Starting phenix.real_space_refine on Thu Sep 26 03:19:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/09_2024/5y4o_6805.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/09_2024/5y4o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/09_2024/5y4o_6805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/09_2024/5y4o_6805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/09_2024/5y4o_6805.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/09_2024/5y4o_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-5461/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: 6.93, per 1000 atoms: 0.56 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=0, symmetry=0 Time building additional restraints: 3.17 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: 1.13 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: 3.09 Time building geometry restraints manager: 3.65 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: 0.47 - 1.36: 46 1.36 - 2.24: 300 2.24 - 3.13: 11135 3.13 - 4.01: 30075 4.01 - 4.90: 53409 Warning: very small nonbonded interaction distances. Nonbonded interactions: 94965 Sorted by model distance: nonbonded pdb=" NE ARG C 235 " pdb=" CZ3 TRP C 302 " model vdw 0.471 3.420 nonbonded pdb=" NE ARG B 235 " pdb=" CZ3 TRP B 302 " model vdw 0.471 3.420 nonbonded pdb=" NE ARG G 235 " pdb=" CZ3 TRP G 302 " model vdw 0.471 3.420 nonbonded pdb=" NE ARG A 235 " pdb=" CZ3 TRP A 302 " model vdw 0.471 3.420 nonbonded pdb=" NE ARG E 235 " pdb=" CZ3 TRP E 302 " model vdw 0.471 3.420 ... (remaining 94960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.150 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.200 ------------------------------------------------------------------------------- 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 : 0.022 0.530 12607 Z= 1.379 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 : 0.471 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 *********************** 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 fitting. rotamer outliers: 273 poor density : 468 time to evaluate : 1.333 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: 0.2405 time to fit residues: 200.9060 Evaluate side-chains 506 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 367 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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: 0.9990 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 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: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 272 GLN C 211 ASN C 218 ASN C 265 HIS C 272 GLN C 307 GLN D 218 ASN D 265 HIS 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 ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12607 Z= 0.263 Angle : 0.820 11.109 17101 Z= 0.445 Chirality : 0.047 0.196 1967 Planarity : 0.006 0.054 2149 Dihedral : 14.641 74.532 2004 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.90 % Allowed : 5.49 % Favored : 93.60 % Rotamer: Outliers : 9.15 % Allowed : 16.67 % Favored : 74.18 % 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: -1.15 (0.20), residues: 1547 helix: 0.52 (0.20), residues: 602 sheet: -2.50 (0.35), residues: 210 loop : -1.26 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP G 184 HIS 0.009 0.002 HIS E 137 PHE 0.018 0.003 PHE G 278 TYR 0.020 0.002 TYR D 310 ARG 0.006 0.001 ARG E 120 *********************** 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 583 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 460 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.2879 (mtt) cc_final: 0.2506 (mtt) REVERT: A 172 MET cc_start: 0.7163 (tpp) cc_final: 0.6412 (ttp) REVERT: A 179 PHE cc_start: 0.4515 (p90) cc_final: 0.4221 (p90) REVERT: A 180 SER cc_start: 0.5461 (m) cc_final: 0.5142 (t) REVERT: A 268 ILE cc_start: 0.6857 (mp) cc_final: 0.6572 (mt) REVERT: B 140 MET cc_start: 0.3558 (mtt) cc_final: 0.2818 (mtt) REVERT: B 180 SER cc_start: 0.5802 (m) cc_final: 0.5398 (t) REVERT: B 275 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8003 (mp) REVERT: B 277 TYR cc_start: 0.8379 (m-80) cc_final: 0.7991 (m-80) REVERT: B 287 ASN cc_start: 0.7412 (m110) cc_final: 0.7056 (m110) REVERT: C 158 MET cc_start: 0.4642 (mmt) cc_final: 0.4321 (mmt) REVERT: C 180 SER cc_start: 0.5419 (m) cc_final: 0.4841 (t) REVERT: C 234 ASN cc_start: 0.6947 (OUTLIER) cc_final: 0.6316 (m110) REVERT: D 180 SER cc_start: 0.6092 (m) cc_final: 0.5404 (t) REVERT: D 314 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7293 (tt) REVERT: E 180 SER cc_start: 0.6235 (m) cc_final: 0.5882 (t) REVERT: E 237 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8279 (pt) REVERT: E 277 TYR cc_start: 0.8655 (m-80) cc_final: 0.8365 (m-80) REVERT: E 314 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7442 (tt) REVERT: F 118 MET cc_start: 0.5824 (ptt) cc_final: 0.5454 (ptp) REVERT: F 140 MET cc_start: 0.3495 (mtt) cc_final: 0.3017 (mtt) REVERT: F 250 LYS cc_start: 0.5270 (ptmt) cc_final: 0.4934 (pttt) REVERT: F 277 TYR cc_start: 0.8252 (m-80) cc_final: 0.7929 (m-80) REVERT: G 172 MET cc_start: 0.6769 (tpp) cc_final: 0.5666 (ttp) REVERT: G 180 SER cc_start: 0.6016 (m) cc_final: 0.5741 (t) outliers start: 123 outliers final: 59 residues processed: 512 average time/residue: 0.2481 time to fit residues: 179.1353 Evaluate side-chains 440 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 376 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 236 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 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 290 VAL Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 236 ARG 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 314 ILE 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 326 PHE 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 77 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 280 GLN A 320 HIS B 218 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS C 228 ASN C 265 HIS C 320 HIS D 218 ASN E 218 ASN E 280 GLN G 211 ASN ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS G 320 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12607 Z= 0.375 Angle : 0.795 10.443 17101 Z= 0.436 Chirality : 0.048 0.237 1967 Planarity : 0.006 0.040 2149 Dihedral : 10.303 74.012 1797 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.89 % Favored : 91.21 % Rotamer: Outliers : 10.19 % Allowed : 18.60 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.20), residues: 1547 helix: 0.84 (0.19), residues: 644 sheet: -2.10 (0.36), residues: 224 loop : -1.98 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP G 184 HIS 0.006 0.002 HIS E 137 PHE 0.019 0.003 PHE B 167 TYR 0.018 0.002 TYR G 174 ARG 0.007 0.001 ARG F 271 *********************** 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 565 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 428 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.2968 (mtt) cc_final: 0.2669 (mtt) REVERT: A 172 MET cc_start: 0.6987 (tpp) cc_final: 0.6221 (ttt) REVERT: A 179 PHE cc_start: 0.5220 (p90) cc_final: 0.5007 (p90) REVERT: A 215 TYR cc_start: 0.8467 (m-80) cc_final: 0.8244 (m-80) REVERT: A 268 ILE cc_start: 0.7353 (mp) cc_final: 0.7063 (mt) REVERT: B 180 SER cc_start: 0.7171 (m) cc_final: 0.6955 (t) REVERT: B 201 TRP cc_start: 0.7073 (m100) cc_final: 0.6864 (m100) REVERT: B 205 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8529 (mtpp) REVERT: B 224 ILE cc_start: 0.8526 (pt) cc_final: 0.8294 (pt) REVERT: B 261 MET cc_start: 0.7422 (tmm) cc_final: 0.7036 (tmm) REVERT: B 289 MET cc_start: 0.8149 (tmm) cc_final: 0.7871 (tmm) REVERT: C 234 ASN cc_start: 0.8151 (m110) cc_final: 0.7871 (m110) REVERT: C 331 LEU cc_start: 0.8192 (mt) cc_final: 0.7870 (mp) REVERT: E 277 TYR cc_start: 0.8583 (m-80) cc_final: 0.8230 (m-80) REVERT: F 118 MET cc_start: 0.5373 (ptt) cc_final: 0.5171 (ptp) REVERT: G 172 MET cc_start: 0.7088 (tpp) cc_final: 0.5817 (ttt) REVERT: G 210 ASP cc_start: 0.7485 (m-30) cc_final: 0.7262 (m-30) REVERT: G 315 ASP cc_start: 0.4556 (OUTLIER) cc_final: 0.4320 (t0) outliers start: 137 outliers final: 88 residues processed: 513 average time/residue: 0.2402 time to fit residues: 174.0575 Evaluate side-chains 465 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 376 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU 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 225 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 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 B residue 214 LEU Chi-restraints excluded: chain B residue 225 SER 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 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 314 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain 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 237 ILE Chi-restraints excluded: chain D residue 254 ILE 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 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 214 LEU 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 290 VAL Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 223 SER 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 239 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 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 186 ARG Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 315 ASP 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 138 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN B 265 HIS ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN D 320 HIS E 228 ASN F 265 HIS G 265 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.7540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12607 Z= 0.300 Angle : 0.697 9.051 17101 Z= 0.383 Chirality : 0.045 0.227 1967 Planarity : 0.005 0.046 2149 Dihedral : 8.568 58.926 1759 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.43 % Favored : 91.66 % Rotamer: Outliers : 9.75 % Allowed : 21.21 % Favored : 69.05 % 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: -0.96 (0.21), residues: 1547 helix: 1.17 (0.19), residues: 651 sheet: -2.10 (0.36), residues: 224 loop : -1.96 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 184 HIS 0.004 0.001 HIS D 320 PHE 0.014 0.002 PHE C 281 TYR 0.021 0.002 TYR B 174 ARG 0.009 0.001 ARG B 231 *********************** 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 511 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 380 time to evaluate : 1.389 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: 0.7345 (tpp) cc_final: 0.6340 (ttt) REVERT: A 268 ILE cc_start: 0.7497 (mp) cc_final: 0.7271 (mt) REVERT: B 161 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.5301 (mttt) REVERT: B 224 ILE cc_start: 0.8628 (pt) cc_final: 0.8395 (pt) REVERT: C 158 MET cc_start: 0.4553 (mmt) cc_final: 0.4349 (mmt) REVERT: C 234 ASN cc_start: 0.7964 (m110) cc_final: 0.7739 (m110) REVERT: D 161 LYS cc_start: 0.6075 (OUTLIER) cc_final: 0.5792 (tppt) REVERT: D 205 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8339 (tttm) REVERT: D 247 ASP cc_start: 0.5244 (m-30) cc_final: 0.4940 (m-30) REVERT: E 161 LYS cc_start: 0.6300 (OUTLIER) cc_final: 0.5736 (tppt) REVERT: F 140 MET cc_start: 0.2679 (mtt) cc_final: 0.2336 (mtt) REVERT: F 161 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5692 (tppt) REVERT: G 138 PHE cc_start: 0.3755 (m-10) cc_final: 0.3461 (m-80) REVERT: G 161 LYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5648 (tppt) REVERT: G 172 MET cc_start: 0.7050 (tpp) cc_final: 0.5592 (ttt) REVERT: G 205 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8328 (mtpp) REVERT: G 237 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8810 (pt) REVERT: G 280 GLN cc_start: 0.7439 (tp40) cc_final: 0.6710 (tp40) REVERT: G 287 ASN cc_start: 0.8104 (m110) cc_final: 0.7701 (m-40) outliers start: 131 outliers final: 89 residues processed: 465 average time/residue: 0.2684 time to fit residues: 172.1059 Evaluate side-chains 442 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 347 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 225 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 317 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 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 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 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 237 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 289 MET 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 218 ASN Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 237 ILE 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 164 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 214 LEU 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 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 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 236 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 186 ARG 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 237 ILE Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 296 THR 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 123 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN ** E 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN F 265 HIS G 265 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.7940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12607 Z= 0.228 Angle : 0.658 9.020 17101 Z= 0.359 Chirality : 0.044 0.232 1967 Planarity : 0.004 0.043 2149 Dihedral : 8.086 58.659 1750 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.30 % Favored : 91.79 % Rotamer: Outliers : 8.71 % Allowed : 24.78 % Favored : 66.52 % 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: -0.82 (0.21), residues: 1547 helix: 1.41 (0.19), residues: 651 sheet: -2.03 (0.36), residues: 224 loop : -2.02 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 184 HIS 0.003 0.001 HIS E 265 PHE 0.018 0.001 PHE E 138 TYR 0.025 0.002 TYR B 174 ARG 0.016 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 376 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7225 (tpp) cc_final: 0.6182 (ttt) REVERT: A 268 ILE cc_start: 0.7496 (mp) cc_final: 0.7189 (mt) REVERT: B 161 LYS cc_start: 0.6024 (OUTLIER) cc_final: 0.5439 (mttt) REVERT: B 237 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8588 (pt) REVERT: C 234 ASN cc_start: 0.7943 (m110) cc_final: 0.7643 (m110) REVERT: D 161 LYS cc_start: 0.6071 (OUTLIER) cc_final: 0.5864 (tppt) REVERT: D 205 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8351 (tttm) REVERT: E 161 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5883 (tppt) REVERT: E 232 MET cc_start: 0.7440 (mtp) cc_final: 0.7206 (mtp) REVERT: F 161 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5941 (tppt) REVERT: F 222 SER cc_start: 0.8479 (m) cc_final: 0.8278 (p) REVERT: G 158 MET cc_start: 0.3954 (OUTLIER) cc_final: 0.3753 (mmt) REVERT: G 161 LYS cc_start: 0.5921 (OUTLIER) cc_final: 0.5720 (tppt) REVERT: G 172 MET cc_start: 0.7094 (tpp) cc_final: 0.5714 (ttt) REVERT: G 173 LEU cc_start: 0.6573 (mm) cc_final: 0.6253 (mm) REVERT: G 205 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8259 (tttm) REVERT: G 237 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8740 (pt) REVERT: G 280 GLN cc_start: 0.7305 (tp40) cc_final: 0.6777 (tp40) outliers start: 117 outliers final: 83 residues processed: 462 average time/residue: 0.2618 time to fit residues: 167.4580 Evaluate side-chains 440 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 349 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 225 SER 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 307 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 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 163 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 222 SER 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 284 SER Chi-restraints excluded: chain C residue 289 MET 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 218 ASN Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 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 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 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 236 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 ARG 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 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 296 THR 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 50 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 0.3980 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN ** E 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.8200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12607 Z= 0.223 Angle : 0.648 9.577 17101 Z= 0.353 Chirality : 0.044 0.244 1967 Planarity : 0.004 0.042 2149 Dihedral : 7.665 56.328 1741 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.24 % Favored : 91.86 % Rotamer: Outliers : 7.44 % Allowed : 26.71 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.21), residues: 1547 helix: 1.53 (0.19), residues: 651 sheet: -2.32 (0.32), residues: 259 loop : -2.04 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 184 HIS 0.001 0.000 HIS E 265 PHE 0.014 0.001 PHE E 138 TYR 0.024 0.002 TYR D 174 ARG 0.008 0.001 ARG E 271 *********************** 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 463 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 363 time to evaluate : 1.374 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: A 140 MET cc_start: 0.2246 (mtt) cc_final: 0.1870 (mtt) REVERT: A 172 MET cc_start: 0.7190 (tpp) cc_final: 0.6130 (ttt) REVERT: A 268 ILE cc_start: 0.7545 (mp) cc_final: 0.7215 (mt) REVERT: B 161 LYS cc_start: 0.6033 (OUTLIER) cc_final: 0.5774 (tppt) REVERT: B 218 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8184 (m110) REVERT: B 237 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8575 (pt) REVERT: B 261 MET cc_start: 0.7210 (tmm) cc_final: 0.6898 (tmm) REVERT: C 234 ASN cc_start: 0.7914 (m110) cc_final: 0.7673 (m110) REVERT: D 161 LYS cc_start: 0.5818 (OUTLIER) cc_final: 0.5477 (tppt) REVERT: D 205 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8331 (tttm) REVERT: E 138 PHE cc_start: 0.4455 (m-80) cc_final: 0.4186 (m-80) REVERT: E 158 MET cc_start: 0.4055 (mmt) cc_final: 0.3788 (mmt) REVERT: E 161 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5780 (tppt) REVERT: E 174 TYR cc_start: 0.5623 (t80) cc_final: 0.5319 (t80) REVERT: F 137 HIS cc_start: 0.4595 (m-70) cc_final: 0.4093 (m-70) REVERT: F 161 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.6017 (tppt) REVERT: F 222 SER cc_start: 0.8468 (m) cc_final: 0.8195 (p) REVERT: F 277 TYR cc_start: 0.8450 (m-80) cc_final: 0.7793 (m-80) REVERT: G 161 LYS cc_start: 0.5949 (OUTLIER) cc_final: 0.5661 (tppt) REVERT: G 172 MET cc_start: 0.7107 (tpp) cc_final: 0.5737 (ttt) REVERT: G 173 LEU cc_start: 0.6514 (mm) cc_final: 0.6309 (mm) REVERT: G 205 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8278 (tttm) REVERT: G 232 MET cc_start: 0.8101 (mtp) cc_final: 0.7678 (mmm) REVERT: G 280 GLN cc_start: 0.7476 (tp40) cc_final: 0.7000 (tp40) REVERT: G 333 MET cc_start: 0.4494 (mmm) cc_final: 0.4234 (mmt) outliers start: 100 outliers final: 82 residues processed: 436 average time/residue: 0.2585 time to fit residues: 156.5322 Evaluate side-chains 433 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 344 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET 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 237 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 285 SER 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 206 ILE Chi-restraints excluded: chain B residue 218 ASN 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 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 163 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 222 SER 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 286 LEU Chi-restraints excluded: chain C residue 289 MET 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 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 317 VAL 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 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 296 THR Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER 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 236 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 268 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 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 ARG 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 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 90 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN ** E 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.8412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12607 Z= 0.215 Angle : 0.646 8.935 17101 Z= 0.350 Chirality : 0.044 0.245 1967 Planarity : 0.004 0.029 2149 Dihedral : 7.260 57.810 1732 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.98 % Favored : 92.11 % Rotamer: Outliers : 7.59 % Allowed : 27.68 % Favored : 64.73 % 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: -0.78 (0.21), residues: 1547 helix: 1.67 (0.19), residues: 651 sheet: -2.31 (0.32), residues: 259 loop : -2.11 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 184 HIS 0.002 0.000 HIS E 265 PHE 0.014 0.001 PHE D 281 TYR 0.027 0.002 TYR C 174 ARG 0.006 0.001 ARG B 231 *********************** 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 474 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 372 time to evaluate : 1.403 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: A 140 MET cc_start: 0.1942 (mtt) cc_final: 0.1741 (mtt) REVERT: A 172 MET cc_start: 0.7229 (tpp) cc_final: 0.6176 (ttt) REVERT: A 268 ILE cc_start: 0.7547 (mp) cc_final: 0.7229 (mt) REVERT: B 218 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.7952 (m110) REVERT: B 237 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8565 (pt) REVERT: C 234 ASN cc_start: 0.7674 (m110) cc_final: 0.7387 (m110) REVERT: C 284 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8182 (t) REVERT: D 161 LYS cc_start: 0.5784 (OUTLIER) cc_final: 0.5535 (tppt) REVERT: D 205 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8339 (tttm) REVERT: D 286 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7729 (tp) REVERT: E 138 PHE cc_start: 0.4551 (m-80) cc_final: 0.4216 (m-80) REVERT: E 158 MET cc_start: 0.4391 (mmt) cc_final: 0.4096 (mmt) REVERT: E 174 TYR cc_start: 0.5644 (t80) cc_final: 0.5320 (t80) REVERT: E 205 LYS cc_start: 0.8397 (mtpp) cc_final: 0.7847 (tttp) REVERT: F 137 HIS cc_start: 0.4660 (OUTLIER) cc_final: 0.4044 (m-70) REVERT: F 161 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6174 (tppt) REVERT: F 222 SER cc_start: 0.8481 (m) cc_final: 0.8204 (p) REVERT: F 277 TYR cc_start: 0.8441 (m-80) cc_final: 0.7830 (m-80) REVERT: G 158 MET cc_start: 0.3735 (OUTLIER) cc_final: 0.3469 (mmt) REVERT: G 172 MET cc_start: 0.7048 (tpp) cc_final: 0.5642 (ttt) REVERT: G 173 LEU cc_start: 0.6528 (mm) cc_final: 0.6326 (mm) REVERT: G 205 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8255 (tttm) REVERT: G 232 MET cc_start: 0.8035 (mtp) cc_final: 0.7642 (mmm) REVERT: G 280 GLN cc_start: 0.7610 (tp40) cc_final: 0.7222 (tp40) REVERT: G 333 MET cc_start: 0.4476 (mmm) cc_final: 0.4171 (mmt) outliers start: 102 outliers final: 77 residues processed: 445 average time/residue: 0.2581 time to fit residues: 158.0586 Evaluate side-chains 438 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 353 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 163 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 237 ILE 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 206 ILE Chi-restraints excluded: chain B residue 218 ASN 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 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 163 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 222 SER 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 284 SER Chi-restraints excluded: chain C residue 289 MET 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 237 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 VAL 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 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 296 THR 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 206 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 268 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 328 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 ARG Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 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 59 optimal weight: 0.0030 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 0.0060 chunk 94 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN D 228 ASN ** E 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS G 320 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.8636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12607 Z= 0.169 Angle : 0.629 8.035 17101 Z= 0.338 Chirality : 0.044 0.258 1967 Planarity : 0.004 0.029 2149 Dihedral : 6.698 59.210 1724 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.40 % Favored : 92.76 % Rotamer: Outliers : 6.03 % Allowed : 29.02 % Favored : 64.96 % 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: -0.60 (0.22), residues: 1547 helix: 1.91 (0.20), residues: 651 sheet: -2.34 (0.31), residues: 266 loop : -2.04 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 201 HIS 0.002 0.000 HIS E 265 PHE 0.011 0.001 PHE A 278 TYR 0.032 0.002 TYR B 174 ARG 0.009 0.001 ARG E 271 *********************** 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 466 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 385 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.3727 (OUTLIER) cc_final: 0.3346 (mmt) REVERT: A 172 MET cc_start: 0.7182 (tpp) cc_final: 0.6291 (ttt) REVERT: A 268 ILE cc_start: 0.7430 (mp) cc_final: 0.7054 (mt) REVERT: A 280 GLN cc_start: 0.7894 (tp40) cc_final: 0.7214 (tp40) REVERT: B 218 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.7840 (m110) REVERT: B 237 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8396 (pt) REVERT: C 232 MET cc_start: 0.7484 (mtp) cc_final: 0.7219 (mmm) REVERT: D 205 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8332 (tttm) REVERT: D 286 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7675 (tp) REVERT: E 138 PHE cc_start: 0.4744 (m-80) cc_final: 0.4454 (m-80) REVERT: E 174 TYR cc_start: 0.5648 (t80) cc_final: 0.5395 (t80) REVERT: E 205 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8088 (tttp) REVERT: E 232 MET cc_start: 0.7225 (mtp) cc_final: 0.6991 (mtp) REVERT: F 137 HIS cc_start: 0.4802 (OUTLIER) cc_final: 0.4116 (m-70) REVERT: F 161 LYS cc_start: 0.6652 (OUTLIER) cc_final: 0.6254 (tppt) REVERT: F 172 MET cc_start: 0.6921 (tpp) cc_final: 0.6238 (ttt) REVERT: F 277 TYR cc_start: 0.8475 (m-80) cc_final: 0.7920 (m-80) REVERT: G 172 MET cc_start: 0.7010 (tpp) cc_final: 0.5562 (ttt) REVERT: G 205 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8297 (tttm) REVERT: G 232 MET cc_start: 0.8002 (mtp) cc_final: 0.7424 (mmm) REVERT: G 237 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8705 (pt) REVERT: G 280 GLN cc_start: 0.7466 (tp40) cc_final: 0.7226 (tp40) outliers start: 81 outliers final: 59 residues processed: 437 average time/residue: 0.2598 time to fit residues: 156.1779 Evaluate side-chains 432 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 366 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 237 ILE 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 206 ILE Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 328 SER 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 286 LEU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 286 LEU 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 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 284 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 296 THR 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 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 130 optimal weight: 0.0770 chunk 137 optimal weight: 0.3980 chunk 90 optimal weight: 0.0060 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS B 234 ASN ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS C 137 HIS C 265 HIS C 320 HIS ** E 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 320 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.8817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12607 Z= 0.155 Angle : 0.623 7.188 17101 Z= 0.334 Chirality : 0.043 0.266 1967 Planarity : 0.004 0.033 2149 Dihedral : 6.510 55.935 1721 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.84 % Allowed : 5.82 % Favored : 93.34 % Rotamer: Outliers : 4.84 % Allowed : 29.61 % Favored : 65.55 % 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: -0.49 (0.22), residues: 1547 helix: 1.97 (0.20), residues: 651 sheet: -2.24 (0.31), residues: 266 loop : -1.98 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 201 HIS 0.002 0.000 HIS E 265 PHE 0.014 0.001 PHE A 278 TYR 0.029 0.002 TYR D 174 ARG 0.008 0.001 ARG B 271 *********************** 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 475 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 410 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.3481 (OUTLIER) cc_final: 0.3078 (mmt) REVERT: A 172 MET cc_start: 0.7188 (tpp) cc_final: 0.6244 (ttt) REVERT: A 173 LEU cc_start: 0.6360 (mm) cc_final: 0.6129 (mm) REVERT: A 268 ILE cc_start: 0.7453 (mp) cc_final: 0.7091 (mt) REVERT: A 280 GLN cc_start: 0.7862 (tp40) cc_final: 0.7226 (tp40) REVERT: B 236 ARG cc_start: 0.7756 (ttp-170) cc_final: 0.7474 (ttp-170) REVERT: B 237 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8361 (pt) REVERT: C 302 TRP cc_start: 0.8781 (t60) cc_final: 0.8435 (t60) REVERT: D 205 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8277 (tttm) REVERT: D 286 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7629 (tp) REVERT: E 205 LYS cc_start: 0.8440 (mtpp) cc_final: 0.8157 (tttp) REVERT: E 237 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8482 (pt) REVERT: F 137 HIS cc_start: 0.4775 (OUTLIER) cc_final: 0.4169 (m-70) REVERT: F 161 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.6403 (tppt) REVERT: F 172 MET cc_start: 0.7144 (tpp) cc_final: 0.6357 (ttt) REVERT: F 173 LEU cc_start: 0.6448 (mm) cc_final: 0.6199 (mp) REVERT: F 237 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8497 (pt) REVERT: F 277 TYR cc_start: 0.8447 (m-80) cc_final: 0.7933 (m-80) REVERT: G 205 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8254 (tttm) REVERT: G 215 TYR cc_start: 0.8879 (m-80) cc_final: 0.8588 (m-80) REVERT: G 232 MET cc_start: 0.7899 (mtp) cc_final: 0.7295 (mmm) REVERT: G 331 LEU cc_start: 0.8232 (mt) cc_final: 0.8026 (mp) outliers start: 65 outliers final: 46 residues processed: 451 average time/residue: 0.2664 time to fit residues: 164.1224 Evaluate side-chains 431 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 378 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 223 SER Chi-restraints excluded: chain A residue 237 ILE 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 206 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 292 CYS 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 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 296 THR 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 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 328 SER 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 146 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 153 optimal weight: 4.9990 chunk 141 optimal weight: 0.0770 chunk 122 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS B 218 ASN ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 320 HIS D 320 HIS ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS G 320 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.8947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12607 Z= 0.165 Angle : 0.640 9.987 17101 Z= 0.339 Chirality : 0.044 0.262 1967 Planarity : 0.004 0.046 2149 Dihedral : 6.246 56.012 1717 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.46 % Favored : 92.76 % Rotamer: Outliers : 3.87 % Allowed : 31.25 % Favored : 64.88 % 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: -0.38 (0.22), residues: 1547 helix: 2.02 (0.20), residues: 651 sheet: -2.21 (0.31), residues: 266 loop : -1.84 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 201 HIS 0.002 0.000 HIS E 265 PHE 0.014 0.001 PHE D 281 TYR 0.027 0.002 TYR B 174 ARG 0.016 0.001 ARG C 271 ********************** 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 437 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 385 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.3690 (OUTLIER) cc_final: 0.3163 (mmt) REVERT: A 172 MET cc_start: 0.7199 (tpp) cc_final: 0.6247 (ttt) REVERT: A 261 MET cc_start: 0.7571 (tmm) cc_final: 0.7350 (tmm) REVERT: A 268 ILE cc_start: 0.7519 (mp) cc_final: 0.7127 (mt) REVERT: B 236 ARG cc_start: 0.7756 (ttp-170) cc_final: 0.7460 (ttp-170) REVERT: B 237 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8353 (pt) REVERT: B 281 PHE cc_start: 0.8259 (t80) cc_final: 0.8037 (t80) REVERT: D 205 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8274 (tttm) REVERT: D 286 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7669 (tp) REVERT: E 205 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8278 (tttp) REVERT: E 232 MET cc_start: 0.7105 (mtp) cc_final: 0.6868 (mtp) REVERT: E 237 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8534 (pt) REVERT: F 172 MET cc_start: 0.7139 (tpp) cc_final: 0.6386 (ttt) REVERT: F 277 TYR cc_start: 0.8461 (m-80) cc_final: 0.7950 (m-80) REVERT: G 215 TYR cc_start: 0.8896 (m-80) cc_final: 0.8653 (m-80) REVERT: G 232 MET cc_start: 0.7890 (mtp) cc_final: 0.7352 (mmm) REVERT: G 333 MET cc_start: 0.5368 (mmm) cc_final: 0.4870 (mmt) outliers start: 52 outliers final: 42 residues processed: 422 average time/residue: 0.2518 time to fit residues: 147.8572 Evaluate side-chains 415 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 369 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 223 SER 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 328 SER Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 HIS 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 237 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 281 PHE 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 237 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 328 SER 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 130 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS B 265 HIS B 320 HIS D 228 ASN D 320 HIS E 320 HIS F 218 ASN ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS G 320 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.185021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.152610 restraints weight = 15605.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.155515 restraints weight = 9193.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.157366 restraints weight = 6307.951| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.9023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12607 Z= 0.185 Angle : 0.649 9.534 17101 Z= 0.344 Chirality : 0.045 0.278 1967 Planarity : 0.004 0.036 2149 Dihedral : 6.028 48.699 1713 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.72 % Favored : 92.57 % Rotamer: Outliers : 4.76 % Allowed : 30.95 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.40 (0.22), residues: 1547 helix: 2.01 (0.20), residues: 651 sheet: -2.27 (0.31), residues: 266 loop : -1.83 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 201 HIS 0.010 0.001 HIS D 320 PHE 0.011 0.001 PHE A 278 TYR 0.029 0.002 TYR D 174 ARG 0.016 0.001 ARG C 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3160.98 seconds wall clock time: 58 minutes 4.57 seconds (3484.57 seconds total)