Starting phenix.real_space_refine on Thu Aug 6 18:09:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9trl_56178/08_2026/9trl_56178.cif Found real_map, /net/cci-nas-00/data/ceres_data/9trl_56178/08_2026/9trl_56178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9trl_56178/08_2026/9trl_56178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9trl_56178/08_2026/9trl_56178.map" model { file = "/net/cci-nas-00/data/ceres_data/9trl_56178/08_2026/9trl_56178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9trl_56178/08_2026/9trl_56178.cif" } resolution = 3.0 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= 0.002 sd= 0.086 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 K 5 8.98 5 P 41 5.49 5 Mg 5 5.21 5 S 87 5.16 5 C 10036 2.51 5 N 2870 2.21 5 O 3162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16206 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 1 Chain: "B" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2409 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain breaks: 1 Chain: "C" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2414 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2413 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 304} Chain breaks: 1 Chain: "E" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2410 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 303} Chain breaks: 1 Chain: "F" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2403 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 133 Unusual residues: {'ACE': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 3, 'TRANS': 13} Chain breaks: 1 Chain: "I" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 141 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 141 Unusual residues: {'ACE': 1} Classifications: {'peptide': 18, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 13} Chain breaks: 1 Chain: "K" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 135 Unusual residues: {'ACE': 1} Classifications: {'peptide': 18, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 13} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 580 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 2 Chain: "Z" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 407 Classifications: {'DNA': 20} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' K': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.28, per 1000 atoms: 0.20 Number of scatterers: 16206 At special positions: 0 Unit cell: (115.92, 120.96, 162.12, 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) K 5 19.00 S 87 16.00 P 41 15.00 Mg 5 11.99 O 3162 8.00 N 2870 7.00 C 10036 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: 1.22 Conformation dependent library (CDL) restraints added in 579.1 milliseconds 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3704 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 19 sheets defined 48.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 25 through 33 removed outlier: 3.601A pdb=" N CYS A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.519A pdb=" N VAL A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.725A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.926A pdb=" N GLU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 167 through 178 removed outlier: 3.658A pdb=" N VAL A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.617A pdb=" N VAL A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 214 removed outlier: 3.816A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.960A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.651A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 32 removed outlier: 4.152A pdb=" N GLN B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.540A pdb=" N ALA B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.579A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 removed outlier: 3.617A pdb=" N ASP B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.730A pdb=" N GLU B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.556A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.768A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 187 removed outlier: 3.666A pdb=" N LEU B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 214 removed outlier: 3.601A pdb=" N THR B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 4.072A pdb=" N THR B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.583A pdb=" N MET B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.837A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 34 through 45 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.925A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 81 removed outlier: 3.749A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.701A pdb=" N PHE C 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.704A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.869A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.531A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 260 Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.775A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 4.275A pdb=" N GLN D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 26 through 31' Processing helix chain 'D' and resid 34 through 45 removed outlier: 3.879A pdb=" N VAL D 38 " --> pdb=" O ASN D 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 40 " --> pdb=" O ASN D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 55 removed outlier: 3.546A pdb=" N VAL D 52 " --> pdb=" O THR D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 63 removed outlier: 3.779A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.585A pdb=" N GLN D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'D' and resid 132 through 144 removed outlier: 4.068A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 146 No H-bonds generated for 'chain 'D' and resid 145 through 146' Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 181 through 186 Processing helix chain 'D' and resid 196 through 211 removed outlier: 4.188A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN D 206 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA D 209 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 210 " --> pdb=" O GLN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 3.893A pdb=" N ARG D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 259 removed outlier: 3.810A pdb=" N ALA D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.656A pdb=" N ILE D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 Processing helix chain 'E' and resid 34 through 45 Processing helix chain 'E' and resid 48 through 55 removed outlier: 3.526A pdb=" N VAL E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 62 removed outlier: 3.501A pdb=" N ASN E 62 " --> pdb=" O LYS E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 82 Processing helix chain 'E' and resid 89 through 98 removed outlier: 3.820A pdb=" N GLU E 98 " --> pdb=" O GLN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 132 through 144 Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 179 removed outlier: 4.184A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'E' and resid 196 through 211 removed outlier: 3.929A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 removed outlier: 3.699A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.872A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 28 removed outlier: 3.528A pdb=" N ARG F 27 " --> pdb=" O PRO F 24 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU F 28 " --> pdb=" O ILE F 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 24 through 28' Processing helix chain 'F' and resid 34 through 43 removed outlier: 3.845A pdb=" N VAL F 38 " --> pdb=" O ASN F 34 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 55 removed outlier: 3.927A pdb=" N VAL F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 removed outlier: 3.563A pdb=" N GLU F 59 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 79 removed outlier: 4.018A pdb=" N GLU F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 98 removed outlier: 3.860A pdb=" N GLU F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 removed outlier: 3.614A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.568A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 178 removed outlier: 3.644A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 176 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 188 Processing helix chain 'F' and resid 196 through 211 removed outlier: 3.910A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 232 removed outlier: 4.100A pdb=" N THR F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 260 Processing helix chain 'F' and resid 288 through 296 removed outlier: 3.638A pdb=" N ILE F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA F 295 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'K' and resid 2 through 6 removed outlier: 3.666A pdb=" N ALA K 6 " --> pdb=" O ARG K 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 83 removed outlier: 3.816A pdb=" N SER O 82 " --> pdb=" O PRO O 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 5.428A pdb=" N LYS B 156 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 218 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B 217 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL B 264 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 219 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR B 266 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL B 221 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 122 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE B 126 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N LYS B 304 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR B 301 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ILE B 314 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ARG B 303 " --> pdb=" O CYS B 312 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N CYS B 312 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS B 312 " --> pdb=" O ALA B 325 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 193 removed outlier: 5.517A pdb=" N LYS A 156 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 218 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 220 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N THR A 123 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASN A 267 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET A 125 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR A 301 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE A 314 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG A 303 " --> pdb=" O CYS A 312 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N CYS A 312 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 88 removed outlier: 6.233A pdb=" N ALA C 157 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA C 192 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR C 159 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 218 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 217 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL C 264 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU C 219 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N THR C 266 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL C 221 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASN C 267 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N MET C 125 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AA9, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.873A pdb=" N TYR E 159 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS E 156 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ILE E 220 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET E 158 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASP E 222 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE E 160 " --> pdb=" O ASP E 222 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA E 217 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL E 264 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR E 266 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL E 221 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AB2, first strand: chain 'D' and resid 192 through 193 removed outlier: 6.866A pdb=" N LYS D 156 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ILE D 220 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET D 158 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ASP D 222 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE D 160 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N VAL D 264 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU D 219 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR D 266 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL D 221 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY D 127 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR D 301 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE D 314 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AB4, first strand: chain 'D' and resid 309 through 310 Processing sheet with id=AB5, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.349A pdb=" N ALA F 157 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ALA F 192 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR F 159 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS F 156 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU F 218 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA F 217 " --> pdb=" O ALA F 262 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL F 264 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU F 219 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR F 266 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL F 221 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR F 123 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN F 267 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET F 125 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB8, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AB9, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AC1, first strand: chain 'O' and resid 42 through 46 removed outlier: 3.616A pdb=" N GLY O 44 " --> pdb=" O LEU O 35 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL O 7 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TYR O 4 " --> pdb=" O VAL O 75 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL O 75 " --> pdb=" O TYR O 4 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER O 6 " --> pdb=" O MET O 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE O 70 " --> pdb=" O LEU O 63 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.66 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: 4783 1.33 - 1.46: 2583 1.46 - 1.58: 8911 1.58 - 1.70: 74 1.70 - 1.82: 141 Bond restraints: 16492 Sorted by residual: bond pdb=" C ACE J 0 " pdb=" N MET J 1 " ideal model delta sigma weight residual 1.329 1.419 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C ACE H 0 " pdb=" N MET H 1 " ideal model delta sigma weight residual 1.329 1.418 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C ACE I 0 " pdb=" N MET I 1 " ideal model delta sigma weight residual 1.329 1.417 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C ACE K 0 " pdb=" N MET K 1 " ideal model delta sigma weight residual 1.329 1.417 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C3' DA Z 2 " pdb=" C2' DA Z 2 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.43e+00 ... (remaining 16487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 21908 2.08 - 4.16: 376 4.16 - 6.23: 46 6.23 - 8.31: 17 8.31 - 10.39: 4 Bond angle restraints: 22351 Sorted by residual: angle pdb=" CB LYS F 80 " pdb=" CG LYS F 80 " pdb=" CD LYS F 80 " ideal model delta sigma weight residual 111.30 121.69 -10.39 2.30e+00 1.89e-01 2.04e+01 angle pdb=" N ILE O 27 " pdb=" CA ILE O 27 " pdb=" C ILE O 27 " ideal model delta sigma weight residual 106.21 110.50 -4.29 1.07e+00 8.73e-01 1.61e+01 angle pdb=" CG MET H 1 " pdb=" SD MET H 1 " pdb=" CE MET H 1 " ideal model delta sigma weight residual 100.90 109.68 -8.78 2.20e+00 2.07e-01 1.59e+01 angle pdb=" CA LYS E 39 " pdb=" CB LYS E 39 " pdb=" CG LYS E 39 " ideal model delta sigma weight residual 114.10 121.96 -7.86 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CG MET K 1 " pdb=" SD MET K 1 " pdb=" CE MET K 1 " ideal model delta sigma weight residual 100.90 109.06 -8.16 2.20e+00 2.07e-01 1.38e+01 ... (remaining 22346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8391 17.77 - 35.54: 1220 35.54 - 53.30: 404 53.30 - 71.07: 89 71.07 - 88.84: 24 Dihedral angle restraints: 10128 sinusoidal: 4354 harmonic: 5774 Sorted by residual: dihedral pdb=" CA ARG C 95 " pdb=" C ARG C 95 " pdb=" N ARG C 96 " pdb=" CA ARG C 96 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA GLU C 98 " pdb=" C GLU C 98 " pdb=" N ILE C 99 " pdb=" CA ILE C 99 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PRO C 83 " pdb=" C PRO C 83 " pdb=" N MET C 84 " pdb=" CA MET C 84 " ideal model delta harmonic sigma weight residual -180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 10125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2117 0.057 - 0.113: 360 0.113 - 0.170: 41 0.170 - 0.227: 1 0.227 - 0.283: 1 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CB VAL O 7 " pdb=" CA VAL O 7 " pdb=" CG1 VAL O 7 " pdb=" CG2 VAL O 7 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE O 70 " pdb=" CA ILE O 70 " pdb=" CG1 ILE O 70 " pdb=" CG2 ILE O 70 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CB ILE A 136 " pdb=" CA ILE A 136 " pdb=" CG1 ILE A 136 " pdb=" CG2 ILE A 136 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 2517 not shown) Planarity restraints: 2800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 96 " 0.165 9.50e-02 1.11e+02 7.46e-02 4.16e+00 pdb=" NE ARG C 96 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 96 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 96 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 96 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 55 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO C 56 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 91 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" CD GLU B 91 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU B 91 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 91 " -0.012 2.00e-02 2.50e+03 ... (remaining 2797 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.55: 5 2.55 - 3.20: 14000 3.20 - 3.84: 30012 3.84 - 4.49: 42919 4.49 - 5.14: 69257 Nonbonded interactions: 156193 Sorted by model distance: nonbonded pdb="MG MG E 401 " pdb=" O1G ATP E 403 " model vdw 1.899 2.170 nonbonded pdb=" N GLN E 30 " pdb=" OE1 GLN E 30 " model vdw 2.476 3.120 nonbonded pdb=" O GLU E 68 " pdb=" OD1 ASP E 72 " model vdw 2.490 3.040 nonbonded pdb=" O GLU A 308 " pdb=" OE1 GLU A 308 " model vdw 2.491 3.040 nonbonded pdb=" O5' DC Z 7 " pdb=" O4' DC Z 7 " model vdw 2.519 2.432 ... (remaining 156188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 339)) selection = (chain 'B' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 273 or resid 283 through 339)) selection = (chain 'C' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 273 or resid 283 through 339)) selection = (chain 'D' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 273 or resid 283 through 339)) selection = (chain 'E' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 273 or resid 283 through 339)) selection = (chain 'F' and (resid 19 through 273 or resid 283 through 339)) } ncs_group { reference = (chain 'H' and (resid 0 through 9 or resid 20 through 24 or (resid 25 and (name \ N or name CA or name C or name O or name CB )) or resid 26)) selection = (chain 'I' and (resid 0 through 9 or resid 20 through 24 or (resid 25 and (name \ N or name CA or name C or name O or name CB )) or resid 26)) selection = (chain 'J' and (resid 0 through 9 or resid 20 through 24 or (resid 25 and (name \ N or name CA or name C or name O or name CB )) or resid 26)) selection = (chain 'K' and (resid 0 through 9 or resid 20 through 26)) } 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: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.950 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 : 0.003 0.090 16492 Z= 0.187 Angle : 0.652 10.389 22351 Z= 0.350 Chirality : 0.043 0.283 2520 Planarity : 0.004 0.075 2800 Dihedral : 18.820 88.840 6424 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.54 % Allowed : 39.09 % Favored : 59.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.51 (0.18), residues: 1985 helix: -0.04 (0.18), residues: 780 sheet: 0.23 (0.31), residues: 290 loop : -0.69 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 96 TYR 0.017 0.001 TYR O 49 PHE 0.016 0.001 PHE C 86 TRP 0.006 0.002 TRP O 9 HIS 0.007 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.19 (16492) covalent geometry : angle 0.65208 / 0.35 (22351) hydrogen bonds : bond 0.22716 / 15.09 ( 681) hydrogen bonds : angle 7.69401 / 5.41 ( 1881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 298 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8317 (tmmm) cc_final: 0.8032 (tmmt) REVERT: B 130 ARG cc_start: 0.7788 (ttp80) cc_final: 0.6592 (ptm160) REVERT: B 247 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7749 (mtp180) REVERT: B 251 MET cc_start: 0.7159 (tpp) cc_final: 0.6757 (mtp) REVERT: B 306 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7353 (mmp-170) REVERT: C 93 HIS cc_start: 0.4648 (t70) cc_final: 0.4305 (t-90) REVERT: C 99 ILE cc_start: 0.6315 (OUTLIER) cc_final: 0.5730 (mm) REVERT: C 197 THR cc_start: 0.8328 (m) cc_final: 0.8119 (m) REVERT: C 247 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7235 (ttm110) REVERT: C 306 ARG cc_start: 0.6826 (mpt180) cc_final: 0.6555 (mmt180) REVERT: D 210 MET cc_start: 0.5105 (ptp) cc_final: 0.4352 (ptp) REVERT: D 261 VAL cc_start: 0.7076 (m) cc_final: 0.6775 (p) REVERT: E 81 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7538 (mt) REVERT: E 108 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7897 (mm-30) REVERT: E 111 LYS cc_start: 0.8514 (mttm) cc_final: 0.8094 (pptt) REVERT: E 247 ARG cc_start: 0.8483 (mmm160) cc_final: 0.8220 (mtm-85) REVERT: E 306 ARG cc_start: 0.7550 (mpt180) cc_final: 0.7337 (mmt180) REVERT: E 316 ASP cc_start: 0.7904 (t0) cc_final: 0.7503 (t0) REVERT: F 57 LYS cc_start: 0.7174 (pmtt) cc_final: 0.6795 (ptpp) REVERT: F 205 TYR cc_start: 0.8013 (m-10) cc_final: 0.7672 (m-10) REVERT: F 216 TYR cc_start: 0.8116 (m-80) cc_final: 0.7728 (m-80) REVERT: F 243 MET cc_start: 0.7742 (ttp) cc_final: 0.7515 (tpt) REVERT: F 250 ARG cc_start: 0.6459 (mtt180) cc_final: 0.4747 (tpt-90) REVERT: O 70 ILE cc_start: 0.6989 (mm) cc_final: 0.6276 (pp) outliers start: 25 outliers final: 8 residues processed: 313 average time/residue: 0.5403 time to fit residues: 187.2776 Evaluate side-chains 215 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 299 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.0970 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 93 HIS D 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.198650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.172094 restraints weight = 22868.840| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.94 r_work: 0.3879 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16492 Z= 0.174 Angle : 0.625 6.739 22351 Z= 0.336 Chirality : 0.045 0.170 2520 Planarity : 0.005 0.077 2800 Dihedral : 11.872 89.982 2722 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 7.31 % Allowed : 31.90 % Favored : 60.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.51 (0.18), residues: 1985 helix: 0.05 (0.18), residues: 846 sheet: 0.08 (0.30), residues: 298 loop : -0.77 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG J 2 TYR 0.023 0.002 TYR D 191 PHE 0.014 0.002 PHE A 248 TRP 0.015 0.003 TRP O 9 HIS 0.005 0.001 HIS E 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (16492) covalent geometry : angle 0.62506 / 0.34 (22351) hydrogen bonds : bond 0.05771 / 3.91 ( 681) hydrogen bonds : angle 5.77249 / 4.09 ( 1881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 206 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8200 (m-40) cc_final: 0.7621 (t0) REVERT: A 39 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7435 (tmmt) REVERT: A 172 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6102 (mp) REVERT: A 213 GLU cc_start: 0.7106 (tt0) cc_final: 0.6906 (tt0) REVERT: A 257 ASP cc_start: 0.6690 (m-30) cc_final: 0.6489 (m-30) REVERT: B 130 ARG cc_start: 0.7885 (ttp80) cc_final: 0.6647 (ptm160) REVERT: B 247 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7862 (ttp-170) REVERT: B 251 MET cc_start: 0.7166 (tpp) cc_final: 0.6859 (mtp) REVERT: B 306 ARG cc_start: 0.7648 (mtp85) cc_final: 0.6998 (mmp-170) REVERT: B 308 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: C 64 LYS cc_start: 0.7903 (mtpp) cc_final: 0.7480 (ttmm) REVERT: C 96 ARG cc_start: 0.5187 (tpp-160) cc_final: 0.4589 (tpp-160) REVERT: C 100 ILE cc_start: 0.5426 (OUTLIER) cc_final: 0.5031 (pt) REVERT: C 214 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7707 (m) REVERT: C 247 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7488 (ttm110) REVERT: C 306 ARG cc_start: 0.6618 (mpt180) cc_final: 0.6364 (mmt180) REVERT: D 261 VAL cc_start: 0.7256 (m) cc_final: 0.6934 (p) REVERT: D 268 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: D 300 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6937 (mt) REVERT: E 81 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7221 (mt) REVERT: E 108 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7745 (mm-30) REVERT: E 111 LYS cc_start: 0.8550 (mttm) cc_final: 0.7890 (pptt) REVERT: E 176 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: E 316 ASP cc_start: 0.8154 (t0) cc_final: 0.7767 (t0) REVERT: F 57 LYS cc_start: 0.6665 (pmtt) cc_final: 0.6248 (ttpt) REVERT: F 98 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5191 (tm-30) REVERT: F 216 TYR cc_start: 0.8024 (m-80) cc_final: 0.7593 (m-80) REVERT: F 250 ARG cc_start: 0.6274 (mtt180) cc_final: 0.4526 (tpt170) REVERT: F 251 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6997 (ttt) outliers start: 119 outliers final: 31 residues processed: 293 average time/residue: 0.5598 time to fit residues: 181.3309 Evaluate side-chains 233 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain O residue 7 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 183 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 179 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 GLN D 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.200444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.173698 restraints weight = 22978.401| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.98 r_work: 0.3895 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16492 Z= 0.114 Angle : 0.525 6.415 22351 Z= 0.282 Chirality : 0.042 0.158 2520 Planarity : 0.004 0.038 2800 Dihedral : 11.723 89.388 2717 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.53 % Allowed : 30.61 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.19 (0.18), residues: 1985 helix: 0.43 (0.19), residues: 829 sheet: 0.10 (0.30), residues: 296 loop : -0.65 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 27 TYR 0.015 0.001 TYR E 315 PHE 0.011 0.001 PHE F 126 TRP 0.008 0.002 TRP O 9 HIS 0.015 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (16492) covalent geometry : angle 0.52543 / 0.28 (22351) hydrogen bonds : bond 0.04102 / 2.80 ( 681) hydrogen bonds : angle 5.18972 / 3.67 ( 1881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 217 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8280 (m-40) cc_final: 0.7726 (t0) REVERT: A 39 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7481 (tmmt) REVERT: A 172 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6183 (mp) REVERT: A 197 THR cc_start: 0.7784 (m) cc_final: 0.7356 (p) REVERT: A 213 GLU cc_start: 0.7139 (tt0) cc_final: 0.6917 (tt0) REVERT: A 237 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6874 (mt-10) REVERT: A 255 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7304 (tp) REVERT: A 257 ASP cc_start: 0.6673 (m-30) cc_final: 0.6463 (m-30) REVERT: B 130 ARG cc_start: 0.7903 (ttp80) cc_final: 0.6637 (ptm160) REVERT: B 158 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7897 (ttt) REVERT: B 247 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7912 (ttp-170) REVERT: B 306 ARG cc_start: 0.7577 (mtp85) cc_final: 0.7008 (mmp-170) REVERT: B 308 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7246 (mm-30) REVERT: C 64 LYS cc_start: 0.7882 (mtpp) cc_final: 0.7518 (ttmt) REVERT: C 198 ASP cc_start: 0.8384 (m-30) cc_final: 0.8174 (m-30) REVERT: C 214 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7681 (m) REVERT: C 247 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7570 (ttm110) REVERT: C 251 MET cc_start: 0.6861 (mtp) cc_final: 0.6658 (tpt) REVERT: C 306 ARG cc_start: 0.6620 (mpt180) cc_final: 0.6388 (mmt180) REVERT: D 30 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.6396 (pt0) REVERT: D 210 MET cc_start: 0.5603 (ptp) cc_final: 0.5368 (ptt) REVERT: D 261 VAL cc_start: 0.7294 (m) cc_final: 0.6984 (p) REVERT: D 268 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: E 108 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7861 (mm-30) REVERT: E 111 LYS cc_start: 0.8596 (mttm) cc_final: 0.8012 (pptt) REVERT: F 57 LYS cc_start: 0.6691 (pmtt) cc_final: 0.6407 (ptpp) REVERT: F 98 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.5077 (tm-30) REVERT: F 110 ASP cc_start: 0.7220 (m-30) cc_final: 0.7011 (m-30) REVERT: F 216 TYR cc_start: 0.7988 (m-80) cc_final: 0.7612 (m-80) REVERT: F 244 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7748 (t-170) REVERT: F 250 ARG cc_start: 0.6177 (mtt180) cc_final: 0.4504 (tpt170) REVERT: F 313 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7483 (tttp) outliers start: 90 outliers final: 37 residues processed: 287 average time/residue: 0.5560 time to fit residues: 176.8332 Evaluate side-chains 238 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 244 HIS Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 313 LYS Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 29 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.200087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173380 restraints weight = 22951.506| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.98 r_work: 0.3894 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16492 Z= 0.117 Angle : 0.519 7.162 22351 Z= 0.279 Chirality : 0.041 0.147 2520 Planarity : 0.003 0.038 2800 Dihedral : 11.677 88.699 2713 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.04 % Allowed : 31.53 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.15 (0.18), residues: 1985 helix: 0.54 (0.19), residues: 832 sheet: 0.06 (0.30), residues: 292 loop : -0.70 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 2 TYR 0.015 0.001 TYR D 159 PHE 0.011 0.001 PHE A 126 TRP 0.021 0.003 TRP O 9 HIS 0.004 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (16492) covalent geometry : angle 0.51881 / 0.28 (22351) hydrogen bonds : bond 0.03637 / 2.49 ( 681) hydrogen bonds : angle 4.91969 / 3.48 ( 1881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 195 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8323 (m-40) cc_final: 0.7667 (t0) REVERT: A 39 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7489 (tmmt) REVERT: A 172 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6343 (mp) REVERT: A 197 THR cc_start: 0.7778 (m) cc_final: 0.7275 (p) REVERT: A 213 GLU cc_start: 0.7222 (tt0) cc_final: 0.7020 (tt0) REVERT: A 237 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6908 (mt-10) REVERT: A 257 ASP cc_start: 0.6670 (m-30) cc_final: 0.6424 (m-30) REVERT: B 130 ARG cc_start: 0.7854 (ttp80) cc_final: 0.6565 (ptm160) REVERT: B 158 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7879 (ttt) REVERT: B 176 GLU cc_start: 0.7044 (mp0) cc_final: 0.6757 (mp0) REVERT: B 247 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7946 (ttp-170) REVERT: B 306 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7093 (mmt-90) REVERT: B 308 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: C 64 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7525 (ttmt) REVERT: C 214 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7586 (m) REVERT: C 247 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7590 (ttm110) REVERT: C 306 ARG cc_start: 0.6662 (mpt180) cc_final: 0.6426 (mmt180) REVERT: D 211 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.6014 (ttt) REVERT: D 268 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: E 50 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6156 (mt-10) REVERT: E 108 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7940 (mm-30) REVERT: E 111 LYS cc_start: 0.8604 (mttm) cc_final: 0.8032 (pptt) REVERT: F 98 GLU cc_start: 0.5617 (OUTLIER) cc_final: 0.5045 (tm-30) REVERT: F 216 TYR cc_start: 0.7976 (m-80) cc_final: 0.7625 (m-80) REVERT: F 244 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7701 (t-170) REVERT: F 250 ARG cc_start: 0.6157 (mtt180) cc_final: 0.4501 (tpt-90) REVERT: J 1 MET cc_start: 0.4538 (mtp) cc_final: 0.4294 (mtm) REVERT: K 1 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7320 (mmm) outliers start: 82 outliers final: 42 residues processed: 261 average time/residue: 0.5793 time to fit residues: 166.7643 Evaluate side-chains 240 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 244 HIS Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 70 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 126 optimal weight: 0.0970 chunk 116 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN A 272 GLN ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS F 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.195861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.169052 restraints weight = 22825.471| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.92 r_work: 0.3851 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16492 Z= 0.163 Angle : 0.580 7.149 22351 Z= 0.310 Chirality : 0.044 0.157 2520 Planarity : 0.004 0.045 2800 Dihedral : 12.028 87.015 2713 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 6.27 % Allowed : 30.36 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.31 (0.18), residues: 1985 helix: 0.44 (0.18), residues: 835 sheet: -0.03 (0.30), residues: 291 loop : -0.81 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 2 TYR 0.024 0.002 TYR E 315 PHE 0.023 0.002 PHE A 129 TRP 0.025 0.004 TRP O 9 HIS 0.005 0.001 HIS E 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (16492) covalent geometry : angle 0.57951 / 0.31 (22351) hydrogen bonds : bond 0.04297 / 2.96 ( 681) hydrogen bonds : angle 4.98600 / 3.53 ( 1881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 197 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8380 (m-40) cc_final: 0.7779 (t0) REVERT: A 39 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7480 (tmmt) REVERT: A 95 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6068 (ttp-110) REVERT: A 172 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6670 (mp) REVERT: A 237 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6868 (mt-10) REVERT: A 254 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7027 (ttm170) REVERT: A 257 ASP cc_start: 0.6673 (m-30) cc_final: 0.6446 (m-30) REVERT: B 84 MET cc_start: 0.7438 (mmm) cc_final: 0.6934 (mtt) REVERT: B 130 ARG cc_start: 0.7925 (ttp80) cc_final: 0.6530 (ptm160) REVERT: B 247 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7880 (ttp-170) REVERT: B 306 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7012 (mmt-90) REVERT: B 308 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: C 61 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7493 (mt) REVERT: C 64 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7558 (ttmt) REVERT: C 214 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7582 (m) REVERT: C 247 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7564 (mtm110) REVERT: C 306 ARG cc_start: 0.6744 (mpt180) cc_final: 0.6496 (mmt180) REVERT: D 158 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.7172 (tpt) REVERT: D 211 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6162 (ttt) REVERT: D 268 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7745 (mt0) REVERT: D 300 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6932 (mt) REVERT: E 50 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6041 (mt-10) REVERT: E 108 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7876 (mm-30) REVERT: E 111 LYS cc_start: 0.8518 (mttm) cc_final: 0.7912 (pptt) REVERT: E 235 ARG cc_start: 0.8018 (ttt-90) cc_final: 0.7639 (tmt-80) REVERT: E 317 SER cc_start: 0.8861 (t) cc_final: 0.8591 (m) REVERT: F 98 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.5133 (tm-30) REVERT: F 216 TYR cc_start: 0.8022 (m-80) cc_final: 0.7813 (m-80) REVERT: F 244 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7558 (t-170) REVERT: F 250 ARG cc_start: 0.6144 (mtt180) cc_final: 0.4417 (tpt-90) REVERT: F 324 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7099 (mm-30) REVERT: K 1 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7584 (mmt) outliers start: 102 outliers final: 51 residues processed: 278 average time/residue: 0.6304 time to fit residues: 193.5448 Evaluate side-chains 248 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 244 HIS Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 85 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 HIS D 135 GLN ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.190879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163227 restraints weight = 22835.746| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.06 r_work: 0.3784 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16492 Z= 0.257 Angle : 0.712 10.042 22351 Z= 0.380 Chirality : 0.049 0.181 2520 Planarity : 0.006 0.073 2800 Dihedral : 12.748 87.318 2713 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 7.68 % Allowed : 29.38 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.85 (0.18), residues: 1985 helix: -0.05 (0.18), residues: 835 sheet: -0.29 (0.30), residues: 297 loop : -1.07 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 2 TYR 0.033 0.002 TYR E 315 PHE 0.027 0.003 PHE A 129 TRP 0.026 0.004 TRP O 9 HIS 0.010 0.002 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.26 (16492) covalent geometry : angle 0.71211 / 0.38 (22351) hydrogen bonds : bond 0.05452 / 3.74 ( 681) hydrogen bonds : angle 5.37812 / 3.83 ( 1881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 188 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8419 (m-40) cc_final: 0.7930 (t0) REVERT: A 39 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7559 (tmmt) REVERT: A 95 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6277 (ttp-110) REVERT: A 172 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.7003 (mp) REVERT: A 254 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7100 (ttm170) REVERT: B 84 MET cc_start: 0.7464 (mmm) cc_final: 0.7194 (mtt) REVERT: B 158 MET cc_start: 0.8381 (ttm) cc_final: 0.8174 (mtt) REVERT: B 247 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8008 (ttp-170) REVERT: B 306 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7159 (mmt-90) REVERT: B 326 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7760 (tmm) REVERT: C 37 ASP cc_start: 0.6966 (m-30) cc_final: 0.6560 (t0) REVERT: C 54 TYR cc_start: 0.6041 (m-10) cc_final: 0.5815 (m-10) REVERT: C 61 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7675 (mt) REVERT: C 64 LYS cc_start: 0.8028 (mtpp) cc_final: 0.7599 (ttmt) REVERT: C 99 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7268 (tp) REVERT: C 214 SER cc_start: 0.7947 (OUTLIER) cc_final: 0.7669 (m) REVERT: D 158 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7652 (tpt) REVERT: D 180 LEU cc_start: 0.7562 (mp) cc_final: 0.7264 (mm) REVERT: D 211 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6205 (ttt) REVERT: D 268 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: D 300 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7091 (mt) REVERT: D 334 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7642 (p) REVERT: E 50 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6221 (mt-10) REVERT: E 108 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7990 (mm-30) REVERT: E 111 LYS cc_start: 0.8580 (mttm) cc_final: 0.8005 (pptt) REVERT: E 235 ARG cc_start: 0.8242 (tmt-80) cc_final: 0.7668 (tmt-80) REVERT: E 317 SER cc_start: 0.8934 (t) cc_final: 0.8728 (m) REVERT: F 98 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5190 (tm-30) REVERT: F 133 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8150 (mppt) REVERT: F 250 ARG cc_start: 0.6414 (mtt180) cc_final: 0.4680 (tpt-90) REVERT: F 313 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7334 (tttp) REVERT: F 324 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7127 (tm-30) REVERT: K 1 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7477 (mmt) outliers start: 125 outliers final: 52 residues processed: 287 average time/residue: 0.5898 time to fit residues: 187.3489 Evaluate side-chains 245 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 175 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 313 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 70 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 34 ASN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.193076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.166398 restraints weight = 22584.259| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.89 r_work: 0.3826 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16492 Z= 0.160 Angle : 0.585 7.531 22351 Z= 0.313 Chirality : 0.043 0.157 2520 Planarity : 0.004 0.050 2800 Dihedral : 12.530 83.393 2713 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.96 % Allowed : 31.59 % Favored : 62.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.59 (0.18), residues: 1985 helix: 0.21 (0.18), residues: 829 sheet: -0.13 (0.31), residues: 279 loop : -0.97 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 130 TYR 0.019 0.001 TYR E 315 PHE 0.019 0.002 PHE D 327 TRP 0.028 0.004 TRP O 9 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (16492) covalent geometry : angle 0.58475 / 0.31 (22351) hydrogen bonds : bond 0.04354 / 3.00 ( 681) hydrogen bonds : angle 5.04981 / 3.59 ( 1881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 191 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8356 (m-40) cc_final: 0.7826 (t0) REVERT: A 39 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7431 (tmmt) REVERT: A 95 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6143 (ttp-110) REVERT: A 254 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6981 (ttm170) REVERT: B 84 MET cc_start: 0.7455 (mmm) cc_final: 0.6998 (mtt) REVERT: B 247 ARG cc_start: 0.8320 (ttp80) cc_final: 0.7862 (ttp-170) REVERT: B 306 ARG cc_start: 0.7772 (mtp85) cc_final: 0.7103 (mmt-90) REVERT: B 308 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7172 (mm-30) REVERT: B 326 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7669 (tmm) REVERT: C 27 ARG cc_start: 0.7679 (ttp-110) cc_final: 0.7472 (ttm-80) REVERT: C 37 ASP cc_start: 0.6877 (m-30) cc_final: 0.6488 (t0) REVERT: C 54 TYR cc_start: 0.5987 (m-10) cc_final: 0.5620 (m-10) REVERT: C 61 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7603 (mt) REVERT: C 64 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7573 (ttmt) REVERT: C 99 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7253 (tp) REVERT: C 214 SER cc_start: 0.7810 (OUTLIER) cc_final: 0.7524 (m) REVERT: D 158 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7519 (tpp) REVERT: D 162 THR cc_start: 0.6695 (OUTLIER) cc_final: 0.6329 (t) REVERT: D 180 LEU cc_start: 0.7467 (mp) cc_final: 0.7156 (mm) REVERT: D 211 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6183 (ttt) REVERT: D 268 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: D 300 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6983 (mt) REVERT: E 50 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: E 108 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7885 (mm-30) REVERT: E 111 LYS cc_start: 0.8496 (mttm) cc_final: 0.7898 (pptt) REVERT: E 235 ARG cc_start: 0.8173 (tmt-80) cc_final: 0.7614 (tmt-80) REVERT: E 317 SER cc_start: 0.8927 (t) cc_final: 0.8682 (m) REVERT: F 98 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.5109 (tm-30) REVERT: F 133 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8027 (mppt) REVERT: F 177 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8465 (ttt180) REVERT: F 250 ARG cc_start: 0.6239 (mtt180) cc_final: 0.4521 (tpt-90) REVERT: F 324 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7040 (tm-30) REVERT: K 1 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7300 (mmt) outliers start: 97 outliers final: 52 residues processed: 271 average time/residue: 0.6047 time to fit residues: 180.9450 Evaluate side-chains 250 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 70 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 6 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 34 ASN C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.194214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.167635 restraints weight = 22801.812| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.91 r_work: 0.3838 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16492 Z= 0.137 Angle : 0.558 8.645 22351 Z= 0.298 Chirality : 0.042 0.157 2520 Planarity : 0.004 0.048 2800 Dihedral : 12.381 82.837 2713 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.79 % Allowed : 33.44 % Favored : 61.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.38 (0.18), residues: 1985 helix: 0.44 (0.19), residues: 823 sheet: -0.07 (0.31), residues: 277 loop : -0.89 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 95 TYR 0.015 0.001 TYR E 315 PHE 0.022 0.002 PHE C 86 TRP 0.030 0.005 TRP O 9 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16492) covalent geometry : angle 0.55770 / 0.30 (22351) hydrogen bonds : bond 0.03944 / 2.72 ( 681) hydrogen bonds : angle 4.87402 / 3.47 ( 1881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 186 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8382 (m-40) cc_final: 0.7825 (t0) REVERT: A 39 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7457 (tmmt) REVERT: A 95 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6110 (ttp-110) REVERT: A 210 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.5894 (mtp) REVERT: A 237 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: B 84 MET cc_start: 0.7375 (mmm) cc_final: 0.6900 (mtt) REVERT: B 247 ARG cc_start: 0.8320 (ttp80) cc_final: 0.7858 (ttp-170) REVERT: B 306 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7093 (mmt-90) REVERT: B 308 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: B 326 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7685 (tmm) REVERT: C 37 ASP cc_start: 0.6850 (m-30) cc_final: 0.6464 (t0) REVERT: C 54 TYR cc_start: 0.5910 (m-10) cc_final: 0.5535 (m-10) REVERT: C 64 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7560 (ttmt) REVERT: C 99 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7164 (tp) REVERT: C 214 SER cc_start: 0.7745 (OUTLIER) cc_final: 0.7464 (m) REVERT: D 41 LEU cc_start: 0.7021 (mt) cc_final: 0.6813 (mt) REVERT: D 158 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7430 (tpt) REVERT: D 162 THR cc_start: 0.6681 (OUTLIER) cc_final: 0.6295 (t) REVERT: D 180 LEU cc_start: 0.7441 (mp) cc_final: 0.7126 (mm) REVERT: D 210 MET cc_start: 0.5398 (ptp) cc_final: 0.5123 (ptt) REVERT: D 211 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6304 (ttt) REVERT: D 268 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7913 (mt0) REVERT: D 300 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6908 (mt) REVERT: E 50 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: E 100 ILE cc_start: 0.7763 (mt) cc_final: 0.7559 (mm) REVERT: E 108 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7864 (mm-30) REVERT: E 111 LYS cc_start: 0.8478 (mttm) cc_final: 0.7877 (pptt) REVERT: E 235 ARG cc_start: 0.8130 (tmt-80) cc_final: 0.7805 (tmt-80) REVERT: E 317 SER cc_start: 0.8899 (t) cc_final: 0.8669 (m) REVERT: F 98 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.5229 (tm-30) REVERT: F 133 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7988 (mppt) REVERT: F 250 ARG cc_start: 0.6201 (mtt180) cc_final: 0.4480 (tpt-90) REVERT: F 324 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7026 (tm-30) REVERT: K 1 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7308 (mmt) outliers start: 78 outliers final: 47 residues processed: 252 average time/residue: 0.5811 time to fit residues: 162.3746 Evaluate side-chains 244 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 70 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 192 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 34 ASN C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.190626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163144 restraints weight = 22727.745| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.05 r_work: 0.3783 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16492 Z= 0.248 Angle : 0.689 10.774 22351 Z= 0.365 Chirality : 0.047 0.171 2520 Planarity : 0.005 0.068 2800 Dihedral : 12.855 87.293 2713 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.59 % Allowed : 32.39 % Favored : 62.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.67 (0.18), residues: 1985 helix: 0.15 (0.18), residues: 823 sheet: -0.30 (0.31), residues: 277 loop : -0.97 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 2 TYR 0.027 0.002 TYR E 315 PHE 0.024 0.003 PHE A 129 TRP 0.031 0.007 TRP O 9 HIS 0.008 0.002 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.25 (16492) covalent geometry : angle 0.68922 / 0.37 (22351) hydrogen bonds : bond 0.05151 / 3.54 ( 681) hydrogen bonds : angle 5.25184 / 3.75 ( 1881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 182 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8458 (m-40) cc_final: 0.7870 (t0) REVERT: A 39 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7485 (tmmt) REVERT: A 95 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6283 (ttp-110) REVERT: A 210 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.5995 (mtm) REVERT: A 237 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: A 308 GLU cc_start: 0.7784 (tp30) cc_final: 0.7426 (tp30) REVERT: B 84 MET cc_start: 0.7516 (mmm) cc_final: 0.7063 (mtt) REVERT: B 247 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8022 (ttp-170) REVERT: B 306 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7265 (mmt-90) REVERT: B 308 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7273 (mm-30) REVERT: B 326 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7761 (tmm) REVERT: C 37 ASP cc_start: 0.6960 (m-30) cc_final: 0.6558 (t0) REVERT: C 61 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7617 (mt) REVERT: C 64 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7620 (ttmt) REVERT: C 99 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7331 (tp) REVERT: C 214 SER cc_start: 0.7913 (OUTLIER) cc_final: 0.7631 (m) REVERT: D 41 LEU cc_start: 0.7120 (mt) cc_final: 0.6863 (mt) REVERT: D 158 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7681 (tpt) REVERT: D 211 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.6110 (ttt) REVERT: D 268 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7913 (mt0) REVERT: D 300 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7097 (mt) REVERT: D 334 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7719 (p) REVERT: E 50 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6209 (mt-10) REVERT: E 108 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7995 (mm-30) REVERT: E 111 LYS cc_start: 0.8548 (mttm) cc_final: 0.7984 (pptt) REVERT: E 317 SER cc_start: 0.8907 (t) cc_final: 0.8677 (m) REVERT: F 98 GLU cc_start: 0.5754 (OUTLIER) cc_final: 0.5226 (tm-30) REVERT: F 133 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8141 (mppt) REVERT: F 177 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8509 (ttt180) REVERT: F 250 ARG cc_start: 0.6372 (mtt180) cc_final: 0.4666 (tpt-90) REVERT: F 324 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7128 (tm-30) REVERT: J 1 MET cc_start: 0.5260 (mtm) cc_final: 0.4912 (mtp) REVERT: K 1 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7268 (mmt) outliers start: 91 outliers final: 50 residues processed: 257 average time/residue: 0.6371 time to fit residues: 180.5267 Evaluate side-chains 240 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 171 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 188 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 191 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 164 optimal weight: 0.0050 chunk 52 optimal weight: 4.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 GLN C 34 ASN C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.195254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.169024 restraints weight = 22757.290| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.91 r_work: 0.3851 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16492 Z= 0.120 Angle : 0.561 11.224 22351 Z= 0.299 Chirality : 0.042 0.162 2520 Planarity : 0.004 0.048 2800 Dihedral : 12.406 81.824 2713 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.38 % Allowed : 34.60 % Favored : 62.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.35 (0.19), residues: 1985 helix: 0.43 (0.18), residues: 829 sheet: -0.06 (0.30), residues: 288 loop : -0.86 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 27 TYR 0.019 0.001 TYR C 54 PHE 0.014 0.001 PHE D 327 TRP 0.040 0.005 TRP O 9 HIS 0.002 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16492) covalent geometry : angle 0.56117 / 0.30 (22351) hydrogen bonds : bond 0.03595 / 2.48 ( 681) hydrogen bonds : angle 4.78423 / 3.41 ( 1881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7448 (tmmt) REVERT: A 144 CYS cc_start: 0.4943 (OUTLIER) cc_final: 0.4737 (m) REVERT: A 237 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6953 (mt-10) REVERT: A 308 GLU cc_start: 0.7708 (tp30) cc_final: 0.7316 (tp30) REVERT: B 247 ARG cc_start: 0.8321 (ttp80) cc_final: 0.7906 (ttp-170) REVERT: B 306 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7180 (mmt-90) REVERT: B 308 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: C 54 TYR cc_start: 0.5889 (m-10) cc_final: 0.5583 (m-10) REVERT: C 64 LYS cc_start: 0.7973 (mtpp) cc_final: 0.7553 (ttmt) REVERT: C 159 TYR cc_start: 0.6609 (t80) cc_final: 0.6243 (t80) REVERT: C 214 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7488 (m) REVERT: D 41 LEU cc_start: 0.6997 (mt) cc_final: 0.6784 (mt) REVERT: D 118 GLU cc_start: 0.5845 (tt0) cc_final: 0.4449 (pt0) REVERT: D 158 MET cc_start: 0.7727 (mmm) cc_final: 0.7436 (tpt) REVERT: D 210 MET cc_start: 0.5756 (ptp) cc_final: 0.5295 (ptt) REVERT: D 300 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6954 (mt) REVERT: E 50 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: E 108 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7862 (mm-30) REVERT: E 111 LYS cc_start: 0.8512 (mttm) cc_final: 0.7913 (pptt) REVERT: E 317 SER cc_start: 0.8863 (t) cc_final: 0.8640 (m) REVERT: F 98 GLU cc_start: 0.5727 (OUTLIER) cc_final: 0.5041 (tm-30) REVERT: F 133 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8023 (mppt) REVERT: F 250 ARG cc_start: 0.6167 (mtt180) cc_final: 0.4499 (tpt-90) REVERT: F 324 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7045 (tm-30) REVERT: J 1 MET cc_start: 0.4934 (mtm) cc_final: 0.4728 (mtp) outliers start: 55 outliers final: 36 residues processed: 236 average time/residue: 0.6474 time to fit residues: 168.6565 Evaluate side-chains 221 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain K residue 3 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 108 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 GLN C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.193109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.166616 restraints weight = 22701.578| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.91 r_work: 0.3829 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16492 Z= 0.166 Angle : 0.599 13.180 22351 Z= 0.317 Chirality : 0.043 0.150 2520 Planarity : 0.004 0.049 2800 Dihedral : 12.517 82.684 2713 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.50 % Allowed : 34.85 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.19), residues: 1985 helix: 0.39 (0.18), residues: 828 sheet: -0.18 (0.31), residues: 277 loop : -0.83 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 254 TYR 0.018 0.002 TYR C 54 PHE 0.020 0.002 PHE A 129 TRP 0.035 0.005 TRP O 9 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (16492) covalent geometry : angle 0.59871 / 0.32 (22351) hydrogen bonds : bond 0.04121 / 2.85 ( 681) hydrogen bonds : angle 4.89184 / 3.49 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6004.78 seconds wall clock time: 102 minutes 54.25 seconds (6174.25 seconds total)