Starting phenix.real_space_refine on Fri Jul 3 22:26:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9trl_56178/07_2026/9trl_56178.cif Found real_map, /net/cci-nas-00/data/ceres_data/9trl_56178/07_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_56178/07_2026/9trl_56178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9trl_56178/07_2026/9trl_56178.map" model { file = "/net/cci-nas-00/data/ceres_data/9trl_56178/07_2026/9trl_56178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9trl_56178/07_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-dev-6108/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, 31 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Chain breaks: 1 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: 3.58, per 1000 atoms: 0.22 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: 1.29 Conformation dependent library (CDL) restraints added in 634.3 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: 0.56 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: 2.38 Time building geometry restraints manager: 1.71 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: 3.240 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.180 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- 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 0.65179 / 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 : 0.613 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: 0.4306 (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: 0.6554 (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: 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: 0.7514 (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: 0.5748 time to fit residues: 199.1029 Evaluate side-chains 214 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 3.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4228 r_free = 0.4228 target = 0.197745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.170896 restraints weight = 22785.691| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.93 r_work: 0.3869 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16492 Z= 0.186 Angle : 0.654 6.539 22351 Z= 0.348 Chirality : 0.046 0.164 2520 Planarity : 0.005 0.064 2800 Dihedral : 12.065 89.608 2722 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 8.30 % Allowed : 30.30 % Favored : 61.40 % 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: -0.62 (0.18), residues: 1985 helix: -0.06 (0.18), residues: 844 sheet: -0.01 (0.29), residues: 297 loop : -0.78 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG J 2 TYR 0.029 0.002 TYR D 191 PHE 0.016 0.002 PHE A 248 TRP 0.017 0.004 TRP O 9 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (16492) covalent geometry : angle 0.65371 / 0.35 (22351) hydrogen bonds : bond 0.05354 / 3.65 ( 681) hydrogen bonds : angle 5.67794 / 4.04 ( 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 346 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 211 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8215 (m-40) cc_final: 0.7588 (t0) REVERT: A 39 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7382 (tmmt) REVERT: A 95 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6002 (ttp-110) REVERT: A 172 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6036 (mp) REVERT: A 210 MET cc_start: 0.6321 (ttm) cc_final: 0.5950 (mtt) REVERT: A 213 GLU cc_start: 0.7173 (tt0) cc_final: 0.6966 (tt0) REVERT: A 237 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6864 (mt-10) REVERT: A 255 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7146 (tp) REVERT: A 257 ASP cc_start: 0.6768 (m-30) cc_final: 0.6561 (m-30) REVERT: B 118 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: B 247 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7879 (ttp-170) REVERT: B 251 MET cc_start: 0.7184 (tpp) cc_final: 0.6859 (mtp) REVERT: B 306 ARG cc_start: 0.7607 (mtp85) cc_final: 0.6957 (mmp-170) REVERT: B 308 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7149 (mm-30) REVERT: C 61 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7495 (mt) REVERT: C 64 LYS cc_start: 0.7852 (mtpp) cc_final: 0.7400 (ttmm) REVERT: C 100 ILE cc_start: 0.5440 (OUTLIER) cc_final: 0.5012 (pt) REVERT: C 214 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7732 (m) REVERT: C 247 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7483 (ttm110) REVERT: C 306 ARG cc_start: 0.6668 (mpt180) cc_final: 0.6376 (mmt180) REVERT: D 261 VAL cc_start: 0.7393 (m) cc_final: 0.7098 (p) REVERT: D 268 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: D 300 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6964 (mt) REVERT: E 81 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7176 (mt) REVERT: E 108 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7729 (mm-30) REVERT: E 111 LYS cc_start: 0.8536 (mttm) cc_final: 0.7863 (pptt) REVERT: E 176 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: F 57 LYS cc_start: 0.6650 (pmtt) cc_final: 0.6179 (ttpt) REVERT: F 98 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.5214 (tm-30) REVERT: F 148 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6204 (tt) REVERT: F 216 TYR cc_start: 0.8008 (m-80) cc_final: 0.7598 (m-80) REVERT: F 250 ARG cc_start: 0.6251 (mtt180) cc_final: 0.4479 (tpt170) REVERT: F 251 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6935 (ttt) outliers start: 135 outliers final: 35 residues processed: 312 average time/residue: 0.6121 time to fit residues: 210.1481 Evaluate side-chains 239 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 119 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 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 90 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 181 SER 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 38 VAL Chi-restraints excluded: chain C residue 60 LEU 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 106 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 233 SER 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 148 ILE Chi-restraints excluded: chain F residue 221 VAL 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: 0.8980 chunk 86 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.199316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.172530 restraints weight = 22952.812| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.92 r_work: 0.3887 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2001 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= 0.119 Angle : 0.530 7.149 22351 Z= 0.285 Chirality : 0.042 0.153 2520 Planarity : 0.004 0.041 2800 Dihedral : 11.858 87.485 2718 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.41 % Allowed : 31.16 % 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: -0.30 (0.18), residues: 1985 helix: 0.34 (0.18), residues: 835 sheet: 0.00 (0.30), residues: 298 loop : -0.71 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 95 TYR 0.016 0.001 TYR E 315 PHE 0.012 0.001 PHE A 129 TRP 0.007 0.002 TRP O 9 HIS 0.014 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (16492) covalent geometry : angle 0.52956 / 0.29 (22351) hydrogen bonds : bond 0.04261 / 2.91 ( 681) hydrogen bonds : angle 5.25242 / 3.72 ( 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 296 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 208 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8268 (m-40) cc_final: 0.7678 (t0) REVERT: A 39 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7398 (tmmt) REVERT: A 172 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6161 (mp) REVERT: A 197 THR cc_start: 0.7746 (m) cc_final: 0.7299 (p) REVERT: A 213 GLU cc_start: 0.7188 (tt0) cc_final: 0.6953 (tt0) REVERT: A 237 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6821 (mt-10) REVERT: A 255 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7132 (tp) REVERT: A 257 ASP cc_start: 0.6630 (m-30) cc_final: 0.6401 (m-30) REVERT: B 130 ARG cc_start: 0.7891 (ttp80) cc_final: 0.6596 (ptm160) REVERT: B 247 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7783 (ttp-170) REVERT: B 251 MET cc_start: 0.7155 (tpp) cc_final: 0.6890 (mtp) REVERT: B 306 ARG cc_start: 0.7568 (mtp85) cc_final: 0.6941 (mmt-90) REVERT: B 308 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: C 64 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7508 (ttmt) REVERT: C 214 SER cc_start: 0.7891 (OUTLIER) cc_final: 0.7610 (m) REVERT: C 247 ARG cc_start: 0.7783 (mtp85) cc_final: 0.7454 (ttm110) REVERT: C 251 MET cc_start: 0.6883 (mtp) cc_final: 0.6540 (tpt) REVERT: C 306 ARG cc_start: 0.6598 (mpt180) cc_final: 0.6316 (mmt180) REVERT: D 210 MET cc_start: 0.5600 (ptp) cc_final: 0.5235 (ptt) REVERT: D 261 VAL cc_start: 0.7269 (m) cc_final: 0.6951 (p) REVERT: D 268 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: E 108 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7734 (mm-30) REVERT: E 111 LYS cc_start: 0.8517 (mttm) cc_final: 0.7892 (pptt) REVERT: F 57 LYS cc_start: 0.6631 (pmtt) cc_final: 0.6331 (ptpp) REVERT: F 98 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.5159 (tm-30) REVERT: F 216 TYR cc_start: 0.7920 (m-80) cc_final: 0.7593 (m-80) REVERT: F 244 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.7535 (t-170) REVERT: F 250 ARG cc_start: 0.6058 (mtt180) cc_final: 0.4348 (tpt170) REVERT: F 251 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6960 (ttt) REVERT: F 313 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7291 (tttp) outliers start: 88 outliers final: 40 residues processed: 275 average time/residue: 0.6037 time to fit residues: 183.8189 Evaluate side-chains 241 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 255 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 99 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 213 GLU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 308 GLU 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 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 82 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 206 GLN 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 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 230 THR Chi-restraints excluded: chain F residue 244 HIS Chi-restraints excluded: chain F residue 251 MET 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: 4.9990 chunk 136 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.198877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.170946 restraints weight = 22852.518| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.02 r_work: 0.3887 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16492 Z= 0.121 Angle : 0.522 6.496 22351 Z= 0.280 Chirality : 0.042 0.148 2520 Planarity : 0.004 0.054 2800 Dihedral : 11.834 89.450 2715 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.84 % Allowed : 30.61 % Favored : 63.55 % 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: -0.18 (0.18), residues: 1985 helix: 0.54 (0.19), residues: 832 sheet: 0.01 (0.29), residues: 296 loop : -0.73 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 2 TYR 0.017 0.001 TYR C 159 PHE 0.013 0.001 PHE A 129 TRP 0.024 0.003 TRP O 9 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16492) covalent geometry : angle 0.52219 / 0.28 (22351) hydrogen bonds : bond 0.03760 / 2.58 ( 681) hydrogen bonds : angle 4.91723 / 3.47 ( 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 290 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 195 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8343 (m-40) cc_final: 0.7703 (t0) REVERT: A 39 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7558 (tmmt) REVERT: A 172 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6553 (mp) REVERT: A 197 THR cc_start: 0.7872 (m) cc_final: 0.7397 (p) REVERT: A 255 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7420 (tp) REVERT: A 257 ASP cc_start: 0.6674 (m-30) cc_final: 0.6419 (m-30) REVERT: B 130 ARG cc_start: 0.7951 (ttp80) cc_final: 0.6795 (ptm160) REVERT: B 247 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8139 (ttp-170) REVERT: B 306 ARG cc_start: 0.7638 (mtp85) cc_final: 0.7178 (mmt-90) REVERT: B 308 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: C 64 LYS cc_start: 0.7939 (mtpp) cc_final: 0.7551 (ttmt) REVERT: C 214 SER cc_start: 0.7909 (OUTLIER) cc_final: 0.7644 (m) REVERT: C 247 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7654 (ttm110) REVERT: C 259 PHE cc_start: 0.6570 (m-80) cc_final: 0.6283 (m-80) REVERT: C 306 ARG cc_start: 0.6786 (mpt180) cc_final: 0.6573 (mmt180) REVERT: D 210 MET cc_start: 0.5605 (ptp) cc_final: 0.5297 (ptt) REVERT: D 261 VAL cc_start: 0.7407 (m) cc_final: 0.7159 (p) REVERT: D 268 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: D 300 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6965 (mt) REVERT: E 50 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6280 (mt-10) REVERT: E 108 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7815 (mm-30) REVERT: E 111 LYS cc_start: 0.8630 (mttm) cc_final: 0.8090 (pptt) REVERT: E 235 ARG cc_start: 0.7971 (ttt-90) cc_final: 0.7647 (tmt-80) REVERT: F 98 GLU cc_start: 0.5471 (OUTLIER) cc_final: 0.5081 (tm-30) REVERT: F 216 TYR cc_start: 0.8095 (m-80) cc_final: 0.7846 (m-80) REVERT: F 244 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7804 (t-170) REVERT: F 250 ARG cc_start: 0.6333 (mtt180) cc_final: 0.4674 (tpt-90) REVERT: K 1 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7271 (mmm) outliers start: 95 outliers final: 46 residues processed: 273 average time/residue: 0.6438 time to fit residues: 194.0027 Evaluate side-chains 238 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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 255 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 99 ILE Chi-restraints excluded: chain B residue 171 LEU 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 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 162 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 206 GLN 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 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 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 230 THR Chi-restraints excluded: chain F residue 244 HIS Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 320 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.195536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168866 restraints weight = 22800.717| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.91 r_work: 0.3855 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16492 Z= 0.159 Angle : 0.574 6.934 22351 Z= 0.307 Chirality : 0.044 0.162 2520 Planarity : 0.004 0.043 2800 Dihedral : 12.095 88.614 2713 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.76 % Allowed : 30.06 % Favored : 63.18 % 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 (0.18), residues: 1985 helix: 0.41 (0.18), residues: 835 sheet: -0.07 (0.30), residues: 293 loop : -0.83 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 2 TYR 0.023 0.002 TYR E 315 PHE 0.023 0.002 PHE A 129 TRP 0.028 0.005 TRP O 9 HIS 0.005 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (16492) covalent geometry : angle 0.57396 / 0.31 (22351) hydrogen bonds : bond 0.04261 / 2.92 ( 681) hydrogen bonds : angle 4.95404 / 3.51 ( 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 308 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 198 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8346 (m-40) cc_final: 0.7776 (t0) REVERT: A 39 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7412 (tmmt) REVERT: A 95 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6014 (ttp-110) REVERT: A 172 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6659 (mp) REVERT: A 254 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6991 (ttm170) REVERT: A 257 ASP cc_start: 0.6655 (m-30) cc_final: 0.6424 (m-30) REVERT: B 84 MET cc_start: 0.7469 (mmm) cc_final: 0.6934 (mtt) REVERT: B 130 ARG cc_start: 0.7943 (ttp80) cc_final: 0.6659 (ptm160) REVERT: B 247 ARG cc_start: 0.8306 (ttp80) cc_final: 0.7818 (ttp-170) REVERT: B 306 ARG cc_start: 0.7621 (mtp85) cc_final: 0.6948 (mmt-90) REVERT: B 308 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: C 61 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7475 (mt) REVERT: C 64 LYS cc_start: 0.7978 (mtpp) cc_final: 0.7547 (ttmt) REVERT: C 91 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6254 (mm-30) REVERT: C 214 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7554 (m) REVERT: C 247 ARG cc_start: 0.7809 (mtp85) cc_final: 0.7504 (mtm110) REVERT: C 306 ARG cc_start: 0.6742 (mpt180) cc_final: 0.6474 (mmt180) REVERT: D 158 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7259 (tpt) REVERT: D 268 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: D 300 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6828 (mt) REVERT: E 50 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.5994 (mt-10) REVERT: E 108 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7838 (mm-30) REVERT: E 111 LYS cc_start: 0.8498 (mttm) cc_final: 0.7877 (pptt) REVERT: E 235 ARG cc_start: 0.8105 (ttt-90) cc_final: 0.7711 (tmt-80) REVERT: F 98 GLU cc_start: 0.5783 (OUTLIER) cc_final: 0.5142 (tm-30) REVERT: F 133 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7838 (mppt) REVERT: F 216 TYR cc_start: 0.7950 (m-80) cc_final: 0.7735 (m-80) REVERT: F 244 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7486 (t-170) REVERT: F 250 ARG cc_start: 0.6075 (mtt180) cc_final: 0.4335 (tpt-90) REVERT: F 324 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7160 (mm-30) REVERT: K 1 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7302 (mmm) outliers start: 110 outliers final: 56 residues processed: 284 average time/residue: 0.6155 time to fit residues: 193.3542 Evaluate side-chains 254 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 182 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 187 ASP 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 A residue 334 VAL 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 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 88 THR Chi-restraints excluded: chain C residue 91 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 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 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 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 133 LYS 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 F residue 320 LEU 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: 0.8980 chunk 197 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 126 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 135 GLN ** 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 = 0.4183 r_free = 0.4183 target = 0.192641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.164930 restraints weight = 22742.102| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.06 r_work: 0.3808 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16492 Z= 0.212 Angle : 0.634 8.084 22351 Z= 0.338 Chirality : 0.046 0.166 2520 Planarity : 0.005 0.058 2800 Dihedral : 12.420 85.568 2713 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 7.44 % Allowed : 30.42 % Favored : 62.14 % 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: -0.62 (0.18), residues: 1985 helix: 0.17 (0.18), residues: 838 sheet: -0.13 (0.30), residues: 290 loop : -1.00 (0.19), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 130 TYR 0.025 0.002 TYR E 315 PHE 0.025 0.002 PHE A 129 TRP 0.027 0.004 TRP O 9 HIS 0.007 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (16492) covalent geometry : angle 0.63383 / 0.34 (22351) hydrogen bonds : bond 0.04796 / 3.30 ( 681) hydrogen bonds : angle 5.11025 / 3.63 ( 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 302 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 181 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8402 (m-40) cc_final: 0.7887 (t0) REVERT: A 39 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7514 (tmmt) REVERT: A 95 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6273 (ttp-110) REVERT: A 125 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.7077 (mtp) REVERT: A 172 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6911 (mp) REVERT: A 254 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7026 (ttm170) REVERT: A 326 MET cc_start: 0.8255 (ttt) cc_final: 0.8000 (tpp) REVERT: B 84 MET cc_start: 0.7442 (mmm) cc_final: 0.6989 (mtt) REVERT: B 118 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: B 247 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8024 (ttp-170) REVERT: B 306 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7155 (mmt-90) REVERT: B 326 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7730 (tmm) REVERT: C 61 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7667 (mt) REVERT: C 64 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7582 (ttmt) REVERT: C 214 SER cc_start: 0.7929 (OUTLIER) cc_final: 0.7633 (m) REVERT: C 247 ARG cc_start: 0.7955 (mtp85) cc_final: 0.7731 (mtm110) REVERT: C 259 PHE cc_start: 0.6641 (m-80) cc_final: 0.6408 (m-80) REVERT: C 306 ARG cc_start: 0.6901 (mpt180) cc_final: 0.6673 (mmt180) REVERT: D 158 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7625 (tpt) REVERT: D 180 LEU cc_start: 0.7578 (mp) cc_final: 0.7296 (mm) REVERT: D 268 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7893 (mt0) REVERT: D 300 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6988 (mt) REVERT: D 334 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7670 (p) REVERT: E 50 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6247 (mt-10) REVERT: E 108 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7928 (mm-30) REVERT: E 111 LYS cc_start: 0.8575 (mttm) cc_final: 0.7998 (pptt) REVERT: E 235 ARG cc_start: 0.8218 (tmt-80) cc_final: 0.7660 (tmt-80) REVERT: F 98 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5140 (tm-30) REVERT: F 133 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8090 (mppt) REVERT: F 250 ARG cc_start: 0.6390 (mtt180) cc_final: 0.4652 (tpt-90) REVERT: F 324 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7143 (tm-30) REVERT: K 1 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7405 (mmt) outliers start: 121 outliers final: 62 residues processed: 279 average time/residue: 0.6140 time to fit residues: 189.3406 Evaluate side-chains 256 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 177 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 125 MET 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 99 ILE Chi-restraints excluded: chain B residue 118 GLU 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 38 VAL 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 187 ASP Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 VAL 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 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 221 VAL 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 61 ILE 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 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 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 320 LEU 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=2.50 ------------------------------------------------------------------------------- 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: 0.9980 chunk 100 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 272 GLN D 30 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 = 0.4208 r_free = 0.4208 target = 0.195267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.167875 restraints weight = 22544.603| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.03 r_work: 0.3834 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16492 Z= 0.132 Angle : 0.548 7.650 22351 Z= 0.293 Chirality : 0.042 0.150 2520 Planarity : 0.004 0.046 2800 Dihedral : 12.205 85.832 2713 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.41 % Allowed : 32.51 % Favored : 62.08 % 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: -0.40 (0.18), residues: 1985 helix: 0.41 (0.18), residues: 836 sheet: -0.11 (0.30), residues: 291 loop : -0.91 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 130 TYR 0.015 0.001 TYR C 54 PHE 0.016 0.002 PHE D 327 TRP 0.028 0.005 TRP O 9 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16492) covalent geometry : angle 0.54840 / 0.29 (22351) hydrogen bonds : bond 0.03857 / 2.66 ( 681) hydrogen bonds : angle 4.81567 / 3.43 ( 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 275 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 187 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8382 (m-40) cc_final: 0.7819 (t0) REVERT: A 39 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7480 (tmmt) REVERT: A 95 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6222 (ttp-110) REVERT: B 84 MET cc_start: 0.7422 (mmm) cc_final: 0.6989 (mtt) REVERT: B 118 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: B 247 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8007 (ttp-170) REVERT: B 306 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7169 (mmt-90) REVERT: B 308 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: B 326 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7716 (tmm) REVERT: C 27 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7514 (ttm-80) REVERT: C 61 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7621 (mt) REVERT: C 64 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7574 (ttmt) REVERT: C 214 SER cc_start: 0.7849 (OUTLIER) cc_final: 0.7566 (m) REVERT: C 247 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7702 (mtm110) REVERT: C 259 PHE cc_start: 0.6558 (m-80) cc_final: 0.6348 (m-80) REVERT: C 306 ARG cc_start: 0.6836 (mpt180) cc_final: 0.6609 (mmt180) REVERT: D 98 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6452 (mm-30) REVERT: D 158 MET cc_start: 0.7762 (mmm) cc_final: 0.7547 (tpt) REVERT: D 162 THR cc_start: 0.6692 (p) cc_final: 0.6387 (t) REVERT: D 180 LEU cc_start: 0.7527 (mp) cc_final: 0.7251 (mm) REVERT: D 210 MET cc_start: 0.5527 (OUTLIER) cc_final: 0.5153 (ptt) REVERT: D 268 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: D 300 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6964 (mt) REVERT: E 50 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: E 108 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7952 (mm-30) REVERT: E 111 LYS cc_start: 0.8556 (mttm) cc_final: 0.7988 (pptt) REVERT: E 235 ARG cc_start: 0.8130 (tmt-80) cc_final: 0.7826 (tmt-80) REVERT: E 317 SER cc_start: 0.8831 (t) cc_final: 0.8601 (m) REVERT: F 98 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5071 (tm-30) REVERT: F 133 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8044 (mppt) REVERT: F 250 ARG cc_start: 0.6353 (mtt180) cc_final: 0.4628 (tpt-90) REVERT: F 324 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7147 (tm-30) REVERT: K 1 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7226 (mmm) outliers start: 88 outliers final: 45 residues processed: 258 average time/residue: 0.6071 time to fit residues: 172.7522 Evaluate side-chains 239 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 187 ASP Chi-restraints excluded: chain A residue 200 GLN 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 118 GLU 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 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 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 206 GLN 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 98 GLU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 210 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 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 329 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 99 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 230 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 6 optimal weight: 0.0170 chunk 117 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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** ** 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 = 0.4221 r_free = 0.4221 target = 0.196628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.170144 restraints weight = 22828.307| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.91 r_work: 0.3864 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16492 Z= 0.114 Angle : 0.528 8.586 22351 Z= 0.282 Chirality : 0.041 0.160 2520 Planarity : 0.004 0.043 2800 Dihedral : 12.020 88.571 2713 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.30 % Allowed : 33.56 % Favored : 62.14 % 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: -0.29 (0.19), residues: 1985 helix: 0.50 (0.18), residues: 846 sheet: -0.15 (0.30), residues: 282 loop : -0.83 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.013 0.001 TYR E 205 PHE 0.015 0.001 PHE D 327 TRP 0.030 0.005 TRP O 9 HIS 0.004 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (16492) covalent geometry : angle 0.52836 / 0.28 (22351) hydrogen bonds : bond 0.03441 / 2.37 ( 681) hydrogen bonds : angle 4.62895 / 3.30 ( 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 257 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 187 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8291 (m-40) cc_final: 0.7645 (t0) REVERT: A 39 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7395 (tmmt) REVERT: A 95 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6048 (ttp-110) REVERT: A 326 MET cc_start: 0.8175 (ttt) cc_final: 0.7880 (tpp) REVERT: B 247 ARG cc_start: 0.8349 (ttp80) cc_final: 0.7871 (ttp-170) REVERT: B 306 ARG cc_start: 0.7653 (mtp85) cc_final: 0.7058 (mmt-90) REVERT: B 308 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7076 (mm-30) REVERT: B 326 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7672 (tmm) REVERT: C 27 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.7385 (ttm-80) REVERT: C 64 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7560 (ttmt) REVERT: C 214 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7498 (m) REVERT: C 247 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7585 (mtm110) REVERT: C 306 ARG cc_start: 0.6763 (mpt180) cc_final: 0.6497 (mmt180) REVERT: C 322 GLU cc_start: 0.6351 (tp30) cc_final: 0.4136 (pp20) REVERT: D 84 MET cc_start: 0.5894 (mtt) cc_final: 0.5529 (mtt) REVERT: D 98 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6442 (mm-30) REVERT: D 158 MET cc_start: 0.7519 (mmm) cc_final: 0.7297 (tpt) REVERT: D 180 LEU cc_start: 0.7486 (mp) cc_final: 0.7200 (mm) REVERT: D 210 MET cc_start: 0.5412 (ptp) cc_final: 0.5012 (ptt) REVERT: D 268 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: E 50 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: E 108 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7822 (mm-30) REVERT: E 111 LYS cc_start: 0.8497 (mttm) cc_final: 0.7881 (pptt) REVERT: E 235 ARG cc_start: 0.8084 (ttt-90) cc_final: 0.7749 (tmt-80) REVERT: E 317 SER cc_start: 0.8815 (t) cc_final: 0.8553 (m) REVERT: F 98 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5096 (tm-30) REVERT: F 133 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7916 (mppt) REVERT: F 216 TYR cc_start: 0.7895 (m-80) cc_final: 0.7606 (m-80) REVERT: F 244 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7422 (t-170) REVERT: F 250 ARG cc_start: 0.6149 (mtt180) cc_final: 0.4438 (tpt-90) REVERT: F 324 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7084 (mm-30) outliers start: 70 outliers final: 40 residues processed: 249 average time/residue: 0.6182 time to fit residues: 170.0349 Evaluate side-chains 232 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 119 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 187 ASP 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 88 THR Chi-restraints excluded: chain C residue 99 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 239 SER Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 99 ILE 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 244 HIS Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 7 VAL 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: 5.9990 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** E 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.191340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.163672 restraints weight = 22649.715| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.05 r_work: 0.3792 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16492 Z= 0.241 Angle : 0.682 10.719 22351 Z= 0.361 Chirality : 0.047 0.191 2520 Planarity : 0.005 0.067 2800 Dihedral : 12.530 84.838 2713 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.10 % Allowed : 32.88 % 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: -0.61 (0.18), residues: 1985 helix: 0.20 (0.18), residues: 836 sheet: -0.16 (0.30), residues: 288 loop : -1.00 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 2 TYR 0.027 0.002 TYR E 315 PHE 0.024 0.003 PHE A 129 TRP 0.032 0.006 TRP O 9 HIS 0.008 0.002 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (16492) covalent geometry : angle 0.68209 / 0.36 (22351) hydrogen bonds : bond 0.05008 / 3.43 ( 681) hydrogen bonds : angle 5.12803 / 3.66 ( 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 270 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 187 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7470 (tmmt) REVERT: A 95 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6277 (ttp-110) REVERT: A 210 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5914 (mtm) REVERT: A 308 GLU cc_start: 0.7751 (tp30) cc_final: 0.7482 (tp30) REVERT: B 247 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8035 (ttp-170) REVERT: B 306 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7248 (mmt-90) REVERT: B 308 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7273 (mm-30) REVERT: C 27 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7559 (ttm-80) REVERT: C 61 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7659 (mt) REVERT: C 214 SER cc_start: 0.7919 (OUTLIER) cc_final: 0.7625 (m) REVERT: C 247 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7763 (mtm110) REVERT: C 306 ARG cc_start: 0.6930 (mpt180) cc_final: 0.6699 (mmt180) REVERT: D 158 MET cc_start: 0.7947 (mmm) cc_final: 0.7696 (tpt) REVERT: D 268 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: D 334 VAL cc_start: 0.7965 (OUTLIER) cc_final: 0.7695 (p) REVERT: E 50 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6274 (mt-10) REVERT: E 108 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7961 (mm-30) REVERT: E 111 LYS cc_start: 0.8558 (mttm) cc_final: 0.7987 (pptt) REVERT: F 98 GLU cc_start: 0.5878 (OUTLIER) cc_final: 0.5082 (tm-30) REVERT: F 133 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8089 (mppt) REVERT: F 177 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8494 (ttt180) REVERT: F 250 ARG cc_start: 0.6387 (mtt180) cc_final: 0.4665 (tpt-90) REVERT: F 324 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7121 (tm-30) REVERT: J 3 ARG cc_start: 0.4871 (mtm180) cc_final: 0.4516 (mtm110) outliers start: 83 outliers final: 46 residues processed: 255 average time/residue: 0.6445 time to fit residues: 181.3830 Evaluate side-chains 229 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 255 LEU 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 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 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 D residue 82 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 90 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 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 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 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: 2.9990 chunk 35 optimal weight: 4.9990 chunk 188 optimal weight: 0.0980 chunk 159 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 191 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 164 optimal weight: 0.0570 chunk 52 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.196543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.169659 restraints weight = 22688.350| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.99 r_work: 0.3856 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16492 Z= 0.114 Angle : 0.566 11.214 22351 Z= 0.300 Chirality : 0.042 0.168 2520 Planarity : 0.004 0.044 2800 Dihedral : 12.139 86.140 2713 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.89 % Allowed : 35.16 % Favored : 61.95 % 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: -0.26 (0.19), residues: 1985 helix: 0.54 (0.19), residues: 829 sheet: -0.06 (0.30), residues: 291 loop : -0.83 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.024 0.001 TYR C 54 PHE 0.014 0.001 PHE D 327 TRP 0.035 0.004 TRP O 9 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (16492) covalent geometry : angle 0.56636 / 0.30 (22351) hydrogen bonds : bond 0.03433 / 2.37 ( 681) hydrogen bonds : angle 4.68082 / 3.34 ( 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 229 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.607 Fit side-chains REVERT: A 34 ASN cc_start: 0.8327 (m-40) cc_final: 0.7708 (t0) REVERT: A 39 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7511 (tmmt) REVERT: A 158 MET cc_start: 0.4734 (ttt) cc_final: 0.4450 (tpp) REVERT: A 326 MET cc_start: 0.8159 (ttt) cc_final: 0.7919 (tpp) REVERT: B 84 MET cc_start: 0.7356 (mmm) cc_final: 0.6865 (mtt) REVERT: B 247 ARG cc_start: 0.8410 (ttp80) cc_final: 0.7992 (ttp-170) REVERT: B 306 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7216 (mmt-90) REVERT: B 308 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7141 (mm-30) REVERT: C 27 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.7479 (ttm-80) REVERT: C 64 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7562 (ttmt) REVERT: C 95 ARG cc_start: 0.4379 (pmm-80) cc_final: 0.2657 (tmt-80) REVERT: C 159 TYR cc_start: 0.6603 (t80) cc_final: 0.6239 (t80) REVERT: C 214 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7468 (m) REVERT: C 247 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7693 (mtm110) REVERT: C 306 ARG cc_start: 0.6853 (mpt180) cc_final: 0.6617 (mmt180) REVERT: D 84 MET cc_start: 0.5989 (mtt) cc_final: 0.5642 (mtt) REVERT: D 118 GLU cc_start: 0.5784 (tt0) cc_final: 0.4432 (pt0) REVERT: D 211 MET cc_start: 0.6203 (mtp) cc_final: 0.5799 (ttt) REVERT: E 50 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: E 108 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7857 (mm-30) REVERT: E 111 LYS cc_start: 0.8550 (mttm) cc_final: 0.7963 (pptt) REVERT: E 317 SER cc_start: 0.8830 (t) cc_final: 0.8575 (m) REVERT: F 73 LYS cc_start: 0.7953 (ptmm) cc_final: 0.7703 (ptmt) REVERT: F 98 GLU cc_start: 0.5624 (OUTLIER) cc_final: 0.5092 (tm-30) REVERT: F 133 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8031 (mppt) REVERT: F 250 ARG cc_start: 0.6260 (mtt180) cc_final: 0.4576 (tpt-90) REVERT: F 324 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7108 (tm-30) outliers start: 47 outliers final: 32 residues processed: 224 average time/residue: 0.6139 time to fit residues: 151.5608 Evaluate side-chains 210 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 165 THR Chi-restraints excluded: chain A residue 266 THR 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 183 SER Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 88 THR 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 239 SER 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 221 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 99 ILE 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 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 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 108 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 GLN ** D 145 GLN ** 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 = 0.4201 r_free = 0.4201 target = 0.194395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.166957 restraints weight = 22661.617| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.07 r_work: 0.3832 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16492 Z= 0.150 Angle : 0.597 13.347 22351 Z= 0.314 Chirality : 0.043 0.204 2520 Planarity : 0.004 0.046 2800 Dihedral : 12.195 88.360 2713 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.13 % Allowed : 35.34 % Favored : 61.52 % 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 (0.19), residues: 1985 helix: 0.50 (0.19), residues: 836 sheet: -0.12 (0.30), residues: 291 loop : -0.85 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.016 0.001 TYR E 315 PHE 0.018 0.002 PHE A 129 TRP 0.032 0.005 TRP O 9 HIS 0.008 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (16492) covalent geometry : angle 0.59739 / 0.31 (22351) hydrogen bonds : bond 0.03876 / 2.66 ( 681) hydrogen bonds : angle 4.75664 / 3.40 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6036.76 seconds wall clock time: 103 minutes 35.11 seconds (6215.11 seconds total)