0.8609 (ttm) cc_final: 0.7756 (tmt) REVERT: F 54 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8740 (tt) REVERT: F 68 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8491 (mt0) REVERT: F 72 ASP cc_start: 0.8787 (m-30) cc_final: 0.8570 (m-30) REVERT: F 93 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8550 (ttmm) REVERT: H 9 ASP cc_start: 0.8936 (t70) cc_final: 0.8596 (t0) REVERT: H 42 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8579 (tm-30) REVERT: H 43 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8939 (mm-30) REVERT: H 47 GLU cc_start: 0.8037 (mp0) cc_final: 0.7754 (mp0) REVERT: K 14 LYS cc_start: 0.8816 (tmmm) cc_final: 0.7772 (mptt) REVERT: K 64 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8841 (tm-30) REVERT: K 68 GLU cc_start: 0.9262 (mp0) cc_final: 0.8826 (mp0) REVERT: K 83 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8756 (mp0) REVERT: K 87 LYS cc_start: 0.9108 (ptmm) cc_final: 0.8711 (pttm) REVERT: K 126 LYS cc_start: 0.9225 (tppt) cc_final: 0.9024 (tppt) REVERT: P 48 GLU cc_start: 0.7762 (tt0) cc_final: 0.7526 (pt0) REVERT: P 76 LYS cc_start: 0.9274 (tttt) cc_final: 0.8766 (tttt) REVERT: Q 11 ARG cc_start: 0.9109 (ptm160) cc_final: 0.8869 (ttm110) REVERT: Q 40 ARG cc_start: 0.8701 (mmp-170) cc_final: 0.8128 (mmp-170) REVERT: R 18 VAL cc_start: 0.8830 (t) cc_final: 0.8451 (p) REVERT: R 22 ASP cc_start: 0.8666 (t0) cc_final: 0.7648 (t0) REVERT: R 24 LYS cc_start: 0.9383 (mtmp) cc_final: 0.9124 (mtmm) REVERT: R 32 TYR cc_start: 0.9271 (m-80) cc_final: 0.9028 (m-80) REVERT: R 33 ILE cc_start: 0.9628 (pt) cc_final: 0.9286 (pp) REVERT: R 51 TYR cc_start: 0.9372 (m-80) cc_final: 0.9047 (m-10) REVERT: U 24 GLU cc_start: 0.8851 (pp20) cc_final: 0.8548 (pp20) REVERT: U 25 LYS cc_start: 0.9453 (mmtt) cc_final: 0.9136 (mttm) REVERT: U 31 GLU cc_start: 0.8896 (tp30) cc_final: 0.8245 (tp30) REVERT: U 33 ARG cc_start: 0.9030 (ptp90) cc_final: 0.8726 (ttp80) REVERT: U 58 LYS cc_start: 0.9421 (mtpt) cc_final: 0.9133 (tmmt) REVERT: W 282 GLN cc_start: 0.9307 (mt0) cc_final: 0.9005 (mt0) REVERT: W 340 LYS cc_start: 0.8856 (ptpt) cc_final: 0.8273 (tptp) REVERT: W 343 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8884 (tptp) outliers start: 89 outliers final: 41 residues processed: 452 average time/residue: 0.7223 time to fit residues: 388.8028 Evaluate side-chains 421 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 378 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 211 ILE Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 272 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: [99, 53, 230, 43, 67, 150, 16, 198, 241, 127, 157] chunk 99 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 241 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 GLN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 118 GLN K 38 GLN ** W 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.035933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.028699 restraints weight = 218596.174| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 1.78 r_work: 0.2431 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2344 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 38870 Z= 0.399 Angle : 1.153 14.798 57821 Z= 0.474 Chirality : 0.087 1.003 7322 Planarity : 0.005 0.050 3334 Dihedral : 18.793 175.680 14778 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 7.32 % Allowed : 28.90 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.21), residues: 1588 helix: 0.50 (0.21), residues: 601 sheet: -0.95 (0.30), residues: 287 loop : -0.60 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 93 TYR 0.017 0.002 TYR R 23 PHE 0.035 0.002 PHE W 172 TRP 0.009 0.001 TRP F 42 HIS 0.005 0.001 HIS L 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.40 (38866) covalent geometry : angle 1.15249 / 0.47 (57818) hydrogen bonds : bond 0.08437 / 4.41 ( 1497) hydrogen bonds : angle 3.94958 / 1.60 ( 3007) metal coordination : bond 0.02244 / 1.12 ( 4) metal coordination : angle 5.88170 / 1.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 380 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8572 (tptp) REVERT: E 23 LYS cc_start: 0.9375 (ttpt) cc_final: 0.8181 (mmtt) REVERT: E 50 TYR cc_start: 0.9259 (t80) cc_final: 0.8907 (t80) REVERT: E 60 ILE cc_start: 0.9596 (pp) cc_final: 0.9260 (mt) REVERT: E 61 GLN cc_start: 0.9329 (tp-100) cc_final: 0.8451 (tp40) REVERT: E 65 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8993 (mm-30) REVERT: E 156 LYS cc_start: 0.9653 (OUTLIER) cc_final: 0.9389 (ptpp) REVERT: F 13 ASP cc_start: 0.8951 (m-30) cc_final: 0.8678 (t0) REVERT: F 54 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8751 (tt) REVERT: F 72 ASP cc_start: 0.8919 (m-30) cc_final: 0.8635 (m-30) REVERT: H 42 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8672 (tm-30) REVERT: H 43 GLU cc_start: 0.9235 (mm-30) cc_final: 0.9014 (mm-30) REVERT: H 47 GLU cc_start: 0.8056 (mp0) cc_final: 0.7784 (mp0) REVERT: H 92 LEU cc_start: 0.9404 (mt) cc_final: 0.9184 (mp) REVERT: H 118 GLN cc_start: 0.9323 (tt0) cc_final: 0.8838 (tm-30) REVERT: K 14 LYS cc_start: 0.8828 (tmmm) cc_final: 0.7816 (mptt) REVERT: K 64 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8857 (tm-30) REVERT: K 68 GLU cc_start: 0.9265 (mp0) cc_final: 0.8813 (mp0) REVERT: K 126 LYS cc_start: 0.9239 (tppt) cc_final: 0.9026 (tppt) REVERT: L 25 GLU cc_start: 0.8914 (mp0) cc_final: 0.8481 (mp0) REVERT: P 48 GLU cc_start: 0.7875 (tt0) cc_final: 0.7481 (pt0) REVERT: P 76 LYS cc_start: 0.9240 (tttt) cc_final: 0.8758 (tttt) REVERT: Q 39 LYS cc_start: 0.9374 (ptpp) cc_final: 0.9121 (ptpp) REVERT: R 18 VAL cc_start: 0.8817 (t) cc_final: 0.8409 (p) REVERT: R 22 ASP cc_start: 0.8693 (t0) cc_final: 0.8007 (t0) REVERT: R 32 TYR cc_start: 0.9352 (m-80) cc_final: 0.9056 (m-80) REVERT: R 51 TYR cc_start: 0.9433 (m-80) cc_final: 0.9110 (m-10) REVERT: U 24 GLU cc_start: 0.8877 (pp20) cc_final: 0.8615 (pp20) REVERT: U 25 LYS cc_start: 0.9479 (mmtt) cc_final: 0.9167 (mttm) REVERT: U 31 GLU cc_start: 0.8750 (tp30) cc_final: 0.8511 (tp30) REVERT: U 39 GLU cc_start: 0.9068 (tt0) cc_final: 0.8747 (tt0) REVERT: U 58 LYS cc_start: 0.9420 (mtpt) cc_final: 0.9137 (tmmt) REVERT: W 282 GLN cc_start: 0.9328 (mt0) cc_final: 0.9099 (mt0) REVERT: W 310 CYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7274 (t) outliers start: 98 outliers final: 50 residues processed: 433 average time/residue: 0.7105 time to fit residues: 369.4385 Evaluate side-chains 411 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 357 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 48 PHE Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 211 ILE Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain W residue 310 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: [248, 253, 17, 249, 125, 152, 146, 212, 140, 220, 214] chunk 248 optimal weight: 4.9990 chunk 253 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 249 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 196 ASN D 198 HIS ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN K 38 GLN O 35 GLN R 74 HIS ** W 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.036810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.029661 restraints weight = 214178.575| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 1.74 r_work: 0.2467 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2380 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 38870 Z= 0.290 Angle : 1.072 13.720 57821 Z= 0.442 Chirality : 0.082 0.907 7322 Planarity : 0.005 0.051 3334 Dihedral : 18.757 178.388 14778 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 6.50 % Allowed : 31.22 % Favored : 62.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.21), residues: 1588 helix: 0.60 (0.21), residues: 595 sheet: -0.85 (0.30), residues: 288 loop : -0.51 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 24 TYR 0.017 0.002 TYR W 329 PHE 0.032 0.002 PHE F 80 TRP 0.009 0.001 TRP F 42 HIS 0.007 0.001 HIS R 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.29 (38866) covalent geometry : angle 1.07138 / 0.44 (57818) hydrogen bonds : bond 0.07996 / 4.19 ( 1497) hydrogen bonds : angle 3.85701 / 1.56 ( 3007) metal coordination : bond 0.01972 / 0.99 ( 4) metal coordination : angle 4.73327 / 1.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 381 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8556 (tptp) REVERT: E 23 LYS cc_start: 0.9398 (ttpt) cc_final: 0.8205 (mmtt) REVERT: E 32 SER cc_start: 0.9466 (OUTLIER) cc_final: 0.9256 (t) REVERT: E 50 TYR cc_start: 0.9264 (t80) cc_final: 0.8972 (t80) REVERT: E 60 ILE cc_start: 0.9603 (pp) cc_final: 0.9246 (mt) REVERT: E 61 GLN cc_start: 0.9339 (tp-100) cc_final: 0.8398 (tp40) REVERT: E 65 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8919 (mm-30) REVERT: E 156 LYS cc_start: 0.9638 (OUTLIER) cc_final: 0.9429 (ptpp) REVERT: F 1 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7751 (tmt) REVERT: F 13 ASP cc_start: 0.8926 (m-30) cc_final: 0.8683 (t0) REVERT: F 54 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8744 (tt) REVERT: F 72 ASP cc_start: 0.8970 (m-30) cc_final: 0.8678 (m-30) REVERT: H 9 ASP cc_start: 0.8998 (t70) cc_final: 0.8685 (t0) REVERT: H 42 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8671 (tm-30) REVERT: H 47 GLU cc_start: 0.8069 (mp0) cc_final: 0.7774 (mp0) REVERT: H 80 ARG cc_start: 0.9502 (OUTLIER) cc_final: 0.9274 (ptt90) REVERT: H 89 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8786 (tmmm) REVERT: H 92 LEU cc_start: 0.9403 (mt) cc_final: 0.9197 (mp) REVERT: K 14 LYS cc_start: 0.8798 (tmmm) cc_final: 0.7778 (mptt) REVERT: K 64 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8879 (tm-30) REVERT: P 48 GLU cc_start: 0.7927 (tt0) cc_final: 0.7592 (pt0) REVERT: P 76 LYS cc_start: 0.9217 (tttt) cc_final: 0.8778 (tttt) REVERT: Q 39 LYS cc_start: 0.9371 (ptpp) cc_final: 0.8917 (ptpp) REVERT: Q 40 ARG cc_start: 0.8834 (mmp-170) cc_final: 0.8474 (mmp-170) REVERT: R 18 VAL cc_start: 0.8811 (t) cc_final: 0.8470 (p) REVERT: R 33 ILE cc_start: 0.9589 (pt) cc_final: 0.9302 (pp) REVERT: R 51 TYR cc_start: 0.9390 (m-80) cc_final: 0.9086 (m-10) REVERT: U 24 GLU cc_start: 0.8868 (pp20) cc_final: 0.8658 (pp20) REVERT: U 31 GLU cc_start: 0.8841 (tp30) cc_final: 0.8417 (tp30) REVERT: U 39 GLU cc_start: 0.9029 (tt0) cc_final: 0.8575 (tt0) REVERT: U 59 LYS cc_start: 0.9185 (mmtt) cc_final: 0.8892 (mmmm) REVERT: W 298 LYS cc_start: 0.8680 (ptmm) cc_final: 0.8335 (pptt) REVERT: W 340 LYS cc_start: 0.8911 (ptpt) cc_final: 0.8394 (tptp) outliers start: 87 outliers final: 51 residues processed: 426 average time/residue: 0.7176 time to fit residues: 365.1867 Evaluate side-chains 425 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 367 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 272 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: [177, 146, 0, 6, 235, 149, 227, 249, 56, 10, 244] chunk 177 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 118 GLN K 38 GLN Q 9 GLN ** W 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.036392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.029219 restraints weight = 216151.943| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 1.75 r_work: 0.2453 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2368 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9201 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 38870 Z= 0.338 Angle : 1.108 14.245 57821 Z= 0.457 Chirality : 0.084 0.941 7322 Planarity : 0.005 0.051 3334 Dihedral : 18.768 178.043 14778 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.65 % Allowed : 32.49 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.21), residues: 1588 helix: 0.58 (0.21), residues: 596 sheet: -0.91 (0.31), residues: 280 loop : -0.54 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 54 TYR 0.020 0.002 TYR R 23 PHE 0.033 0.002 PHE W 172 TRP 0.014 0.001 TRP F 42 HIS 0.007 0.001 HIS K 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.34 (38866) covalent geometry : angle 1.10716 / 0.46 (57818) hydrogen bonds : bond 0.08175 / 4.27 ( 1497) hydrogen bonds : angle 3.88083 / 1.57 ( 3007) metal coordination : bond 0.02080 / 1.04 ( 4) metal coordination : angle 5.02707 / 1.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 374 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8530 (tptp) REVERT: E 23 LYS cc_start: 0.9373 (ttpt) cc_final: 0.8213 (mmtt) REVERT: E 50 TYR cc_start: 0.9270 (t80) cc_final: 0.8965 (t80) REVERT: E 60 ILE cc_start: 0.9636 (pp) cc_final: 0.9320 (mt) REVERT: E 61 GLN cc_start: 0.9349 (tp-100) cc_final: 0.8414 (tp40) REVERT: E 65 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8931 (mm-30) REVERT: E 156 LYS cc_start: 0.9642 (OUTLIER) cc_final: 0.9421 (ptpp) REVERT: F 1 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8097 (tmt) REVERT: F 13 ASP cc_start: 0.8928 (m-30) cc_final: 0.8690 (t0) REVERT: F 54 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8753 (tt) REVERT: F 72 ASP cc_start: 0.8935 (m-30) cc_final: 0.8670 (m-30) REVERT: H 9 ASP cc_start: 0.8987 (t70) cc_final: 0.8660 (t0) REVERT: H 47 GLU cc_start: 0.8051 (mp0) cc_final: 0.7759 (mp0) REVERT: H 89 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8833 (tmmm) REVERT: H 92 LEU cc_start: 0.9417 (mt) cc_final: 0.9205 (mp) REVERT: H 118 GLN cc_start: 0.9283 (tt0) cc_final: 0.8746 (tm-30) REVERT: K 14 LYS cc_start: 0.8790 (tmmm) cc_final: 0.7780 (mptt) REVERT: K 64 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8857 (tm-30) REVERT: K 87 LYS cc_start: 0.9128 (ptmm) cc_final: 0.8707 (pttm) REVERT: O 10 LYS cc_start: 0.9474 (tppp) cc_final: 0.8673 (tppt) REVERT: P 48 GLU cc_start: 0.7922 (tt0) cc_final: 0.7551 (pt0) REVERT: P 76 LYS cc_start: 0.9203 (tttt) cc_final: 0.8762 (tttt) REVERT: R 18 VAL cc_start: 0.8800 (t) cc_final: 0.8442 (p) REVERT: R 51 TYR cc_start: 0.9419 (m-80) cc_final: 0.9111 (m-10) REVERT: T 28 MET cc_start: 0.9451 (ttp) cc_final: 0.9133 (ttm) REVERT: U 24 GLU cc_start: 0.8893 (pp20) cc_final: 0.8680 (pp20) REVERT: U 31 GLU cc_start: 0.8848 (tp30) cc_final: 0.8446 (tp30) REVERT: U 39 GLU cc_start: 0.9037 (tt0) cc_final: 0.8712 (tt0) REVERT: U 59 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8922 (mmmm) REVERT: W 282 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.9072 (mt0) REVERT: W 340 LYS cc_start: 0.8899 (ptpt) cc_final: 0.8329 (tptp) outliers start: 89 outliers final: 57 residues processed: 420 average time/residue: 0.6904 time to fit residues: 346.5860 Evaluate side-chains 424 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 361 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 48 PHE Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 167 ASP Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 245 LEU Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain W residue 282 GLN Chi-restraints excluded: chain W residue 310 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: [108, 218, 86, 69, 76, 153, 178, 240, 2, 122, 110] chunk 108 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 GLN D 196 ASN D 198 HIS H 21 ASN K 38 GLN Q 9 GLN T 61 GLN W 282 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.038174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.031057 restraints weight = 211203.091| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 1.74 r_work: 0.2525 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 38870 Z= 0.196 Angle : 1.025 14.178 57821 Z= 0.427 Chirality : 0.078 0.945 7322 Planarity : 0.004 0.052 3334 Dihedral : 18.671 177.727 14778 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.53 % Allowed : 35.18 % Favored : 59.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.21), residues: 1588 helix: 0.56 (0.21), residues: 597 sheet: -0.80 (0.30), residues: 286 loop : -0.44 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 54 TYR 0.020 0.002 TYR D 51 PHE 0.039 0.002 PHE F 80 TRP 0.013 0.001 TRP F 42 HIS 0.006 0.001 HIS K 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (38866) covalent geometry : angle 1.02459 / 0.43 (57818) hydrogen bonds : bond 0.07875 / 4.12 ( 1497) hydrogen bonds : angle 3.83401 / 1.56 ( 3007) metal coordination : bond 0.01141 / 0.57 ( 4) metal coordination : angle 3.10899 / 1.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 390 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 ASN cc_start: 0.9441 (OUTLIER) cc_final: 0.9060 (t0) REVERT: E 14 LYS cc_start: 0.9209 (mtpp) cc_final: 0.8664 (ptpt) REVERT: E 23 LYS cc_start: 0.9395 (ttpt) cc_final: 0.8206 (mmtt) REVERT: E 50 TYR cc_start: 0.9275 (t80) cc_final: 0.8939 (t80) REVERT: E 61 GLN cc_start: 0.9329 (tp-100) cc_final: 0.8413 (tp40) REVERT: E 65 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8956 (mm-30) REVERT: E 68 ARG cc_start: 0.9149 (mmt90) cc_final: 0.8946 (mmt90) REVERT: E 156 LYS cc_start: 0.9633 (OUTLIER) cc_final: 0.9409 (ptpp) REVERT: F 1 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8110 (tmt) REVERT: F 13 ASP cc_start: 0.8895 (m-30) cc_final: 0.8679 (t0) REVERT: F 54 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8703 (tt) REVERT: F 72 ASP cc_start: 0.8919 (m-30) cc_final: 0.8648 (m-30) REVERT: H 9 ASP cc_start: 0.8977 (t70) cc_final: 0.8654 (t0) REVERT: H 42 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8629 (tm-30) REVERT: H 47 GLU cc_start: 0.8101 (mp0) cc_final: 0.7820 (mp0) REVERT: H 80 ARG cc_start: 0.9458 (OUTLIER) cc_final: 0.9228 (ptt90) REVERT: H 89 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8850 (tmmm) REVERT: K 14 LYS cc_start: 0.8937 (tmmm) cc_final: 0.7959 (mptt) REVERT: K 64 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8816 (tm-30) REVERT: K 68 GLU cc_start: 0.9201 (mp0) cc_final: 0.8863 (mp0) REVERT: O 10 LYS cc_start: 0.9239 (tppp) cc_final: 0.8922 (tppt) REVERT: P 48 GLU cc_start: 0.8029 (tt0) cc_final: 0.7741 (pt0) REVERT: P 76 LYS cc_start: 0.9191 (tttt) cc_final: 0.8663 (tttt) REVERT: Q 18 GLU cc_start: 0.8795 (pt0) cc_final: 0.8560 (pm20) REVERT: Q 39 LYS cc_start: 0.9305 (ptpp) cc_final: 0.8798 (pttp) REVERT: Q 40 ARG cc_start: 0.8690 (mmp-170) cc_final: 0.8366 (mmp-170) REVERT: Q 60 GLU cc_start: 0.8722 (tt0) cc_final: 0.8438 (tm-30) REVERT: R 18 VAL cc_start: 0.8814 (t) cc_final: 0.8445 (p) REVERT: R 33 ILE cc_start: 0.9573 (pt) cc_final: 0.9291 (pp) REVERT: R 51 TYR cc_start: 0.9348 (m-80) cc_final: 0.9042 (m-10) REVERT: U 24 GLU cc_start: 0.8938 (pp20) cc_final: 0.8701 (pp20) REVERT: U 31 GLU cc_start: 0.8701 (tp30) cc_final: 0.8409 (tp30) REVERT: U 39 GLU cc_start: 0.9025 (tt0) cc_final: 0.8710 (tt0) REVERT: U 59 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8867 (mmmm) REVERT: W 215 GLN cc_start: 0.9097 (mt0) cc_final: 0.8770 (tt0) REVERT: W 282 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.9076 (mt0) REVERT: W 298 LYS cc_start: 0.8518 (pptt) cc_final: 0.8295 (pptt) REVERT: W 340 LYS cc_start: 0.8826 (ptpt) cc_final: 0.8315 (tptp) outliers start: 74 outliers final: 46 residues processed: 427 average time/residue: 0.6771 time to fit residues: 345.4440 Evaluate side-chains 419 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 366 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 245 LEU Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain W residue 282 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: [212, 149, 120, 137, 24, 108, 32, 158, 96, 90, 134] chunk 212 optimal weight: 0.1980 chunk 149 optimal weight: 8.9990 chunk 120 optimal weight: 0.2980 chunk 137 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 196 ASN H 21 ASN K 38 GLN Q 9 GLN T 61 GLN ** W 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 282 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.038585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.031487 restraints weight = 210826.109| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 1.75 r_work: 0.2542 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 38870 Z= 0.183 Angle : 1.022 15.169 57821 Z= 0.427 Chirality : 0.077 0.943 7322 Planarity : 0.004 0.055 3334 Dihedral : 18.632 177.943 14778 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 5.08 % Allowed : 36.07 % Favored : 58.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.21), residues: 1588 helix: 0.49 (0.21), residues: 599 sheet: -0.82 (0.30), residues: 292 loop : -0.38 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 33 TYR 0.021 0.001 TYR W 329 PHE 0.032 0.001 PHE W 172 TRP 0.015 0.002 TRP F 42 HIS 0.006 0.001 HIS K 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (38866) covalent geometry : angle 1.02226 / 0.43 (57818) hydrogen bonds : bond 0.07856 / 4.11 ( 1497) hydrogen bonds : angle 3.86623 / 1.57 ( 3007) metal coordination : bond 0.01073 / 0.54 ( 4) metal coordination : angle 2.89918 / 0.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 382 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 GLU cc_start: 0.9024 (mp0) cc_final: 0.8822 (mp0) REVERT: E 14 LYS cc_start: 0.9201 (mtpp) cc_final: 0.8937 (ptpt) REVERT: E 23 LYS cc_start: 0.9367 (ttpt) cc_final: 0.8157 (mmtt) REVERT: E 33 PHE cc_start: 0.9376 (m-80) cc_final: 0.9035 (m-80) REVERT: E 50 TYR cc_start: 0.9264 (t80) cc_final: 0.8937 (t80) REVERT: E 61 GLN cc_start: 0.9271 (tp-100) cc_final: 0.8328 (tp40) REVERT: E 65 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8849 (mm-30) REVERT: E 68 ARG cc_start: 0.9154 (mmt90) cc_final: 0.8888 (mmt90) REVERT: E 116 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8550 (pp20) REVERT: E 152 MET cc_start: 0.9332 (pmm) cc_final: 0.9109 (pmm) REVERT: E 156 LYS cc_start: 0.9633 (OUTLIER) cc_final: 0.9400 (ptpp) REVERT: F 1 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7752 (tmt) REVERT: F 13 ASP cc_start: 0.8879 (m-30) cc_final: 0.8653 (t0) REVERT: F 25 TYR cc_start: 0.8760 (m-80) cc_final: 0.8449 (m-80) REVERT: F 54 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8708 (tt) REVERT: F 72 ASP cc_start: 0.8948 (m-30) cc_final: 0.8708 (m-30) REVERT: F 91 ARG cc_start: 0.9352 (mmm-85) cc_final: 0.9114 (mmm-85) REVERT: F 97 THR cc_start: 0.8604 (m) cc_final: 0.8381 (p) REVERT: H 9 ASP cc_start: 0.8984 (t70) cc_final: 0.8659 (t0) REVERT: H 47 GLU cc_start: 0.8121 (mp0) cc_final: 0.7814 (mp0) REVERT: H 80 ARG cc_start: 0.9448 (OUTLIER) cc_final: 0.9214 (ptt90) REVERT: H 124 GLU cc_start: 0.8607 (tt0) cc_final: 0.8344 (tt0) REVERT: H 125 ILE cc_start: 0.9088 (pp) cc_final: 0.8877 (pp) REVERT: K 14 LYS cc_start: 0.8948 (tmmm) cc_final: 0.7974 (mptt) REVERT: K 64 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8841 (tm-30) REVERT: K 87 LYS cc_start: 0.9054 (ptmm) cc_final: 0.8547 (pttm) REVERT: O 10 LYS cc_start: 0.9227 (tppp) cc_final: 0.8968 (tppt) REVERT: P 48 GLU cc_start: 0.7987 (tt0) cc_final: 0.7647 (pt0) REVERT: P 76 LYS cc_start: 0.9184 (tttt) cc_final: 0.8812 (tttt) REVERT: Q 18 GLU cc_start: 0.8761 (pt0) cc_final: 0.8544 (pm20) REVERT: Q 40 ARG cc_start: 0.8642 (mmp-170) cc_final: 0.8379 (mmp-170) REVERT: Q 60 GLU cc_start: 0.8701 (tt0) cc_final: 0.8402 (tm-30) REVERT: R 18 VAL cc_start: 0.8803 (t) cc_final: 0.8441 (p) REVERT: R 51 TYR cc_start: 0.9341 (m-80) cc_final: 0.9030 (m-10) REVERT: U 24 GLU cc_start: 0.8966 (pp20) cc_final: 0.8696 (pp20) REVERT: U 31 GLU cc_start: 0.8665 (tp30) cc_final: 0.8180 (tp30) REVERT: U 39 GLU cc_start: 0.8991 (tt0) cc_final: 0.8722 (tt0) REVERT: U 58 LYS cc_start: 0.9411 (mtpt) cc_final: 0.9122 (tmmt) REVERT: W 215 GLN cc_start: 0.9080 (mt0) cc_final: 0.8780 (tt0) REVERT: W 282 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.9122 (mt0) REVERT: W 298 LYS cc_start: 0.8482 (pptt) cc_final: 0.8210 (pptt) REVERT: W 340 LYS cc_start: 0.8816 (ptpt) cc_final: 0.8335 (tptp) outliers start: 68 outliers final: 44 residues processed: 414 average time/residue: 0.6757 time to fit residues: 333.7558 Evaluate side-chains 419 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 369 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 167 ASP Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 245 LEU Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain W residue 282 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: [32, 53, 177, 1, 17, 67, 132, 221, 214, 48, 28] chunk 32 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 GLN H 21 ASN K 38 GLN L 5 ASN Q 9 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN W 282 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.036834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.029646 restraints weight = 215205.304| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 1.76 r_work: 0.2468 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2380 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 38870 Z= 0.326 Angle : 1.108 15.794 57821 Z= 0.463 Chirality : 0.082 0.991 7322 Planarity : 0.005 0.065 3334 Dihedral : 18.731 179.731 14778 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.78 % Allowed : 36.45 % Favored : 58.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.21), residues: 1588 helix: 0.39 (0.21), residues: 599 sheet: -0.84 (0.30), residues: 292 loop : -0.40 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 54 TYR 0.024 0.002 TYR D 51 PHE 0.035 0.002 PHE F 80 TRP 0.015 0.002 TRP F 42 HIS 0.008 0.001 HIS R 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.33 (38866) covalent geometry : angle 1.10801 / 0.46 (57818) hydrogen bonds : bond 0.08183 / 4.27 ( 1497) hydrogen bonds : angle 3.98483 / 1.63 ( 3007) metal coordination : bond 0.01964 / 0.98 ( 4) metal coordination : angle 4.43651 / 1.48 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 365 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 14 LYS cc_start: 0.9152 (mtpp) cc_final: 0.8873 (ptpt) REVERT: E 23 LYS cc_start: 0.9327 (ttpt) cc_final: 0.8174 (mmtt) REVERT: E 31 PHE cc_start: 0.9122 (m-10) cc_final: 0.8385 (m-10) REVERT: E 50 TYR cc_start: 0.9262 (t80) cc_final: 0.8956 (t80) REVERT: E 54 ARG cc_start: 0.8867 (tpp-160) cc_final: 0.8414 (mmm160) REVERT: E 61 GLN cc_start: 0.9195 (tp-100) cc_final: 0.8217 (tp40) REVERT: E 65 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8862 (mm-30) REVERT: E 116 GLU cc_start: 0.8900 (pp20) cc_final: 0.8642 (pp20) REVERT: E 152 MET cc_start: 0.9361 (pmm) cc_final: 0.9125 (pmm) REVERT: E 156 LYS cc_start: 0.9641 (OUTLIER) cc_final: 0.9342 (ptpp) REVERT: F 1 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8026 (tmt) REVERT: F 13 ASP cc_start: 0.8931 (m-30) cc_final: 0.8682 (t0) REVERT: F 54 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8675 (tt) REVERT: F 59 TYR cc_start: 0.8566 (m-80) cc_final: 0.8356 (m-80) REVERT: F 72 ASP cc_start: 0.8949 (m-30) cc_final: 0.8664 (m-30) REVERT: H 9 ASP cc_start: 0.9024 (t70) cc_final: 0.8717 (t0) REVERT: H 47 GLU cc_start: 0.8112 (mp0) cc_final: 0.7799 (mp0) REVERT: H 80 ARG cc_start: 0.9523 (OUTLIER) cc_final: 0.9321 (ptt90) REVERT: H 118 GLN cc_start: 0.9212 (tt0) cc_final: 0.8590 (tm-30) REVERT: K 14 LYS cc_start: 0.8961 (tmmm) cc_final: 0.7970 (mptt) REVERT: K 64 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8862 (tm-30) REVERT: K 87 LYS cc_start: 0.9056 (ptmm) cc_final: 0.8539 (pttm) REVERT: O 10 LYS cc_start: 0.9262 (tppp) cc_final: 0.9039 (tppt) REVERT: P 48 GLU cc_start: 0.7972 (tt0) cc_final: 0.7600 (pt0) REVERT: P 76 LYS cc_start: 0.9183 (tttt) cc_final: 0.8849 (tttt) REVERT: Q 18 GLU cc_start: 0.8788 (pt0) cc_final: 0.8474 (pm20) REVERT: Q 39 LYS cc_start: 0.9314 (ptpp) cc_final: 0.8881 (ptpp) REVERT: Q 40 ARG cc_start: 0.8843 (mmp-170) cc_final: 0.8491 (mmp-170) REVERT: R 18 VAL cc_start: 0.8831 (t) cc_final: 0.8440 (p) REVERT: R 51 TYR cc_start: 0.9393 (m-80) cc_final: 0.9064 (m-10) REVERT: T 28 MET cc_start: 0.9423 (ttp) cc_final: 0.9083 (ttm) REVERT: U 24 GLU cc_start: 0.8930 (pp20) cc_final: 0.8700 (pp20) REVERT: U 31 GLU cc_start: 0.8693 (tp30) cc_final: 0.8415 (tp30) REVERT: U 39 GLU cc_start: 0.9087 (tt0) cc_final: 0.8784 (tt0) REVERT: U 59 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8904 (mmmm) REVERT: W 282 GLN cc_start: 0.9416 (OUTLIER) cc_final: 0.9134 (mt0) REVERT: W 340 LYS cc_start: 0.8859 (ptpt) cc_final: 0.8382 (tptp) outliers start: 64 outliers final: 48 residues processed: 403 average time/residue: 0.6658 time to fit residues: 321.7014 Evaluate side-chains 409 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 356 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 245 LEU Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain W residue 282 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: [256, 13, 35, 22, 46, 218, 193, 17, 9, 230, 120] chunk 256 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 218 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 71 GLN H 21 ASN K 38 GLN Q 9 GLN T 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.030103 restraints weight = 211808.960| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 1.74 r_work: 0.2485 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2397 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 38870 Z= 0.271 Angle : 1.083 15.485 57821 Z= 0.454 Chirality : 0.080 0.965 7322 Planarity : 0.005 0.064 3334 Dihedral : 18.728 179.654 14778 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.48 % Allowed : 37.04 % Favored : 58.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.21), residues: 1588 helix: 0.39 (0.21), residues: 599 sheet: -0.89 (0.30), residues: 293 loop : -0.43 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 54 TYR 0.029 0.002 TYR D 51 PHE 0.033 0.002 PHE W 172 TRP 0.014 0.002 TRP F 42 HIS 0.007 0.001 HIS R 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.27 (38866) covalent geometry : angle 1.08258 / 0.45 (57818) hydrogen bonds : bond 0.08023 / 4.19 ( 1497) hydrogen bonds : angle 3.97811 / 1.62 ( 3007) metal coordination : bond 0.01835 / 0.92 ( 4) metal coordination : angle 4.41025 / 1.47 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12967.20 seconds wall clock time: 221 minutes 26.78 seconds (13286.78 seconds total)