Starting phenix.real_space_refine on Wed Sep 17 22:45:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5y4o_6805/09_2025/5y4o_6805.cif Found real_map, /net/cci-nas-00/data/ceres_data/5y4o_6805/09_2025/5y4o_6805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5y4o_6805/09_2025/5y4o_6805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5y4o_6805/09_2025/5y4o_6805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5y4o_6805/09_2025/5y4o_6805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5y4o_6805/09_2025/5y4o_6805.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7966 2.51 5 N 2072 2.21 5 O 2240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12341 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "B" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "C" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "D" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "E" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "F" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "G" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Time building chain proxies: 3.00, per 1000 atoms: 0.24 Number of scatterers: 12341 At special positions: 0 Unit cell: (100.32, 99, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2240 8.00 N 2072 7.00 C 7966 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 520.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 15 sheets defined 52.9% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 114 through 138 removed outlier: 3.819A pdb=" N ILE A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 176 " --> pdb=" O MET A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.531A pdb=" N LEU A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'B' and resid 114 through 138 removed outlier: 3.818A pdb=" N ILE B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS B 161 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 removed outlier: 3.532A pdb=" N LEU B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 244 through 249 removed outlier: 4.854A pdb=" N ALA B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS B 263 " --> pdb=" O ARG B 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'C' and resid 114 through 138 removed outlier: 3.817A pdb=" N ILE C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ASP C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE C 167 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE C 168 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 223 removed outlier: 3.531A pdb=" N LEU C 220 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 265 removed outlier: 3.596A pdb=" N LEU C 262 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'D' and resid 114 through 138 removed outlier: 3.819A pdb=" N ILE D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP D 162 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE D 167 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 223 removed outlier: 3.531A pdb=" N LEU D 220 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS D 263 " --> pdb=" O ARG D 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'E' and resid 114 through 138 removed outlier: 3.818A pdb=" N ILE E 122 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 143 No H-bonds generated for 'chain 'E' and resid 141 through 143' Processing helix chain 'E' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY E 153 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS E 161 " --> pdb=" O GLY E 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP E 162 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP E 176 " --> pdb=" O MET E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 223 removed outlier: 3.530A pdb=" N LEU E 220 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU E 262 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 320 Processing helix chain 'F' and resid 114 through 138 removed outlier: 3.819A pdb=" N ILE F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL F 128 " --> pdb=" O ILE F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 143 No H-bonds generated for 'chain 'F' and resid 141 through 143' Processing helix chain 'F' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE F 151 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 152 " --> pdb=" O PHE F 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS F 161 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP F 162 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE F 163 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE F 168 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP F 176 " --> pdb=" O MET F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 223 removed outlier: 3.531A pdb=" N LEU F 220 " --> pdb=" O PRO F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS F 263 " --> pdb=" O ARG F 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 264 " --> pdb=" O GLU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 320 Processing helix chain 'G' and resid 114 through 138 removed outlier: 3.819A pdb=" N ILE G 122 " --> pdb=" O MET G 118 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL G 128 " --> pdb=" O ILE G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 143 No H-bonds generated for 'chain 'G' and resid 141 through 143' Processing helix chain 'G' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE G 151 " --> pdb=" O THR G 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY G 152 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY G 153 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS G 161 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP G 162 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE G 167 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE G 168 " --> pdb=" O LEU G 164 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP G 176 " --> pdb=" O MET G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 223 removed outlier: 3.531A pdb=" N LEU G 220 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU G 262 " --> pdb=" O VAL G 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS G 263 " --> pdb=" O ARG G 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU A 198 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 238 removed outlier: 3.628A pdb=" N TYR A 277 " --> pdb=" O MET A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU B 198 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 238 removed outlier: 3.627A pdb=" N TYR B 277 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU C 198 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 235 through 238 removed outlier: 3.628A pdb=" N TYR C 277 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU D 198 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 235 through 238 removed outlier: 3.628A pdb=" N TYR D 277 " --> pdb=" O MET D 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU E 198 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 235 through 238 removed outlier: 3.627A pdb=" N TYR E 277 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 330 through 331 removed outlier: 6.052A pdb=" N THR E 330 " --> pdb=" O GLN F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU F 198 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 235 through 238 removed outlier: 3.627A pdb=" N TYR F 277 " --> pdb=" O MET F 289 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU G 198 " --> pdb=" O LYS G 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 235 through 238 removed outlier: 3.627A pdb=" N TYR G 277 " --> pdb=" O MET G 289 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.01: 3 1.01 - 1.22: 350 1.22 - 1.43: 4964 1.43 - 1.64: 7164 1.64 - 1.84: 126 Bond restraints: 12607 Sorted by residual: bond pdb=" C MET E 140 " pdb=" N SER E 141 " ideal model delta sigma weight residual 1.332 0.802 0.530 1.40e-02 5.10e+03 1.44e+03 bond pdb=" C PHE E 148 " pdb=" N GLY E 149 " ideal model delta sigma weight residual 1.334 1.822 -0.487 1.42e-02 4.96e+03 1.18e+03 bond pdb=" C PHE F 148 " pdb=" N GLY F 149 " ideal model delta sigma weight residual 1.334 1.821 -0.487 1.42e-02 4.96e+03 1.17e+03 bond pdb=" C PHE B 148 " pdb=" N GLY B 149 " ideal model delta sigma weight residual 1.334 1.821 -0.486 1.42e-02 4.96e+03 1.17e+03 bond pdb=" C PHE A 148 " pdb=" N GLY A 149 " ideal model delta sigma weight residual 1.334 1.821 -0.486 1.42e-02 4.96e+03 1.17e+03 ... (remaining 12602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.65: 17021 10.65 - 21.30: 57 21.30 - 31.95: 17 31.95 - 42.60: 4 42.60 - 53.25: 2 Bond angle restraints: 17101 Sorted by residual: angle pdb=" CA MET A 140 " pdb=" C MET A 140 " pdb=" N SER A 141 " ideal model delta sigma weight residual 114.60 65.47 49.13 1.30e+00 5.92e-01 1.43e+03 angle pdb=" CA MET G 140 " pdb=" C MET G 140 " pdb=" N SER G 141 " ideal model delta sigma weight residual 114.60 77.96 36.64 1.30e+00 5.92e-01 7.94e+02 angle pdb=" CA MET E 140 " pdb=" C MET E 140 " pdb=" N SER E 141 " ideal model delta sigma weight residual 114.87 72.68 42.19 1.55e+00 4.16e-01 7.41e+02 angle pdb=" CA MET B 140 " pdb=" C MET B 140 " pdb=" N SER B 141 " ideal model delta sigma weight residual 114.87 73.17 41.70 1.55e+00 4.16e-01 7.24e+02 angle pdb=" CA MET F 140 " pdb=" C MET F 140 " pdb=" N SER F 141 " ideal model delta sigma weight residual 117.65 64.40 53.25 1.98e+00 2.55e-01 7.23e+02 ... (remaining 17096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.56: 6461 21.56 - 43.13: 675 43.13 - 64.69: 270 64.69 - 86.25: 7 86.25 - 107.81: 7 Dihedral angle restraints: 7420 sinusoidal: 2926 harmonic: 4494 Sorted by residual: dihedral pdb=" CA MET C 140 " pdb=" C MET C 140 " pdb=" N SER C 141 " pdb=" CA SER C 141 " ideal model delta harmonic sigma weight residual 180.00 72.19 107.81 0 5.00e+00 4.00e-02 4.65e+02 dihedral pdb=" CA MET F 140 " pdb=" C MET F 140 " pdb=" N SER F 141 " pdb=" CA SER F 141 " ideal model delta harmonic sigma weight residual 180.00 77.81 102.19 0 5.00e+00 4.00e-02 4.18e+02 dihedral pdb=" CA MET D 140 " pdb=" C MET D 140 " pdb=" N SER D 141 " pdb=" CA SER D 141 " ideal model delta harmonic sigma weight residual 180.00 78.33 101.67 0 5.00e+00 4.00e-02 4.13e+02 ... (remaining 7417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 1629 0.142 - 0.284: 271 0.284 - 0.425: 54 0.425 - 0.567: 6 0.567 - 0.709: 7 Chirality restraints: 1967 Sorted by residual: chirality pdb=" CG LEU E 146 " pdb=" CB LEU E 146 " pdb=" CD1 LEU E 146 " pdb=" CD2 LEU E 146 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CG LEU F 146 " pdb=" CB LEU F 146 " pdb=" CD1 LEU F 146 " pdb=" CD2 LEU F 146 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CG LEU A 146 " pdb=" CB LEU A 146 " pdb=" CD1 LEU A 146 " pdb=" CD2 LEU A 146 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.24e+01 ... (remaining 1964 not shown) Planarity restraints: 2149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 140 " 0.070 2.00e-02 2.50e+03 2.69e-01 7.21e+02 pdb=" C MET F 140 " -0.456 2.00e-02 2.50e+03 pdb=" O MET F 140 " 0.173 2.00e-02 2.50e+03 pdb=" N SER F 141 " 0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 140 " 0.106 2.00e-02 2.50e+03 2.55e-01 6.48e+02 pdb=" C MET D 140 " -0.436 2.00e-02 2.50e+03 pdb=" O MET D 140 " 0.208 2.00e-02 2.50e+03 pdb=" N SER D 141 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 140 " -0.077 2.00e-02 2.50e+03 2.39e-01 5.69e+02 pdb=" C MET B 140 " 0.408 2.00e-02 2.50e+03 pdb=" O MET B 140 " -0.178 2.00e-02 2.50e+03 pdb=" N SER B 141 " -0.154 2.00e-02 2.50e+03 ... (remaining 2146 not shown) Histogram of nonbonded interaction distances: 0.70 - 1.54: 51 1.54 - 2.38: 326 2.38 - 3.22: 13639 3.22 - 4.06: 28887 4.06 - 4.90: 51970 Warning: very small nonbonded interaction distances. Nonbonded interactions: 94873 Sorted by model distance: nonbonded pdb=" OE1 GLU F 136 " pdb=" O MET G 140 " model vdw 0.701 3.040 nonbonded pdb=" OE1 GLU D 136 " pdb=" O MET E 140 " model vdw 0.849 3.040 nonbonded pdb=" CD GLU C 136 " pdb=" O MET D 140 " model vdw 0.895 3.270 nonbonded pdb=" O MET A 140 " pdb=" OE1 GLU G 136 " model vdw 0.918 3.040 nonbonded pdb=" CD GLU B 136 " pdb=" O MET C 140 " model vdw 1.059 3.270 ... (remaining 94868 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.720 Find NCS groups from input model: 0.110 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 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 : 0.032 0.959 12628 Z= 2.779 Angle : 2.442 53.248 17101 Z= 1.699 Chirality : 0.121 0.709 1967 Planarity : 0.022 0.269 2149 Dihedral : 19.883 107.815 4536 Min Nonbonded Distance : 0.701 Molprobity Statistics. All-atom Clashscore : 78.50 Ramachandran Plot: Outliers : 4.46 % Allowed : 7.76 % Favored : 87.78 % Rotamer: Outliers : 20.31 % Allowed : 10.42 % Favored : 69.27 % Cbeta Deviations : 1.94 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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 aren not related in a simple way. whole: -2.08 (0.21), residues: 1547 helix: -1.35 (0.18), residues: 637 sheet: -3.24 (0.29), residues: 245 loop : -0.33 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.005 ARG A 116 TYR 0.069 0.007 TYR D 134 PHE 0.096 0.008 PHE C 138 TRP 0.031 0.004 TRP C 184 HIS 0.048 0.012 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.02223 (12607) covalent geometry : angle 2.44237 (17101) hydrogen bonds : bond 0.27375 ( 574) hydrogen bonds : angle 9.83626 ( 1533) Misc. bond : bond 0.57379 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 273 poor density : 468 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ILE cc_start: 0.7167 (mp) cc_final: 0.6710 (mt) REVERT: B 164 LEU cc_start: 0.4522 (mp) cc_final: 0.4257 (mp) REVERT: C 174 TYR cc_start: 0.5682 (t80) cc_final: 0.5437 (t80) REVERT: D 158 MET cc_start: 0.4077 (OUTLIER) cc_final: 0.3865 (mmt) REVERT: D 179 PHE cc_start: 0.4696 (p90) cc_final: 0.4464 (p90) REVERT: D 181 ILE cc_start: 0.7017 (mp) cc_final: 0.6810 (mt) REVERT: D 268 ILE cc_start: 0.7249 (mp) cc_final: 0.6907 (mt) REVERT: D 316 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.6039 (mm) REVERT: E 237 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8327 (pp) REVERT: E 268 ILE cc_start: 0.7263 (mp) cc_final: 0.7023 (mt) REVERT: E 277 TYR cc_start: 0.8561 (m-80) cc_final: 0.8200 (m-80) REVERT: G 268 ILE cc_start: 0.7186 (mp) cc_final: 0.6971 (mt) outliers start: 273 outliers final: 136 residues processed: 599 average time/residue: 0.1092 time to fit residues: 92.8032 Evaluate side-chains 506 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 367 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 TRP Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 302 TRP Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 302 TRP Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 235 ARG Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 302 TRP Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 316 ILE Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 270 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 302 TRP Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain G residue 236 ARG Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 243 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 270 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 302 TRP Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 316 ILE Chi-restraints excluded: chain G residue 326 PHE Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN B 320 HIS C 218 ASN C 272 GLN C 307 GLN D 218 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN E 264 ASN E 272 GLN E 320 HIS F 272 GLN F 307 GLN F 320 HIS ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.187878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.155405 restraints weight = 15884.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.158226 restraints weight = 9397.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.159886 restraints weight = 6525.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.161056 restraints weight = 5176.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.161602 restraints weight = 4475.120| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12628 Z= 0.239 Angle : 0.864 11.433 17101 Z= 0.467 Chirality : 0.050 0.212 1967 Planarity : 0.007 0.081 2149 Dihedral : 14.526 73.131 2004 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.90 % Allowed : 5.82 % Favored : 93.28 % Rotamer: Outliers : 9.52 % Allowed : 16.44 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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 aren not related in a simple way. whole: -1.53 (0.19), residues: 1547 helix: 0.11 (0.19), residues: 630 sheet: -2.21 (0.36), residues: 224 loop : -1.59 (0.20), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG G 186 TYR 0.019 0.002 TYR D 310 PHE 0.020 0.003 PHE B 278 TRP 0.033 0.004 TRP G 184 HIS 0.025 0.004 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00510 (12607) covalent geometry : angle 0.86357 (17101) hydrogen bonds : bond 0.06865 ( 574) hydrogen bonds : angle 5.57191 ( 1533) Misc. bond : bond 0.00392 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 470 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.2775 (mtt) cc_final: 0.2331 (mtt) REVERT: A 158 MET cc_start: 0.4587 (mmt) cc_final: 0.4246 (mmt) REVERT: A 172 MET cc_start: 0.7741 (tpp) cc_final: 0.6542 (ttp) REVERT: A 179 PHE cc_start: 0.5863 (p90) cc_final: 0.5490 (p90) REVERT: A 180 SER cc_start: 0.6690 (m) cc_final: 0.6242 (t) REVERT: A 268 ILE cc_start: 0.7720 (mp) cc_final: 0.7265 (mt) REVERT: A 284 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.7968 (t) REVERT: B 140 MET cc_start: 0.2884 (mtt) cc_final: 0.2326 (mtt) REVERT: B 173 LEU cc_start: 0.7495 (tt) cc_final: 0.7084 (mm) REVERT: B 180 SER cc_start: 0.7081 (m) cc_final: 0.6553 (t) REVERT: C 158 MET cc_start: 0.5031 (mmt) cc_final: 0.4720 (mmt) REVERT: C 180 SER cc_start: 0.6132 (m) cc_final: 0.5730 (t) REVERT: D 140 MET cc_start: 0.2554 (mtt) cc_final: 0.2242 (ttm) REVERT: D 173 LEU cc_start: 0.6786 (tp) cc_final: 0.6488 (mm) REVERT: E 180 SER cc_start: 0.6909 (m) cc_final: 0.6616 (t) REVERT: E 181 ILE cc_start: 0.7721 (mp) cc_final: 0.7439 (mm) REVERT: E 237 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8293 (pt) REVERT: E 277 TYR cc_start: 0.8703 (m-80) cc_final: 0.8196 (m-80) REVERT: E 281 PHE cc_start: 0.8886 (t80) cc_final: 0.8583 (t80) REVERT: E 284 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8535 (t) REVERT: E 314 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7769 (tt) REVERT: F 118 MET cc_start: 0.4746 (ptt) cc_final: 0.4472 (ptp) REVERT: F 140 MET cc_start: 0.2749 (mtt) cc_final: 0.2335 (mtt) REVERT: F 277 TYR cc_start: 0.8342 (m-80) cc_final: 0.7762 (m-80) REVERT: G 172 MET cc_start: 0.7388 (tpp) cc_final: 0.6282 (ttt) REVERT: G 174 TYR cc_start: 0.5373 (t80) cc_final: 0.5046 (t80) REVERT: G 180 SER cc_start: 0.6907 (m) cc_final: 0.6524 (t) REVERT: G 234 ASN cc_start: 0.7814 (m110) cc_final: 0.7612 (m110) REVERT: G 250 LYS cc_start: 0.6101 (ptmt) cc_final: 0.5753 (pttt) REVERT: G 314 ILE cc_start: 0.7928 (tt) cc_final: 0.7649 (tt) outliers start: 128 outliers final: 59 residues processed: 514 average time/residue: 0.1143 time to fit residues: 82.7518 Evaluate side-chains 441 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 378 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 326 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 HIS B 218 ASN ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 HIS D 320 HIS ** E 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 GLN G 320 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.188975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.151519 restraints weight = 16108.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.154593 restraints weight = 9911.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.156591 restraints weight = 7153.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.157609 restraints weight = 5804.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.158532 restraints weight = 5145.832| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12628 Z= 0.184 Angle : 0.714 8.376 17101 Z= 0.388 Chirality : 0.043 0.212 1967 Planarity : 0.005 0.075 2149 Dihedral : 9.494 73.037 1786 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.98 % Favored : 92.11 % Rotamer: Outliers : 9.52 % Allowed : 18.01 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.20), residues: 1547 helix: 0.94 (0.19), residues: 637 sheet: -2.05 (0.36), residues: 224 loop : -1.96 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 235 TYR 0.017 0.002 TYR B 174 PHE 0.017 0.002 PHE B 278 TRP 0.032 0.004 TRP G 184 HIS 0.006 0.002 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00396 (12607) covalent geometry : angle 0.71417 (17101) hydrogen bonds : bond 0.05583 ( 574) hydrogen bonds : angle 4.93071 ( 1533) Misc. bond : bond 0.00354 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 419 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.5078 (mmt) cc_final: 0.4795 (mmt) REVERT: A 172 MET cc_start: 0.7739 (tpp) cc_final: 0.6340 (ttt) REVERT: A 179 PHE cc_start: 0.6078 (p90) cc_final: 0.5803 (p90) REVERT: A 180 SER cc_start: 0.7109 (m) cc_final: 0.6729 (t) REVERT: A 207 THR cc_start: 0.9149 (m) cc_final: 0.8829 (p) REVERT: A 215 TYR cc_start: 0.8485 (m-80) cc_final: 0.7952 (m-80) REVERT: A 268 ILE cc_start: 0.7542 (mp) cc_final: 0.7205 (mt) REVERT: A 277 TYR cc_start: 0.8190 (m-80) cc_final: 0.7984 (m-80) REVERT: A 281 PHE cc_start: 0.8869 (t80) cc_final: 0.8538 (t80) REVERT: A 291 TYR cc_start: 0.8487 (t80) cc_final: 0.8273 (t80) REVERT: B 173 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.6942 (mm) REVERT: B 180 SER cc_start: 0.7293 (m) cc_final: 0.6976 (t) REVERT: B 201 TRP cc_start: 0.7719 (m100) cc_final: 0.7496 (m100) REVERT: B 237 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8309 (pt) REVERT: C 161 LYS cc_start: 0.5411 (OUTLIER) cc_final: 0.4719 (tppt) REVERT: C 174 TYR cc_start: 0.6491 (t80) cc_final: 0.6255 (t80) REVERT: C 180 SER cc_start: 0.6307 (m) cc_final: 0.6033 (t) REVERT: C 301 GLU cc_start: 0.6346 (mm-30) cc_final: 0.6105 (mm-30) REVERT: D 173 LEU cc_start: 0.6884 (tp) cc_final: 0.6460 (mm) REVERT: D 180 SER cc_start: 0.7110 (m) cc_final: 0.6862 (t) REVERT: E 118 MET cc_start: 0.5335 (ptt) cc_final: 0.4820 (mmt) REVERT: E 180 SER cc_start: 0.7275 (m) cc_final: 0.6887 (t) REVERT: E 237 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8330 (pt) REVERT: E 250 LYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5897 (pttt) REVERT: E 281 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8578 (t80) REVERT: F 118 MET cc_start: 0.5207 (ptt) cc_final: 0.4981 (ptp) REVERT: F 158 MET cc_start: 0.4732 (mmt) cc_final: 0.4381 (mmt) REVERT: F 277 TYR cc_start: 0.8370 (m-80) cc_final: 0.7778 (m-80) REVERT: G 172 MET cc_start: 0.7496 (tpp) cc_final: 0.6293 (ttt) REVERT: G 237 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8237 (pt) REVERT: G 287 ASN cc_start: 0.7896 (m110) cc_final: 0.7554 (m-40) outliers start: 128 outliers final: 69 residues processed: 493 average time/residue: 0.1123 time to fit residues: 77.5754 Evaluate side-chains 446 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 370 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 299 TRP Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 299 TRP Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 326 PHE Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 139 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 148 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 218 ASN ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN E 228 ASN F 218 ASN ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 ASN ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.183293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.149948 restraints weight = 16135.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.152871 restraints weight = 9400.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.154752 restraints weight = 6495.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.155982 restraints weight = 5102.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.156518 restraints weight = 4373.737| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.7263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12628 Z= 0.213 Angle : 0.751 17.040 17101 Z= 0.404 Chirality : 0.045 0.180 1967 Planarity : 0.006 0.050 2149 Dihedral : 8.224 58.948 1746 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.37 % Favored : 91.73 % Rotamer: Outliers : 9.30 % Allowed : 21.50 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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 aren not related in a simple way. whole: -1.05 (0.21), residues: 1547 helix: 1.05 (0.19), residues: 651 sheet: -2.05 (0.36), residues: 224 loop : -2.00 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG G 186 TYR 0.018 0.002 TYR B 174 PHE 0.021 0.002 PHE E 138 TRP 0.025 0.004 TRP F 184 HIS 0.041 0.005 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00472 (12607) covalent geometry : angle 0.75091 (17101) hydrogen bonds : bond 0.05676 ( 574) hydrogen bonds : angle 4.72439 ( 1533) Misc. bond : bond 0.00647 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 409 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 PHE cc_start: 0.5331 (m-10) cc_final: 0.4950 (m-80) REVERT: A 158 MET cc_start: 0.5170 (mmt) cc_final: 0.4791 (mmt) REVERT: A 172 MET cc_start: 0.7833 (tpp) cc_final: 0.6729 (ttp) REVERT: A 174 TYR cc_start: 0.6344 (t80) cc_final: 0.6102 (t80) REVERT: A 179 PHE cc_start: 0.5824 (p90) cc_final: 0.5489 (p90) REVERT: B 161 LYS cc_start: 0.5338 (OUTLIER) cc_final: 0.4535 (mttt) REVERT: B 173 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6939 (mm) REVERT: B 232 MET cc_start: 0.8575 (mtt) cc_final: 0.8328 (mtp) REVERT: B 237 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8418 (pt) REVERT: C 180 SER cc_start: 0.6941 (m) cc_final: 0.6572 (t) REVERT: C 284 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8366 (t) REVERT: C 301 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6300 (mm-30) REVERT: D 161 LYS cc_start: 0.5497 (OUTLIER) cc_final: 0.4777 (tppt) REVERT: D 173 LEU cc_start: 0.7205 (tp) cc_final: 0.6778 (mm) REVERT: D 205 LYS cc_start: 0.8995 (mtpp) cc_final: 0.8376 (tttm) REVERT: D 232 MET cc_start: 0.8296 (mtt) cc_final: 0.7986 (mtt) REVERT: D 235 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7259 (mmt-90) REVERT: E 118 MET cc_start: 0.5500 (ptt) cc_final: 0.4962 (mmt) REVERT: E 161 LYS cc_start: 0.5683 (OUTLIER) cc_final: 0.4896 (tppt) REVERT: E 232 MET cc_start: 0.7690 (mtt) cc_final: 0.7464 (mtp) REVERT: E 237 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8534 (pt) REVERT: F 174 TYR cc_start: 0.6312 (t80) cc_final: 0.6049 (t80) REVERT: F 277 TYR cc_start: 0.8449 (m-80) cc_final: 0.7877 (m-80) REVERT: G 172 MET cc_start: 0.7377 (tpp) cc_final: 0.6074 (ttt) REVERT: G 205 LYS cc_start: 0.8879 (mtpt) cc_final: 0.8535 (mtpp) REVERT: G 232 MET cc_start: 0.8635 (mtt) cc_final: 0.7835 (mtt) REVERT: G 235 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7336 (mmt-90) REVERT: G 237 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8524 (pt) REVERT: G 280 GLN cc_start: 0.7874 (tp40) cc_final: 0.7182 (tp40) REVERT: G 287 ASN cc_start: 0.8178 (m110) cc_final: 0.7847 (m-40) REVERT: G 329 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8210 (mt0) outliers start: 125 outliers final: 82 residues processed: 490 average time/residue: 0.1170 time to fit residues: 80.3062 Evaluate side-chains 439 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 347 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 326 PHE Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 139 optimal weight: 0.0570 chunk 25 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 153 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN ** G 265 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 = 0.4007 r_free = 0.4007 target = 0.187532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.152255 restraints weight = 15922.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.155401 restraints weight = 9614.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.157438 restraints weight = 6767.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.158599 restraints weight = 5398.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.159211 restraints weight = 4690.632| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.7612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12628 Z= 0.130 Angle : 0.704 16.613 17101 Z= 0.371 Chirality : 0.042 0.192 1967 Planarity : 0.004 0.053 2149 Dihedral : 7.409 54.514 1732 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.90 % Allowed : 5.75 % Favored : 93.34 % Rotamer: Outliers : 7.59 % Allowed : 23.81 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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 aren not related in a simple way. whole: -0.85 (0.21), residues: 1547 helix: 1.42 (0.19), residues: 651 sheet: -2.04 (0.35), residues: 224 loop : -2.10 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 186 TYR 0.019 0.001 TYR B 174 PHE 0.017 0.001 PHE C 278 TRP 0.019 0.003 TRP F 184 HIS 0.012 0.001 HIS E 265 Details of bonding type rmsd covalent geometry : bond 0.00259 (12607) covalent geometry : angle 0.70419 (17101) hydrogen bonds : bond 0.04962 ( 574) hydrogen bonds : angle 4.45982 ( 1533) Misc. bond : bond 0.00349 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 391 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 PHE cc_start: 0.5405 (m-10) cc_final: 0.5139 (m-80) REVERT: A 172 MET cc_start: 0.7702 (tpp) cc_final: 0.6318 (ttt) REVERT: A 174 TYR cc_start: 0.6371 (t80) cc_final: 0.6108 (t80) REVERT: A 207 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8993 (p) REVERT: A 291 TYR cc_start: 0.8234 (t80) cc_final: 0.7846 (t80) REVERT: A 318 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7586 (mm-40) REVERT: B 161 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.4873 (mttt) REVERT: B 173 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6975 (mm) REVERT: B 235 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6780 (mmt-90) REVERT: B 237 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8208 (pt) REVERT: B 277 TYR cc_start: 0.8067 (m-80) cc_final: 0.7810 (m-10) REVERT: C 180 SER cc_start: 0.6981 (m) cc_final: 0.6670 (t) REVERT: C 284 SER cc_start: 0.8460 (p) cc_final: 0.8145 (t) REVERT: D 161 LYS cc_start: 0.5597 (OUTLIER) cc_final: 0.5046 (tppt) REVERT: D 173 LEU cc_start: 0.7076 (tp) cc_final: 0.6638 (mm) REVERT: D 205 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8349 (tttm) REVERT: E 118 MET cc_start: 0.5421 (ptt) cc_final: 0.4877 (mmt) REVERT: E 161 LYS cc_start: 0.5450 (OUTLIER) cc_final: 0.4982 (tppt) REVERT: E 212 ARG cc_start: 0.7742 (mtt180) cc_final: 0.7428 (mtt180) REVERT: E 237 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8417 (pt) REVERT: E 281 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8471 (t80) REVERT: F 172 MET cc_start: 0.7819 (tpp) cc_final: 0.6550 (ttt) REVERT: F 277 TYR cc_start: 0.8396 (m-80) cc_final: 0.7762 (m-80) REVERT: G 138 PHE cc_start: 0.5665 (m-10) cc_final: 0.5388 (m-80) REVERT: G 161 LYS cc_start: 0.5581 (OUTLIER) cc_final: 0.4650 (tppt) REVERT: G 172 MET cc_start: 0.7418 (tpp) cc_final: 0.6277 (ttt) REVERT: G 232 MET cc_start: 0.7833 (mtt) cc_final: 0.7465 (mtt) REVERT: G 237 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8377 (pt) REVERT: G 287 ASN cc_start: 0.7979 (m110) cc_final: 0.7666 (m-40) outliers start: 102 outliers final: 61 residues processed: 462 average time/residue: 0.1200 time to fit residues: 76.6891 Evaluate side-chains 442 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 370 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 326 PHE Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 329 GLN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN E 228 ASN ** E 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.189236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.154695 restraints weight = 15787.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.157726 restraints weight = 9610.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.159726 restraints weight = 6831.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.160881 restraints weight = 5441.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.161745 restraints weight = 4731.711| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.7853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12628 Z= 0.134 Angle : 0.729 20.325 17101 Z= 0.378 Chirality : 0.042 0.187 1967 Planarity : 0.004 0.039 2149 Dihedral : 7.255 56.030 1731 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.27 % Favored : 92.82 % Rotamer: Outliers : 7.07 % Allowed : 25.67 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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 aren not related in a simple way. whole: -0.79 (0.21), residues: 1547 helix: 1.59 (0.20), residues: 651 sheet: -1.96 (0.34), residues: 224 loop : -2.22 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 186 TYR 0.022 0.001 TYR F 174 PHE 0.014 0.001 PHE A 278 TRP 0.021 0.003 TRP F 302 HIS 0.016 0.002 HIS E 265 Details of bonding type rmsd covalent geometry : bond 0.00281 (12607) covalent geometry : angle 0.72870 (17101) hydrogen bonds : bond 0.04868 ( 574) hydrogen bonds : angle 4.38764 ( 1533) Misc. bond : bond 0.00422 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 391 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7653 (tpp) cc_final: 0.6385 (ttp) REVERT: A 174 TYR cc_start: 0.6379 (t80) cc_final: 0.6155 (t80) REVERT: A 291 TYR cc_start: 0.8241 (t80) cc_final: 0.7883 (t80) REVERT: B 161 LYS cc_start: 0.5901 (OUTLIER) cc_final: 0.5042 (mttt) REVERT: B 173 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7014 (mm) REVERT: B 235 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6903 (mmt-90) REVERT: B 237 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8216 (pt) REVERT: C 180 SER cc_start: 0.7280 (m) cc_final: 0.6912 (t) REVERT: C 212 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.7859 (mtt180) REVERT: C 284 SER cc_start: 0.8321 (p) cc_final: 0.7966 (t) REVERT: D 161 LYS cc_start: 0.5533 (OUTLIER) cc_final: 0.5043 (tppt) REVERT: D 173 LEU cc_start: 0.7072 (tp) cc_final: 0.6678 (mm) REVERT: D 205 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8369 (tttm) REVERT: D 228 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8411 (p0) REVERT: D 232 MET cc_start: 0.8183 (mtt) cc_final: 0.7977 (mtp) REVERT: E 118 MET cc_start: 0.5487 (ptt) cc_final: 0.4979 (mmt) REVERT: E 161 LYS cc_start: 0.5603 (OUTLIER) cc_final: 0.5309 (tppt) REVERT: E 237 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8387 (pt) REVERT: F 172 MET cc_start: 0.7840 (tpp) cc_final: 0.6610 (ttt) REVERT: F 277 TYR cc_start: 0.8394 (m-80) cc_final: 0.7787 (m-80) REVERT: G 138 PHE cc_start: 0.5292 (m-10) cc_final: 0.5074 (m-80) REVERT: G 161 LYS cc_start: 0.5693 (OUTLIER) cc_final: 0.4991 (tppt) REVERT: G 172 MET cc_start: 0.7438 (tpp) cc_final: 0.6095 (ttt) REVERT: G 173 LEU cc_start: 0.6338 (mp) cc_final: 0.6120 (mm) REVERT: G 205 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8433 (tttm) REVERT: G 234 ASN cc_start: 0.7830 (m110) cc_final: 0.7579 (m110) REVERT: G 237 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8484 (pt) outliers start: 95 outliers final: 68 residues processed: 467 average time/residue: 0.1191 time to fit residues: 77.4439 Evaluate side-chains 454 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 376 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 299 TRP Chi-restraints excluded: chain G residue 326 PHE Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 20 optimal weight: 0.0870 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS B 329 GLN C 137 HIS C 320 HIS D 218 ASN D 228 ASN E 320 HIS ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN G 218 ASN G 228 ASN ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.187190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.153439 restraints weight = 15720.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.156519 restraints weight = 9523.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.158542 restraints weight = 6685.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.159779 restraints weight = 5281.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.160315 restraints weight = 4545.750| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.8084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 12628 Z= 0.143 Angle : 0.765 20.402 17101 Z= 0.399 Chirality : 0.043 0.224 1967 Planarity : 0.004 0.047 2149 Dihedral : 7.187 59.523 1729 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.90 % Allowed : 5.95 % Favored : 93.15 % Rotamer: Outliers : 6.99 % Allowed : 25.89 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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 aren not related in a simple way. whole: -0.76 (0.21), residues: 1547 helix: 1.69 (0.20), residues: 651 sheet: -2.10 (0.33), residues: 231 loop : -2.22 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 271 TYR 0.024 0.001 TYR F 174 PHE 0.013 0.001 PHE C 278 TRP 0.044 0.004 TRP E 302 HIS 0.072 0.005 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00300 (12607) covalent geometry : angle 0.76462 (17101) hydrogen bonds : bond 0.04941 ( 574) hydrogen bonds : angle 4.39746 ( 1533) Misc. bond : bond 0.00582 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 385 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7802 (tpp) cc_final: 0.6578 (ttt) REVERT: A 174 TYR cc_start: 0.6397 (t80) cc_final: 0.6166 (t80) REVERT: A 291 TYR cc_start: 0.8219 (t80) cc_final: 0.7903 (t80) REVERT: B 161 LYS cc_start: 0.5951 (OUTLIER) cc_final: 0.5406 (tppt) REVERT: B 173 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7250 (mm) REVERT: B 218 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8546 (m110) REVERT: B 235 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6864 (mmt-90) REVERT: B 237 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8192 (pt) REVERT: C 180 SER cc_start: 0.7471 (m) cc_final: 0.7007 (t) REVERT: C 284 SER cc_start: 0.8296 (p) cc_final: 0.7929 (t) REVERT: D 161 LYS cc_start: 0.5513 (OUTLIER) cc_final: 0.5290 (tppt) REVERT: D 173 LEU cc_start: 0.7121 (tp) cc_final: 0.6751 (mm) REVERT: D 205 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8503 (tttm) REVERT: E 118 MET cc_start: 0.5464 (ptt) cc_final: 0.4901 (mmt) REVERT: E 161 LYS cc_start: 0.5619 (OUTLIER) cc_final: 0.5273 (tppt) REVERT: E 205 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8250 (tttp) REVERT: E 237 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8425 (pt) REVERT: F 173 LEU cc_start: 0.6991 (tp) cc_final: 0.6612 (mm) REVERT: F 277 TYR cc_start: 0.8447 (m-80) cc_final: 0.7967 (m-80) REVERT: G 138 PHE cc_start: 0.5241 (m-10) cc_final: 0.5027 (m-80) REVERT: G 161 LYS cc_start: 0.5716 (OUTLIER) cc_final: 0.4977 (tppt) REVERT: G 172 MET cc_start: 0.7508 (tpp) cc_final: 0.6170 (ttt) REVERT: G 173 LEU cc_start: 0.6332 (mp) cc_final: 0.6108 (mm) REVERT: G 205 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8459 (tttm) REVERT: G 232 MET cc_start: 0.7813 (mtt) cc_final: 0.7541 (mtt) REVERT: G 237 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8462 (pt) REVERT: G 280 GLN cc_start: 0.7876 (tp40) cc_final: 0.7594 (tp40) outliers start: 94 outliers final: 65 residues processed: 461 average time/residue: 0.1188 time to fit residues: 76.7427 Evaluate side-chains 438 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 363 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 299 TRP Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 148 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 94 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 306 GLN B 320 HIS B 329 GLN D 218 ASN D 228 ASN D 264 ASN E 218 ASN E 320 HIS F 280 GLN G 218 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.187006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.154016 restraints weight = 15656.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.157052 restraints weight = 9474.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.159042 restraints weight = 6679.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.160225 restraints weight = 5267.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.161095 restraints weight = 4536.666| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.8289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 12628 Z= 0.141 Angle : 0.783 22.456 17101 Z= 0.414 Chirality : 0.043 0.301 1967 Planarity : 0.004 0.051 2149 Dihedral : 7.174 58.736 1725 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.27 % Favored : 92.82 % Rotamer: Outliers : 6.55 % Allowed : 27.01 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.16 % 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 aren not related in a simple way. whole: -0.73 (0.21), residues: 1547 helix: 1.74 (0.20), residues: 651 sheet: -2.20 (0.32), residues: 231 loop : -2.19 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 235 TYR 0.025 0.002 TYR F 174 PHE 0.013 0.001 PHE C 278 TRP 0.027 0.003 TRP E 302 HIS 0.079 0.004 HIS G 265 Details of bonding type rmsd covalent geometry : bond 0.00301 (12607) covalent geometry : angle 0.78337 (17101) hydrogen bonds : bond 0.05020 ( 574) hydrogen bonds : angle 4.43218 ( 1533) Misc. bond : bond 0.00616 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 390 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7776 (tpp) cc_final: 0.6609 (ttt) REVERT: B 161 LYS cc_start: 0.6016 (OUTLIER) cc_final: 0.5449 (tppt) REVERT: B 173 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7257 (mm) REVERT: B 218 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8525 (m110) REVERT: B 235 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6783 (mmt-90) REVERT: B 237 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8043 (pt) REVERT: C 180 SER cc_start: 0.7514 (m) cc_final: 0.7220 (t) REVERT: D 161 LYS cc_start: 0.5578 (OUTLIER) cc_final: 0.5140 (tppt) REVERT: D 205 LYS cc_start: 0.8936 (mtpp) cc_final: 0.8384 (tttm) REVERT: E 118 MET cc_start: 0.5496 (ptt) cc_final: 0.4924 (mmt) REVERT: E 161 LYS cc_start: 0.5679 (OUTLIER) cc_final: 0.5358 (tppt) REVERT: E 205 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8239 (tttp) REVERT: E 237 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8332 (pt) REVERT: F 172 MET cc_start: 0.7519 (tpp) cc_final: 0.6429 (ttt) REVERT: F 173 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6557 (mm) REVERT: F 277 TYR cc_start: 0.8428 (m-80) cc_final: 0.7893 (m-80) REVERT: G 138 PHE cc_start: 0.5211 (m-10) cc_final: 0.5009 (m-80) REVERT: G 172 MET cc_start: 0.7495 (tpp) cc_final: 0.6138 (ttt) REVERT: G 173 LEU cc_start: 0.6279 (mp) cc_final: 0.6037 (mm) REVERT: G 205 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8465 (tttm) REVERT: G 237 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8353 (pt) REVERT: G 280 GLN cc_start: 0.7915 (tp40) cc_final: 0.7622 (tp40) outliers start: 88 outliers final: 65 residues processed: 458 average time/residue: 0.1157 time to fit residues: 74.0597 Evaluate side-chains 450 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 375 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 299 TRP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 299 TRP Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 299 TRP Chi-restraints excluded: chain E residue 302 TRP Chi-restraints excluded: chain E residue 320 HIS Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 299 TRP Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 0.3980 chunk 106 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 86 optimal weight: 0.0030 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN C 264 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN E 234 ASN E 320 HIS ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN G 218 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.188472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.153499 restraints weight = 15815.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.156642 restraints weight = 9849.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.158386 restraints weight = 7091.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.159890 restraints weight = 5790.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.160562 restraints weight = 5016.646| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.8492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12628 Z= 0.138 Angle : 0.831 24.118 17101 Z= 0.431 Chirality : 0.044 0.256 1967 Planarity : 0.004 0.042 2149 Dihedral : 7.107 56.547 1721 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.21 % Favored : 93.21 % Rotamer: Outliers : 5.88 % Allowed : 27.98 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.16 % 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 aren not related in a simple way. whole: -0.69 (0.21), residues: 1547 helix: 1.78 (0.20), residues: 651 sheet: -2.25 (0.32), residues: 231 loop : -2.13 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 235 TYR 0.026 0.002 TYR F 174 PHE 0.012 0.001 PHE C 278 TRP 0.026 0.003 TRP E 302 HIS 0.066 0.005 HIS G 265 Details of bonding type rmsd covalent geometry : bond 0.00294 (12607) covalent geometry : angle 0.83091 (17101) hydrogen bonds : bond 0.04973 ( 574) hydrogen bonds : angle 4.42481 ( 1533) Misc. bond : bond 0.00570 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 384 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7772 (tpp) cc_final: 0.6578 (ttt) REVERT: B 161 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5397 (tppt) REVERT: B 173 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7276 (mm) REVERT: B 218 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8463 (m110) REVERT: B 235 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6806 (mmt-90) REVERT: B 237 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8057 (pt) REVERT: C 180 SER cc_start: 0.7628 (m) cc_final: 0.7369 (t) REVERT: D 161 LYS cc_start: 0.5618 (OUTLIER) cc_final: 0.5185 (tppt) REVERT: D 205 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8385 (tttm) REVERT: E 118 MET cc_start: 0.5405 (ptt) cc_final: 0.4812 (mmt) REVERT: E 161 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.5577 (tppt) REVERT: E 174 TYR cc_start: 0.6386 (t80) cc_final: 0.5881 (t80) REVERT: E 205 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8345 (tttp) REVERT: E 237 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8385 (pt) REVERT: F 172 MET cc_start: 0.7529 (tpp) cc_final: 0.6463 (ttt) REVERT: F 173 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6572 (mm) REVERT: F 277 TYR cc_start: 0.8450 (m-80) cc_final: 0.7883 (m-80) REVERT: G 172 MET cc_start: 0.7587 (tpp) cc_final: 0.7261 (tpp) REVERT: G 205 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8448 (tttm) REVERT: G 237 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8339 (pt) REVERT: G 280 GLN cc_start: 0.7919 (tp40) cc_final: 0.7705 (tp40) REVERT: G 287 ASN cc_start: 0.7855 (m-40) cc_final: 0.7566 (m-40) outliers start: 79 outliers final: 61 residues processed: 443 average time/residue: 0.1213 time to fit residues: 74.8608 Evaluate side-chains 441 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 370 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 299 TRP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 299 TRP Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 302 TRP Chi-restraints excluded: chain E residue 320 HIS Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 299 TRP Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 0.0770 chunk 151 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 126 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 7 optimal weight: 0.0770 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN G 218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.187934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.153069 restraints weight = 15713.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.156077 restraints weight = 9770.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.157832 restraints weight = 7077.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.159285 restraints weight = 5774.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.160057 restraints weight = 5006.872| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.8484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.747 12628 Z= 0.392 Angle : 1.397 59.199 17101 Z= 0.732 Chirality : 0.049 0.684 1967 Planarity : 0.009 0.216 2149 Dihedral : 7.138 56.508 1719 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.66 % Favored : 92.82 % Rotamer: Outliers : 5.36 % Allowed : 29.02 % Favored : 65.62 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.20 % 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 aren not related in a simple way. whole: -0.72 (0.21), residues: 1547 helix: 1.79 (0.20), residues: 651 sheet: -2.31 (0.32), residues: 231 loop : -2.17 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG D 231 TYR 0.024 0.002 TYR D 174 PHE 0.027 0.001 PHE B 281 TRP 0.023 0.004 TRP E 302 HIS 0.301 0.021 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00978 (12607) covalent geometry : angle 1.39658 (17101) hydrogen bonds : bond 0.05013 ( 574) hydrogen bonds : angle 4.46470 ( 1533) Misc. bond : bond 0.02285 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 366 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7769 (tpp) cc_final: 0.6587 (ttt) REVERT: B 161 LYS cc_start: 0.5998 (OUTLIER) cc_final: 0.5420 (tppt) REVERT: B 173 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7286 (mm) REVERT: B 218 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8448 (m110) REVERT: B 235 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6871 (mmt-90) REVERT: B 237 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8060 (pt) REVERT: B 312 LYS cc_start: 0.4826 (OUTLIER) cc_final: 0.4509 (mmmt) REVERT: C 180 SER cc_start: 0.7594 (m) cc_final: 0.7353 (t) REVERT: D 161 LYS cc_start: 0.5632 (OUTLIER) cc_final: 0.5221 (tppt) REVERT: D 205 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8394 (tttm) REVERT: E 118 MET cc_start: 0.5400 (ptt) cc_final: 0.4821 (mmt) REVERT: E 161 LYS cc_start: 0.5923 (OUTLIER) cc_final: 0.5614 (tppt) REVERT: E 174 TYR cc_start: 0.6355 (t80) cc_final: 0.5871 (t80) REVERT: E 205 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8353 (tttp) REVERT: E 237 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8400 (pt) REVERT: E 261 MET cc_start: 0.6471 (tmm) cc_final: 0.6226 (tmm) REVERT: F 172 MET cc_start: 0.7530 (tpp) cc_final: 0.6454 (ttt) REVERT: F 173 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6593 (mm) REVERT: F 277 TYR cc_start: 0.8422 (m-80) cc_final: 0.7969 (m-80) REVERT: F 280 GLN cc_start: 0.7745 (tp40) cc_final: 0.7502 (tp40) REVERT: G 172 MET cc_start: 0.7534 (tpp) cc_final: 0.7265 (tpp) REVERT: G 205 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8435 (tttm) REVERT: G 237 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8362 (pt) REVERT: G 279 ASN cc_start: 0.8460 (t0) cc_final: 0.8216 (m-40) REVERT: G 280 GLN cc_start: 0.7931 (tp40) cc_final: 0.7648 (tp40) REVERT: G 287 ASN cc_start: 0.7831 (m-40) cc_final: 0.7530 (m-40) outliers start: 72 outliers final: 57 residues processed: 420 average time/residue: 0.1172 time to fit residues: 69.0362 Evaluate side-chains 434 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 366 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 299 TRP Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 299 TRP Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 201 TRP Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 302 TRP Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 139 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 84 optimal weight: 0.0970 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** G 265 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 = 0.3999 r_free = 0.3999 target = 0.187576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.152870 restraints weight = 15601.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.155902 restraints weight = 9721.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.157905 restraints weight = 7033.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.159050 restraints weight = 5674.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.159877 restraints weight = 4964.166| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.8496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.961 12628 Z= 1.028 Angle : 1.391 55.358 17101 Z= 0.732 Chirality : 0.049 0.684 1967 Planarity : 0.009 0.216 2149 Dihedral : 7.138 56.508 1719 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.66 % Favored : 92.82 % Rotamer: Outliers : 5.06 % Allowed : 29.54 % Favored : 65.40 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.20 % 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 aren not related in a simple way. whole: -0.72 (0.21), residues: 1547 helix: 1.79 (0.20), residues: 651 sheet: -2.31 (0.32), residues: 231 loop : -2.17 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG D 231 TYR 0.024 0.002 TYR D 174 PHE 0.027 0.001 PHE B 281 TRP 0.023 0.004 TRP E 302 HIS 0.301 0.021 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00978 (12607) covalent geometry : angle 1.39082 (17101) hydrogen bonds : bond 0.05013 ( 574) hydrogen bonds : angle 4.46470 ( 1533) Misc. bond : bond 0.23434 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2252.16 seconds wall clock time: 39 minutes 39.66 seconds (2379.66 seconds total)