Starting phenix.real_space_refine on Wed Jul 30 03:37:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5y4o_6805/07_2025/5y4o_6805.cif Found real_map, /net/cci-nas-00/data/ceres_data/5y4o_6805/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5y4o_6805/07_2025/5y4o_6805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5y4o_6805/07_2025/5y4o_6805.map" model { file = "/net/cci-nas-00/data/ceres_data/5y4o_6805/07_2025/5y4o_6805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5y4o_6805/07_2025/5y4o_6805.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.44, per 1000 atoms: 0.60 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: 3.32 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.07 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: 3.02 Time building geometry restraints manager: 3.80 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.250 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.130 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.031 0.004 TRP C 184 HIS 0.048 0.012 HIS F 137 PHE 0.096 0.008 PHE C 138 TYR 0.069 0.007 TYR D 134 ARG 0.074 0.005 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.27375 ( 574) hydrogen bonds : angle 9.83626 ( 1533) covalent geometry : bond 0.02223 (12607) covalent geometry : angle 2.44237 (17101) 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 : 1.434 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: 0.2522 time to fit residues: 210.4803 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 : 1.411 ------------------------------------------------------------------------------- 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 130 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 211 ASN C 218 ASN C 272 GLN C 307 GLN D 218 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 280 GLN E 264 ASN E 272 GLN E 280 GLN E 320 HIS F 272 GLN F 280 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.188490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.155416 restraints weight = 15899.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.158427 restraints weight = 9105.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.160405 restraints weight = 6189.885| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12628 Z= 0.232 Angle : 0.854 11.146 17101 Z= 0.461 Chirality : 0.048 0.198 1967 Planarity : 0.007 0.076 2149 Dihedral : 14.500 74.927 2004 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.90 % Allowed : 5.82 % Favored : 93.28 % Rotamer: Outliers : 8.85 % Allowed : 17.41 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.86 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.20), residues: 1547 helix: 0.22 (0.19), residues: 630 sheet: -2.17 (0.36), residues: 224 loop : -1.41 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP G 184 HIS 0.021 0.004 HIS A 265 PHE 0.018 0.003 PHE G 278 TYR 0.021 0.002 TYR D 310 ARG 0.017 0.001 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.06951 ( 574) hydrogen bonds : angle 5.61068 ( 1533) covalent geometry : bond 0.00473 (12607) covalent geometry : angle 0.85447 (17101) Misc. bond : bond 0.00402 ( 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 577 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 458 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.2486 (mtt) cc_final: 0.2059 (mtt) REVERT: A 158 MET cc_start: 0.4529 (mmt) cc_final: 0.4228 (mmt) REVERT: A 172 MET cc_start: 0.7729 (tpp) cc_final: 0.6515 (ttp) REVERT: A 179 PHE cc_start: 0.5871 (p90) cc_final: 0.5553 (p90) REVERT: A 180 SER cc_start: 0.6424 (m) cc_final: 0.5953 (t) REVERT: A 268 ILE cc_start: 0.7705 (mp) cc_final: 0.7300 (mt) REVERT: B 140 MET cc_start: 0.2632 (mtt) cc_final: 0.1961 (mtt) REVERT: B 173 LEU cc_start: 0.7431 (tt) cc_final: 0.7065 (mm) REVERT: B 180 SER cc_start: 0.6535 (m) cc_final: 0.5942 (t) REVERT: B 275 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8038 (mp) REVERT: B 329 GLN cc_start: 0.7940 (mt0) cc_final: 0.7649 (mt0) REVERT: C 158 MET cc_start: 0.4911 (mmt) cc_final: 0.4575 (mmt) REVERT: C 180 SER cc_start: 0.6297 (m) cc_final: 0.5769 (t) REVERT: C 234 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7301 (m110) REVERT: D 140 MET cc_start: 0.2430 (mtt) cc_final: 0.2047 (ttm) REVERT: D 173 LEU cc_start: 0.6727 (tp) cc_final: 0.6484 (mm) REVERT: D 180 SER cc_start: 0.6567 (m) cc_final: 0.5799 (t) REVERT: E 180 SER cc_start: 0.6696 (m) cc_final: 0.6215 (t) REVERT: E 237 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8233 (pt) REVERT: E 277 TYR cc_start: 0.8663 (m-80) cc_final: 0.8136 (m-80) REVERT: E 281 PHE cc_start: 0.8795 (t80) cc_final: 0.8515 (t80) REVERT: E 284 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8379 (t) REVERT: E 314 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7676 (tt) REVERT: F 118 MET cc_start: 0.4439 (ptt) cc_final: 0.4155 (ptp) REVERT: F 140 MET cc_start: 0.2791 (mtt) cc_final: 0.2316 (mtt) REVERT: F 250 LYS cc_start: 0.5238 (ptmt) cc_final: 0.4691 (pttt) REVERT: F 277 TYR cc_start: 0.8346 (m-80) cc_final: 0.8002 (m-80) REVERT: G 158 MET cc_start: 0.3917 (OUTLIER) cc_final: 0.3693 (mmt) REVERT: G 172 MET cc_start: 0.7370 (tpp) cc_final: 0.6301 (ttt) REVERT: G 180 SER cc_start: 0.6739 (m) cc_final: 0.6375 (t) REVERT: G 250 LYS cc_start: 0.6089 (ptmt) cc_final: 0.5814 (pttt) REVERT: G 314 ILE cc_start: 0.7835 (tt) cc_final: 0.7565 (tt) outliers start: 119 outliers final: 56 residues processed: 510 average time/residue: 0.2554 time to fit residues: 184.4640 Evaluate side-chains 423 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 361 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 247 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 326 PHE 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 275 LEU 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 234 ASN 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 254 ILE 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 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 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 236 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 247 ASP 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 296 THR Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain G residue 158 MET 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 247 ASP Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 286 LEU 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 49 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 0.0670 overall best weight: 1.5124 ------------------------------------------------------------------------------- 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 218 ASN D 280 GLN ** 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 320 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.190379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.156813 restraints weight = 15895.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.159830 restraints weight = 9295.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.161702 restraints weight = 6401.945| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12628 Z= 0.164 Angle : 0.702 7.952 17101 Z= 0.380 Chirality : 0.042 0.200 1967 Planarity : 0.005 0.031 2149 Dihedral : 9.916 73.478 1788 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.14 % Favored : 92.95 % Rotamer: Outliers : 9.08 % Allowed : 19.20 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 1547 helix: 0.99 (0.19), residues: 637 sheet: -2.08 (0.36), residues: 224 loop : -1.88 (0.20), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP G 184 HIS 0.007 0.002 HIS A 265 PHE 0.019 0.002 PHE G 278 TYR 0.018 0.002 TYR G 174 ARG 0.026 0.001 ARG G 235 Details of bonding type rmsd hydrogen bonds : bond 0.05510 ( 574) hydrogen bonds : angle 4.91662 ( 1533) covalent geometry : bond 0.00347 (12607) covalent geometry : angle 0.70236 (17101) Misc. bond : bond 0.00293 ( 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 542 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 420 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7701 (tpp) cc_final: 0.6351 (ttt) REVERT: A 179 PHE cc_start: 0.5810 (p90) cc_final: 0.5581 (p90) REVERT: A 180 SER cc_start: 0.6584 (m) cc_final: 0.6233 (t) REVERT: A 215 TYR cc_start: 0.8517 (m-80) cc_final: 0.8300 (m-80) REVERT: A 268 ILE cc_start: 0.7785 (mp) cc_final: 0.7480 (mt) REVERT: A 281 PHE cc_start: 0.8664 (t80) cc_final: 0.8337 (t80) REVERT: B 173 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7058 (mm) REVERT: B 232 MET cc_start: 0.7910 (mtt) cc_final: 0.7616 (mtt) REVERT: B 237 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8165 (pt) REVERT: C 140 MET cc_start: 0.2655 (mtt) cc_final: 0.2308 (ttm) REVERT: C 174 TYR cc_start: 0.6335 (t80) cc_final: 0.5987 (t80) REVERT: C 180 SER cc_start: 0.6235 (m) cc_final: 0.5627 (t) REVERT: C 186 ARG cc_start: 0.7354 (ttt90) cc_final: 0.7072 (ttt90) REVERT: C 234 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7733 (m110) REVERT: C 301 GLU cc_start: 0.6470 (mm-30) cc_final: 0.6195 (mm-30) REVERT: D 173 LEU cc_start: 0.6891 (tp) cc_final: 0.6504 (mm) REVERT: D 180 SER cc_start: 0.7033 (m) cc_final: 0.6368 (t) REVERT: D 235 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7133 (mmt-90) REVERT: D 329 GLN cc_start: 0.8142 (mt0) cc_final: 0.7917 (mt0) REVERT: E 118 MET cc_start: 0.5426 (ptt) cc_final: 0.5046 (mmt) REVERT: E 180 SER cc_start: 0.6945 (m) cc_final: 0.6689 (t) REVERT: E 237 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8230 (pt) REVERT: E 281 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8566 (t80) REVERT: F 118 MET cc_start: 0.5308 (ptt) cc_final: 0.5069 (ptp) REVERT: F 158 MET cc_start: 0.4718 (mmt) cc_final: 0.4488 (mmt) REVERT: F 172 MET cc_start: 0.7642 (tpp) cc_final: 0.6486 (ttt) REVERT: F 277 TYR cc_start: 0.8275 (m-80) cc_final: 0.7698 (m-80) REVERT: G 172 MET cc_start: 0.7460 (tpp) cc_final: 0.6226 (ttp) REVERT: G 180 SER cc_start: 0.6691 (m) cc_final: 0.6281 (t) REVERT: G 237 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8346 (pt) outliers start: 122 outliers final: 81 residues processed: 483 average time/residue: 0.2508 time to fit residues: 168.8336 Evaluate side-chains 460 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 372 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE 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 254 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 LEU 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 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 254 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 VAL 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 137 HIS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 235 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 254 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 206 ILE 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 254 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 284 SER 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 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 206 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 239 THR 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 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 240 THR 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 296 THR 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 237 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 254 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 50 optimal weight: 0.0980 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 HIS E 218 ASN ** E 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN F 218 ASN ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN G 218 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.185545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.151629 restraints weight = 15989.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.154570 restraints weight = 9374.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.156418 restraints weight = 6504.555| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12628 Z= 0.203 Angle : 0.749 13.752 17101 Z= 0.404 Chirality : 0.044 0.196 1967 Planarity : 0.006 0.085 2149 Dihedral : 8.172 58.562 1759 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.24 % Favored : 91.86 % Rotamer: Outliers : 10.42 % Allowed : 20.76 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1547 helix: 1.13 (0.19), residues: 644 sheet: -2.07 (0.36), residues: 224 loop : -2.02 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP B 302 HIS 0.021 0.002 HIS D 265 PHE 0.013 0.002 PHE B 326 TYR 0.019 0.001 TYR B 174 ARG 0.012 0.001 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.05630 ( 574) hydrogen bonds : angle 4.64016 ( 1533) covalent geometry : bond 0.00448 (12607) covalent geometry : angle 0.74919 (17101) Misc. bond : bond 0.00489 ( 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 560 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 420 time to evaluate : 1.443 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: A 172 MET cc_start: 0.7779 (tpp) cc_final: 0.6738 (ttp) REVERT: A 174 TYR cc_start: 0.6289 (t80) cc_final: 0.6030 (t80) REVERT: A 179 PHE cc_start: 0.6103 (p90) cc_final: 0.5832 (p90) REVERT: A 284 SER cc_start: 0.8405 (p) cc_final: 0.8031 (t) REVERT: B 161 LYS cc_start: 0.5373 (OUTLIER) cc_final: 0.4584 (tppt) REVERT: B 173 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6901 (mm) REVERT: B 237 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8439 (pt) REVERT: C 161 LYS cc_start: 0.5664 (OUTLIER) cc_final: 0.5208 (tppt) REVERT: C 174 TYR cc_start: 0.6490 (t80) cc_final: 0.6181 (t80) REVERT: C 301 GLU cc_start: 0.6543 (mm-30) cc_final: 0.6284 (mm-30) REVERT: D 161 LYS cc_start: 0.5506 (OUTLIER) cc_final: 0.4763 (tppt) REVERT: D 173 LEU cc_start: 0.6908 (tp) cc_final: 0.6484 (mm) REVERT: D 174 TYR cc_start: 0.6144 (t80) cc_final: 0.5792 (t80) REVERT: D 284 SER cc_start: 0.8159 (p) cc_final: 0.7836 (t) REVERT: E 118 MET cc_start: 0.5463 (ptt) cc_final: 0.5049 (ptm) REVERT: E 161 LYS cc_start: 0.5468 (OUTLIER) cc_final: 0.4700 (tppt) REVERT: E 237 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8471 (pt) REVERT: E 277 TYR cc_start: 0.8644 (m-80) cc_final: 0.8216 (m-80) REVERT: E 281 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8578 (t80) REVERT: F 161 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.5115 (tppt) REVERT: G 138 PHE cc_start: 0.5740 (m-10) cc_final: 0.5459 (m-80) REVERT: G 161 LYS cc_start: 0.5164 (OUTLIER) cc_final: 0.4563 (tppt) REVERT: G 172 MET cc_start: 0.7362 (tpp) cc_final: 0.6154 (ttt) REVERT: G 180 SER cc_start: 0.7047 (m) cc_final: 0.6808 (t) REVERT: G 237 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8414 (pt) REVERT: G 280 GLN cc_start: 0.7840 (tp40) cc_final: 0.7122 (tp40) REVERT: G 287 ASN cc_start: 0.8277 (m110) cc_final: 0.7900 (m-40) REVERT: G 329 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8262 (mt0) outliers start: 140 outliers final: 87 residues processed: 517 average time/residue: 0.2565 time to fit residues: 184.9161 Evaluate side-chains 463 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 365 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE 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 223 SER 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 246 GLU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 285 SER 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 225 SER 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 284 SER Chi-restraints excluded: chain B residue 285 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 B residue 330 THR Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 233 THR 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 264 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE 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 237 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 285 SER 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 163 ILE 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 237 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU 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 206 ILE Chi-restraints excluded: chain F residue 214 LEU 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 285 SER 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 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 238 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 285 SER 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 88 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN E 218 ASN ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.185540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.152417 restraints weight = 15909.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.155384 restraints weight = 9341.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.157136 restraints weight = 6475.947| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12628 Z= 0.163 Angle : 0.734 14.268 17101 Z= 0.388 Chirality : 0.043 0.193 1967 Planarity : 0.004 0.037 2149 Dihedral : 7.610 57.607 1734 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.33 % Favored : 92.76 % Rotamer: Outliers : 8.56 % Allowed : 25.07 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.21), residues: 1547 helix: 1.32 (0.19), residues: 651 sheet: -2.36 (0.35), residues: 217 loop : -2.13 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 302 HIS 0.043 0.004 HIS F 265 PHE 0.018 0.001 PHE C 278 TYR 0.019 0.001 TYR G 174 ARG 0.007 0.001 ARG E 271 Details of bonding type rmsd hydrogen bonds : bond 0.05208 ( 574) hydrogen bonds : angle 4.48897 ( 1533) covalent geometry : bond 0.00352 (12607) covalent geometry : angle 0.73421 (17101) Misc. bond : bond 0.00482 ( 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 507 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 392 time to evaluate : 1.391 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: A 138 PHE cc_start: 0.5628 (m-10) cc_final: 0.5283 (m-80) REVERT: A 172 MET cc_start: 0.7854 (tpp) cc_final: 0.6510 (ttt) REVERT: A 207 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8923 (p) REVERT: A 270 GLN cc_start: 0.8301 (pm20) cc_final: 0.8048 (pm20) REVERT: B 173 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6957 (mm) REVERT: B 235 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7028 (mmt-90) REVERT: B 237 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8355 (pt) REVERT: B 277 TYR cc_start: 0.8154 (m-80) cc_final: 0.7851 (m-10) REVERT: C 161 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.5450 (tppt) REVERT: C 174 TYR cc_start: 0.6510 (t80) cc_final: 0.5943 (t80) REVERT: C 301 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6195 (mm-30) REVERT: D 140 MET cc_start: 0.1940 (ttm) cc_final: 0.1735 (ttp) REVERT: D 173 LEU cc_start: 0.6946 (tp) cc_final: 0.6515 (mm) REVERT: D 205 LYS cc_start: 0.8977 (mtpp) cc_final: 0.8573 (tttm) REVERT: D 228 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8492 (p0) REVERT: D 235 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6972 (mmt-90) REVERT: E 118 MET cc_start: 0.5222 (ptt) cc_final: 0.4883 (ptm) REVERT: E 161 LYS cc_start: 0.5433 (OUTLIER) cc_final: 0.4949 (tppt) REVERT: E 237 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8441 (pt) REVERT: E 263 LYS cc_start: 0.7444 (mmtm) cc_final: 0.7238 (mmtp) REVERT: E 277 TYR cc_start: 0.8668 (m-80) cc_final: 0.8101 (m-80) REVERT: F 161 LYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5134 (tppt) REVERT: F 172 MET cc_start: 0.7823 (tpp) cc_final: 0.6664 (ttt) REVERT: G 138 PHE cc_start: 0.5777 (m-10) cc_final: 0.5537 (m-80) REVERT: G 161 LYS cc_start: 0.5206 (OUTLIER) cc_final: 0.4738 (tppt) REVERT: G 172 MET cc_start: 0.7457 (tpp) cc_final: 0.6061 (ttt) REVERT: G 173 LEU cc_start: 0.6417 (mp) cc_final: 0.6109 (mm) REVERT: G 180 SER cc_start: 0.7285 (m) cc_final: 0.6871 (t) REVERT: G 237 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8437 (pt) REVERT: G 280 GLN cc_start: 0.7810 (tp40) cc_final: 0.7164 (tp40) outliers start: 115 outliers final: 81 residues processed: 472 average time/residue: 0.2599 time to fit residues: 170.1913 Evaluate side-chains 460 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 367 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 223 SER 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 285 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER 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 225 SER 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 240 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 285 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 161 LYS 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 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 C residue 326 PHE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 163 ILE 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 228 ASN Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 264 ASN 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 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 163 ILE 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 222 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 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 164 LEU Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 218 ASN 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 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 F residue 330 THR Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 222 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 268 ILE Chi-restraints excluded: chain G residue 285 SER 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 21 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- 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** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN E 228 ASN ** E 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN G 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.181117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.148372 restraints weight = 16026.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.151367 restraints weight = 9333.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.153249 restraints weight = 6404.010| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.7839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12628 Z= 0.196 Angle : 0.748 13.600 17101 Z= 0.397 Chirality : 0.044 0.170 1967 Planarity : 0.005 0.058 2149 Dihedral : 7.578 57.333 1734 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.56 % Favored : 91.53 % Rotamer: Outliers : 8.48 % Allowed : 25.82 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.21), residues: 1547 helix: 1.43 (0.19), residues: 637 sheet: -2.09 (0.35), residues: 224 loop : -2.11 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 184 HIS 0.013 0.002 HIS A 265 PHE 0.014 0.002 PHE C 278 TYR 0.024 0.002 TYR B 174 ARG 0.011 0.001 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.05369 ( 574) hydrogen bonds : angle 4.54299 ( 1533) covalent geometry : bond 0.00434 (12607) covalent geometry : angle 0.74760 (17101) Misc. bond : bond 0.00413 ( 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 496 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 382 time to evaluate : 1.326 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: A 138 PHE cc_start: 0.5678 (m-10) cc_final: 0.5324 (m-80) REVERT: A 172 MET cc_start: 0.7770 (tpp) cc_final: 0.6668 (ttp) REVERT: A 174 TYR cc_start: 0.6252 (t80) cc_final: 0.5761 (t80) REVERT: B 158 MET cc_start: 0.5179 (mmt) cc_final: 0.4732 (mmp) REVERT: B 161 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.4860 (tppt) REVERT: B 173 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7193 (mm) REVERT: B 201 TRP cc_start: 0.7572 (m100) cc_final: 0.7248 (m100) REVERT: B 235 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7001 (mmt-90) REVERT: B 237 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8379 (pt) REVERT: B 277 TYR cc_start: 0.8326 (m-80) cc_final: 0.8071 (m-10) REVERT: C 161 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.5625 (tppt) REVERT: D 161 LYS cc_start: 0.5496 (OUTLIER) cc_final: 0.4992 (tppt) REVERT: D 173 LEU cc_start: 0.7238 (tp) cc_final: 0.6768 (mm) REVERT: D 205 LYS cc_start: 0.9000 (mtpp) cc_final: 0.8481 (tttm) REVERT: D 235 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7225 (mmt-90) REVERT: D 247 ASP cc_start: 0.5738 (m-30) cc_final: 0.5446 (m-30) REVERT: D 333 MET cc_start: 0.5601 (mmm) cc_final: 0.5348 (mmm) REVERT: E 161 LYS cc_start: 0.5647 (OUTLIER) cc_final: 0.4978 (tppt) REVERT: E 237 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8476 (pt) REVERT: E 277 TYR cc_start: 0.8642 (m-80) cc_final: 0.8288 (m-80) REVERT: F 161 LYS cc_start: 0.5653 (OUTLIER) cc_final: 0.4850 (tppt) REVERT: F 173 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6524 (mm) REVERT: G 138 PHE cc_start: 0.5319 (m-10) cc_final: 0.5102 (m-80) REVERT: G 161 LYS cc_start: 0.5398 (OUTLIER) cc_final: 0.4786 (tppt) REVERT: G 172 MET cc_start: 0.7499 (tpp) cc_final: 0.6161 (ttt) REVERT: G 173 LEU cc_start: 0.6320 (mp) cc_final: 0.5990 (mm) REVERT: G 180 SER cc_start: 0.7493 (m) cc_final: 0.7069 (t) REVERT: G 205 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8448 (mtpp) REVERT: G 237 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8528 (pt) REVERT: G 280 GLN cc_start: 0.7851 (tp40) cc_final: 0.7276 (tp40) outliers start: 114 outliers final: 87 residues processed: 463 average time/residue: 0.2579 time to fit residues: 165.8033 Evaluate side-chains 450 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 350 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE 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 223 SER 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 285 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 147 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 225 SER 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 284 SER Chi-restraints excluded: chain B residue 285 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 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 199 ILE Chi-restraints excluded: chain C residue 223 SER 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 239 THR Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 223 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 285 SER 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 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 235 ARG Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 239 THR 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 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 164 LEU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 303 LEU 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 161 LYS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 222 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 290 VAL Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 140 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 C 137 HIS ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN ** E 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 228 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.179402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.146784 restraints weight = 15795.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.149711 restraints weight = 9451.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.151624 restraints weight = 6632.091| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.8178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12628 Z= 0.202 Angle : 0.818 17.661 17101 Z= 0.424 Chirality : 0.045 0.235 1967 Planarity : 0.005 0.068 2149 Dihedral : 7.507 58.979 1727 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.50 % Favored : 91.60 % Rotamer: Outliers : 8.78 % Allowed : 26.56 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1547 helix: 1.44 (0.19), residues: 637 sheet: -2.12 (0.35), residues: 224 loop : -2.17 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 302 HIS 0.015 0.002 HIS C 265 PHE 0.020 0.002 PHE E 138 TYR 0.033 0.002 TYR D 174 ARG 0.010 0.001 ARG G 244 Details of bonding type rmsd hydrogen bonds : bond 0.05389 ( 574) hydrogen bonds : angle 4.56286 ( 1533) covalent geometry : bond 0.00445 (12607) covalent geometry : angle 0.81806 (17101) Misc. bond : bond 0.00519 ( 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 499 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 381 time to evaluate : 1.495 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: A 138 PHE cc_start: 0.5848 (m-10) cc_final: 0.5554 (m-80) REVERT: A 172 MET cc_start: 0.7652 (tpp) cc_final: 0.6360 (ttt) REVERT: A 174 TYR cc_start: 0.6234 (t80) cc_final: 0.5787 (t80) REVERT: A 235 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7233 (mmt-90) REVERT: A 291 TYR cc_start: 0.8293 (t80) cc_final: 0.7929 (t80) REVERT: B 137 HIS cc_start: 0.5802 (t-90) cc_final: 0.5447 (t70) REVERT: B 161 LYS cc_start: 0.5584 (OUTLIER) cc_final: 0.4947 (tppt) REVERT: B 173 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7180 (mm) REVERT: B 201 TRP cc_start: 0.7532 (m100) cc_final: 0.7315 (m100) REVERT: B 205 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8710 (tttm) REVERT: B 235 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6994 (mmt-90) REVERT: B 237 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8414 (pt) REVERT: B 277 TYR cc_start: 0.8400 (m-80) cc_final: 0.8172 (m-10) REVERT: C 161 LYS cc_start: 0.5902 (OUTLIER) cc_final: 0.5656 (tppt) REVERT: C 174 TYR cc_start: 0.6469 (t80) cc_final: 0.6112 (t80) REVERT: C 244 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7447 (mtm-85) REVERT: C 333 MET cc_start: 0.5867 (mmm) cc_final: 0.5660 (mmp) REVERT: D 161 LYS cc_start: 0.5703 (OUTLIER) cc_final: 0.5134 (tppt) REVERT: D 173 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6876 (mm) REVERT: D 205 LYS cc_start: 0.9000 (mtpp) cc_final: 0.8452 (tttm) REVERT: D 235 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7101 (mmt-90) REVERT: D 333 MET cc_start: 0.5842 (mmm) cc_final: 0.5602 (mmm) REVERT: E 161 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.4930 (tppt) REVERT: E 237 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8562 (pt) REVERT: F 161 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5149 (tppt) REVERT: F 173 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6608 (mm) REVERT: F 277 TYR cc_start: 0.8464 (m-80) cc_final: 0.7762 (m-80) REVERT: G 172 MET cc_start: 0.7544 (tpp) cc_final: 0.6156 (ttt) REVERT: G 173 LEU cc_start: 0.6592 (mp) cc_final: 0.6175 (mm) REVERT: G 180 SER cc_start: 0.7632 (m) cc_final: 0.7417 (t) REVERT: G 205 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8456 (tttm) REVERT: G 234 ASN cc_start: 0.8398 (m110) cc_final: 0.8179 (m110) REVERT: G 280 GLN cc_start: 0.7891 (tp40) cc_final: 0.7374 (tp40) outliers start: 118 outliers final: 86 residues processed: 463 average time/residue: 0.2562 time to fit residues: 164.9708 Evaluate side-chains 463 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 364 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 223 SER 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 285 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 147 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 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 239 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 285 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 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 199 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 223 SER 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 268 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 223 SER 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 290 VAL Chi-restraints excluded: chain D residue 292 CYS 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 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 223 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 284 SER 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 E residue 330 THR Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 164 LEU 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 223 SER Chi-restraints excluded: chain F residue 237 ILE 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 F residue 330 THR Chi-restraints excluded: chain G residue 158 MET 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 268 ILE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 289 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 296 THR 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 28 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS C 264 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN D 228 ASN E 218 ASN ** E 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.183967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.151445 restraints weight = 15820.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.154450 restraints weight = 9192.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.156411 restraints weight = 6321.647| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.8392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12628 Z= 0.153 Angle : 0.789 21.055 17101 Z= 0.419 Chirality : 0.044 0.221 1967 Planarity : 0.004 0.051 2149 Dihedral : 7.384 57.010 1723 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.92 % Favored : 92.18 % Rotamer: Outliers : 8.33 % Allowed : 26.56 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1547 helix: 1.60 (0.20), residues: 637 sheet: -2.10 (0.34), residues: 224 loop : -2.16 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 302 HIS 0.022 0.003 HIS B 265 PHE 0.012 0.001 PHE C 278 TYR 0.024 0.001 TYR F 174 ARG 0.007 0.001 ARG G 244 Details of bonding type rmsd hydrogen bonds : bond 0.05271 ( 574) hydrogen bonds : angle 4.47082 ( 1533) covalent geometry : bond 0.00329 (12607) covalent geometry : angle 0.78865 (17101) Misc. bond : bond 0.00495 ( 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 490 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 378 time to evaluate : 1.315 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 138 PHE cc_start: 0.5873 (m-10) cc_final: 0.5578 (m-80) REVERT: A 172 MET cc_start: 0.7790 (tpp) cc_final: 0.6520 (ttt) REVERT: A 207 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9006 (p) REVERT: A 291 TYR cc_start: 0.8188 (t80) cc_final: 0.7830 (t80) REVERT: B 137 HIS cc_start: 0.5847 (t-90) cc_final: 0.5504 (t70) REVERT: B 158 MET cc_start: 0.4979 (OUTLIER) cc_final: 0.4474 (mmp) REVERT: B 161 LYS cc_start: 0.5611 (OUTLIER) cc_final: 0.5106 (tppt) REVERT: B 173 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7204 (mm) REVERT: B 205 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8696 (tttm) REVERT: B 235 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6855 (mmt-90) REVERT: B 237 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8284 (pt) REVERT: B 277 TYR cc_start: 0.8399 (m-80) cc_final: 0.8152 (m-10) REVERT: C 161 LYS cc_start: 0.5949 (OUTLIER) cc_final: 0.5632 (tppt) REVERT: D 161 LYS cc_start: 0.5546 (OUTLIER) cc_final: 0.4933 (tppt) REVERT: D 173 LEU cc_start: 0.7078 (tp) cc_final: 0.6622 (mm) REVERT: D 205 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8454 (tttm) REVERT: D 235 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7005 (mmt-90) REVERT: D 333 MET cc_start: 0.5801 (mmm) cc_final: 0.5549 (mmm) REVERT: E 161 LYS cc_start: 0.5745 (OUTLIER) cc_final: 0.5391 (tppt) REVERT: E 237 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8431 (pt) REVERT: F 161 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5192 (tppt) REVERT: F 173 LEU cc_start: 0.7040 (tp) cc_final: 0.6661 (mm) REVERT: F 277 TYR cc_start: 0.8569 (m-80) cc_final: 0.7932 (m-80) REVERT: G 172 MET cc_start: 0.7584 (tpp) cc_final: 0.6264 (ttt) REVERT: G 173 LEU cc_start: 0.6201 (mp) cc_final: 0.5945 (mm) REVERT: G 180 SER cc_start: 0.7647 (m) cc_final: 0.7447 (t) REVERT: G 205 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8393 (tttm) REVERT: G 237 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8424 (pt) REVERT: G 280 GLN cc_start: 0.8073 (tp40) cc_final: 0.7618 (tp40) outliers start: 112 outliers final: 79 residues processed: 460 average time/residue: 0.2559 time to fit residues: 162.9314 Evaluate side-chains 450 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 358 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 207 THR Chi-restraints excluded: chain A residue 223 SER 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 290 VAL Chi-restraints excluded: chain A residue 296 THR 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 158 MET 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 225 SER 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 285 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 223 SER 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 268 ILE Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 264 ASN 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 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 223 SER Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 235 ARG 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 328 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 246 GLU 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 158 MET 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 235 ARG 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 285 SER Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 320 HIS ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN ** E 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.180615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.148298 restraints weight = 16010.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.151277 restraints weight = 9287.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.153220 restraints weight = 6396.167| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.8631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 12628 Z= 0.209 Angle : 0.904 24.919 17101 Z= 0.475 Chirality : 0.047 0.377 1967 Planarity : 0.005 0.066 2149 Dihedral : 7.651 59.865 1721 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.76 % Favored : 91.34 % Rotamer: Outliers : 7.37 % Allowed : 27.46 % Favored : 65.18 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.21), residues: 1547 helix: 1.46 (0.19), residues: 637 sheet: -2.30 (0.34), residues: 231 loop : -2.15 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP E 201 HIS 0.096 0.006 HIS G 265 PHE 0.014 0.002 PHE E 221 TYR 0.028 0.002 TYR F 174 ARG 0.012 0.001 ARG D 271 Details of bonding type rmsd hydrogen bonds : bond 0.05584 ( 574) hydrogen bonds : angle 4.64640 ( 1533) covalent geometry : bond 0.00469 (12607) covalent geometry : angle 0.90438 (17101) Misc. bond : bond 0.00738 ( 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: 99 poor density : 364 time to evaluate : 1.417 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 138 PHE cc_start: 0.5922 (m-10) cc_final: 0.5718 (m-80) REVERT: A 172 MET cc_start: 0.7596 (tpp) cc_final: 0.6292 (ttt) REVERT: A 191 ASN cc_start: 0.6837 (t0) cc_final: 0.6601 (t0) REVERT: A 207 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9046 (p) REVERT: A 291 TYR cc_start: 0.8184 (t80) cc_final: 0.7854 (t80) REVERT: B 158 MET cc_start: 0.5117 (OUTLIER) cc_final: 0.4594 (mmp) REVERT: B 161 LYS cc_start: 0.5618 (OUTLIER) cc_final: 0.5319 (tppt) REVERT: B 173 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7047 (mm) REVERT: B 205 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8613 (tttm) REVERT: B 235 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7146 (mmt-90) REVERT: B 237 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8378 (pt) REVERT: B 277 TYR cc_start: 0.8473 (m-80) cc_final: 0.8225 (m-10) REVERT: C 161 LYS cc_start: 0.5831 (OUTLIER) cc_final: 0.5586 (tppt) REVERT: C 174 TYR cc_start: 0.6575 (t80) cc_final: 0.6199 (t80) REVERT: C 222 SER cc_start: 0.8824 (m) cc_final: 0.8526 (p) REVERT: C 333 MET cc_start: 0.5872 (mmm) cc_final: 0.5624 (mmp) REVERT: D 161 LYS cc_start: 0.5569 (OUTLIER) cc_final: 0.4901 (tppt) REVERT: D 173 LEU cc_start: 0.6931 (tp) cc_final: 0.6583 (mm) REVERT: D 205 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8620 (tttm) REVERT: D 235 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6974 (mmt-90) REVERT: D 333 MET cc_start: 0.5906 (mmm) cc_final: 0.5673 (mmm) REVERT: E 158 MET cc_start: 0.5590 (mmt) cc_final: 0.4941 (mmt) REVERT: E 174 TYR cc_start: 0.6736 (t80) cc_final: 0.6063 (t80) REVERT: E 237 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8539 (pt) REVERT: F 137 HIS cc_start: 0.6576 (OUTLIER) cc_final: 0.6135 (t-90) REVERT: F 140 MET cc_start: 0.1647 (ttm) cc_final: 0.1322 (ttm) REVERT: F 161 LYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5366 (tppt) REVERT: F 173 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6803 (mm) REVERT: F 277 TYR cc_start: 0.8472 (m-80) cc_final: 0.7797 (m-80) REVERT: G 173 LEU cc_start: 0.6269 (mp) cc_final: 0.6016 (mm) REVERT: G 180 SER cc_start: 0.7721 (m) cc_final: 0.7422 (t) REVERT: G 205 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8479 (tttm) REVERT: G 280 GLN cc_start: 0.8071 (tp40) cc_final: 0.7705 (tp40) outliers start: 99 outliers final: 78 residues processed: 435 average time/residue: 0.2611 time to fit residues: 158.0739 Evaluate side-chains 442 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 351 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 158 MET 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 285 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 223 SER 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 268 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE 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 275 LEU Chi-restraints excluded: chain D residue 279 ASN 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 328 SER Chi-restraints excluded: chain E residue 147 THR 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 223 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 284 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 164 LEU 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 223 SER Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 246 GLU 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 296 THR 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 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 268 ILE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 74 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 145 optimal weight: 0.8980 chunk 112 optimal weight: 0.0000 chunk 63 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 130 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 overall best weight: 0.3902 ------------------------------------------------------------------------------- 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 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN D 228 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.186896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.155594 restraints weight = 15789.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.158628 restraints weight = 9349.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.160702 restraints weight = 6487.395| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.8809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12628 Z= 0.153 Angle : 0.948 25.730 17101 Z= 0.486 Chirality : 0.045 0.342 1967 Planarity : 0.005 0.067 2149 Dihedral : 7.410 59.454 1719 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.27 % Favored : 92.82 % Rotamer: Outliers : 5.36 % Allowed : 29.69 % Favored : 64.96 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.21), residues: 1547 helix: 1.72 (0.20), residues: 637 sheet: -2.41 (0.32), residues: 231 loop : -2.20 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 302 HIS 0.101 0.006 HIS G 265 PHE 0.012 0.001 PHE F 278 TYR 0.027 0.001 TYR F 174 ARG 0.011 0.001 ARG D 271 Details of bonding type rmsd hydrogen bonds : bond 0.05333 ( 574) hydrogen bonds : angle 4.51991 ( 1533) covalent geometry : bond 0.00322 (12607) covalent geometry : angle 0.94772 (17101) Misc. bond : bond 0.00761 ( 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 454 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 382 time to evaluate : 1.407 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: A 138 PHE cc_start: 0.5846 (m-10) cc_final: 0.5585 (m-80) REVERT: A 172 MET cc_start: 0.7723 (tpp) cc_final: 0.6485 (ttt) REVERT: B 158 MET cc_start: 0.5011 (OUTLIER) cc_final: 0.4511 (mmt) REVERT: B 173 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7021 (mm) REVERT: B 205 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8572 (tttm) REVERT: B 237 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8064 (pt) REVERT: B 277 TYR cc_start: 0.8442 (m-80) cc_final: 0.8159 (m-10) REVERT: C 333 MET cc_start: 0.5953 (mmm) cc_final: 0.5612 (mmp) REVERT: D 161 LYS cc_start: 0.5595 (OUTLIER) cc_final: 0.5031 (tppt) REVERT: D 173 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6461 (mm) REVERT: D 205 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8466 (tttm) REVERT: D 236 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7473 (ttm170) REVERT: D 280 GLN cc_start: 0.8559 (tp40) cc_final: 0.8153 (tm-30) REVERT: D 289 MET cc_start: 0.8020 (tmm) cc_final: 0.7806 (tmm) REVERT: D 333 MET cc_start: 0.5842 (mmm) cc_final: 0.5641 (mmm) REVERT: E 174 TYR cc_start: 0.6505 (t80) cc_final: 0.5877 (t80) REVERT: E 237 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8410 (pt) REVERT: F 161 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.5340 (tppt) REVERT: F 173 LEU cc_start: 0.7184 (tp) cc_final: 0.6758 (mm) REVERT: F 277 TYR cc_start: 0.8544 (m-80) cc_final: 0.7953 (m-80) REVERT: G 172 MET cc_start: 0.7559 (tpp) cc_final: 0.7222 (tpp) REVERT: G 173 LEU cc_start: 0.6195 (mp) cc_final: 0.5955 (mm) REVERT: G 205 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8394 (tttm) REVERT: G 237 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8408 (pt) REVERT: G 280 GLN cc_start: 0.7937 (tp40) cc_final: 0.7683 (tp40) REVERT: G 324 PHE cc_start: 0.7898 (m-80) cc_final: 0.7566 (m-80) outliers start: 72 outliers final: 48 residues processed: 437 average time/residue: 0.2613 time to fit residues: 158.0976 Evaluate side-chains 412 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 356 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 158 MET 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 235 ARG Chi-restraints excluded: chain B residue 237 ILE 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 C residue 163 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 223 SER 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 290 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain E residue 147 THR 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 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 328 SER Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 292 CYS 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 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 268 ILE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 71 optimal weight: 5.9990 chunk 101 optimal weight: 0.0970 chunk 50 optimal weight: 0.2980 chunk 7 optimal weight: 0.0000 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 overall best weight: 0.3782 ------------------------------------------------------------------------------- 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 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.188716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.157216 restraints weight = 15782.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.160164 restraints weight = 9463.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.162222 restraints weight = 6607.990| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.9063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 12628 Z= 0.149 Angle : 0.917 26.127 17101 Z= 0.472 Chirality : 0.046 0.395 1967 Planarity : 0.004 0.059 2149 Dihedral : 7.211 55.952 1719 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.14 % Favored : 93.02 % Rotamer: Outliers : 4.09 % Allowed : 31.18 % Favored : 64.73 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1547 helix: 1.62 (0.20), residues: 651 sheet: -2.34 (0.32), residues: 231 loop : -2.27 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 201 HIS 0.091 0.005 HIS G 265 PHE 0.012 0.001 PHE C 278 TYR 0.027 0.001 TYR F 174 ARG 0.011 0.001 ARG E 271 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 574) hydrogen bonds : angle 4.58600 ( 1533) covalent geometry : bond 0.00311 (12607) covalent geometry : angle 0.91697 (17101) Misc. bond : bond 0.00744 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4532.40 seconds wall clock time: 79 minutes 0.33 seconds (4740.33 seconds total)