Starting phenix.real_space_refine on Wed Mar 4 20:38:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nuw_0523/03_2026/6nuw_0523.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nuw_0523/03_2026/6nuw_0523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nuw_0523/03_2026/6nuw_0523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nuw_0523/03_2026/6nuw_0523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nuw_0523/03_2026/6nuw_0523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nuw_0523/03_2026/6nuw_0523.map" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 49 5.16 5 C 10236 2.51 5 N 2921 2.21 5 O 3086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16292 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1962 Classifications: {'peptide': 244} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 232} Chain: "C" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1601 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 2 Chain: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1578 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2851 Classifications: {'peptide': 369} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 45} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 5, 'PHE:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "F" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1360 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 3, 'TRANS': 186} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "G" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1114 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'TYR:plan': 5, 'ASN:plan1': 9, 'PHE:plan': 2, 'GLU:plan': 7, 'ASP:plan': 11, 'ARG:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 152 Chain: "I" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1295 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 1668 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 15, 'TRANS': 286} Chain breaks: 5 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 839 Unresolved non-hydrogen angles: 1077 Unresolved non-hydrogen dihedrals: 723 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 11, 'TRP:plan': 8, 'HIS:plan': 9, 'TYR:plan': 5, 'PHE:plan': 9, 'ASN:plan1': 12, 'ASP:plan': 10, 'ARG:plan': 12, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 408 Chain: "J" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 997 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 7, 'ASP:plan': 5, 'ASN:plan1': 5, 'GLN:plan1': 6, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 119 Chain: "Y" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 561 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 9, 'ARG:plan': 6, 'HIS:plan': 6, 'GLU:plan': 5, 'TRP:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 212 Chain: "Y" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 185 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Chain: "X" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "M" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 375 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'UNK:plan-1': 75} Unresolved non-hydrogen planarities: 75 Chain: "U" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 3.47, per 1000 atoms: 0.21 Number of scatterers: 16292 At special positions: 0 Unit cell: (147.6, 143.91, 188.19, 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 49 16.00 O 3086 8.00 N 2921 7.00 C 10236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 577.0 milliseconds 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4570 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 9 sheets defined 74.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 94 through 108 removed outlier: 4.185A pdb=" N VAL B 98 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 153 through 157 removed outlier: 3.936A pdb=" N LYS B 156 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 229 through 240 removed outlier: 3.935A pdb=" N ILE B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 173 Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 261 through 286 removed outlier: 4.155A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 338 through 345 Processing helix chain 'C' and resid 347 through 359 removed outlier: 3.921A pdb=" N LEU C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 140 removed outlier: 3.846A pdb=" N GLU D 137 " --> pdb=" O ASN D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 236 through 263 removed outlier: 4.260A pdb=" N ASN D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 Processing helix chain 'D' and resid 349 through 363 removed outlier: 3.814A pdb=" N LEU D 354 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS D 355 " --> pdb=" O LYS D 351 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 363 " --> pdb=" O ASN D 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 27 removed outlier: 3.863A pdb=" N LYS E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU E 27 " --> pdb=" O GLN E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 41 Processing helix chain 'E' and resid 51 through 64 removed outlier: 3.921A pdb=" N GLU E 56 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 79 Processing helix chain 'E' and resid 87 through 99 removed outlier: 3.717A pdb=" N ASP E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N CYS E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 220 through 232 removed outlier: 3.610A pdb=" N ARG E 230 " --> pdb=" O GLN E 226 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE E 232 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 256 Processing helix chain 'E' and resid 270 through 275 Processing helix chain 'E' and resid 285 through 290 removed outlier: 3.893A pdb=" N HIS E 289 " --> pdb=" O ASP E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 309 Processing helix chain 'E' and resid 318 through 334 Processing helix chain 'E' and resid 408 through 418 removed outlier: 3.506A pdb=" N GLY E 412 " --> pdb=" O ASP E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'F' and resid 163 through 190 Processing helix chain 'F' and resid 197 through 221 Processing helix chain 'F' and resid 234 through 293 removed outlier: 4.174A pdb=" N GLN F 293 " --> pdb=" O GLU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 330 Processing helix chain 'F' and resid 346 through 355 removed outlier: 4.422A pdb=" N LYS F 350 " --> pdb=" O ARG F 347 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 351 " --> pdb=" O LEU F 348 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL F 353 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU F 354 " --> pdb=" O GLU F 351 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER F 355 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 375 Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.667A pdb=" N ASP F 380 " --> pdb=" O MET F 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 27 removed outlier: 3.746A pdb=" N LEU G 19 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 removed outlier: 3.803A pdb=" N LEU G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 84 removed outlier: 4.494A pdb=" N GLY G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS G 58 " --> pdb=" O MET G 54 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 140 through 177 removed outlier: 3.715A pdb=" N GLU G 161 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR G 171 " --> pdb=" O ILE G 167 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN G 172 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 173 " --> pdb=" O SER G 169 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASN G 175 " --> pdb=" O THR G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 204 Processing helix chain 'I' and resid 125 through 150 removed outlier: 3.537A pdb=" N ASP I 149 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 230 removed outlier: 4.580A pdb=" N TYR I 204 " --> pdb=" O ASN I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 250 removed outlier: 3.612A pdb=" N GLN I 240 " --> pdb=" O TRP I 236 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN I 247 " --> pdb=" O GLN I 243 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP I 248 " --> pdb=" O ALA I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 266 Processing helix chain 'I' and resid 268 through 273 Processing helix chain 'I' and resid 290 through 300 Processing helix chain 'I' and resid 302 through 321 Processing helix chain 'H' and resid 44 through 54 Processing helix chain 'H' and resid 57 through 65 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 105 through 120 Processing helix chain 'H' and resid 130 through 146 removed outlier: 5.106A pdb=" N TRP H 136 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU H 137 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE H 142 " --> pdb=" O HIS H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 Proline residue: H 160 - end of helix Processing helix chain 'H' and resid 167 through 183 removed outlier: 3.789A pdb=" N HIS H 177 " --> pdb=" O ARG H 173 " (cutoff:3.500A) Proline residue: H 178 - end of helix Processing helix chain 'H' and resid 189 through 201 removed outlier: 3.697A pdb=" N ARG H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 209 removed outlier: 3.547A pdb=" N THR H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE H 209 " --> pdb=" O THR H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 232 removed outlier: 3.526A pdb=" N ARG H 215 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 324 Proline residue: H 304 - end of helix Proline residue: H 309 - end of helix Proline residue: H 318 - end of helix Processing helix chain 'H' and resid 326 through 348 Processing helix chain 'H' and resid 355 through 374 removed outlier: 4.259A pdb=" N HIS H 370 " --> pdb=" O ARG H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 386 Processing helix chain 'H' and resid 387 through 396 Processing helix chain 'H' and resid 412 through 430 Proline residue: H 422 - end of helix Proline residue: H 426 - end of helix Processing helix chain 'H' and resid 437 through 457 removed outlier: 3.587A pdb=" N ALA H 441 " --> pdb=" O VAL H 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 29 removed outlier: 3.884A pdb=" N LEU J 15 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR J 18 " --> pdb=" O SER J 14 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS J 26 " --> pdb=" O PHE J 22 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLN J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU J 29 " --> pdb=" O PHE J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 46 Processing helix chain 'J' and resid 50 through 73 removed outlier: 5.574A pdb=" N PHE J 64 " --> pdb=" O ARG J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 127 removed outlier: 4.024A pdb=" N PHE J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU J 123 " --> pdb=" O LEU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 153 removed outlier: 3.571A pdb=" N GLY J 138 " --> pdb=" O ASN J 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 326 Processing helix chain 'Y' and resid 329 through 335 Processing helix chain 'Y' and resid 340 through 369 removed outlier: 3.906A pdb=" N ILE Y 344 " --> pdb=" O TYR Y 340 " (cutoff:3.500A) Proline residue: Y 356 - end of helix Processing helix chain 'Y' and resid 480 through 490 removed outlier: 3.801A pdb=" N GLN Y 490 " --> pdb=" O LEU Y 486 " (cutoff:3.500A) Processing helix chain 'Y' and resid 655 through 666 Processing helix chain 'Y' and resid 673 through 678 removed outlier: 3.778A pdb=" N HIS Y 677 " --> pdb=" O PHE Y 673 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS Y 678 " --> pdb=" O PHE Y 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 673 through 678' Processing helix chain 'Y' and resid 684 through 696 Processing helix chain 'Y' and resid 1197 through 1204 Processing helix chain 'Y' and resid 1206 through 1212 Processing helix chain 'Y' and resid 1668 through 1681 removed outlier: 4.334A pdb=" N UNK Y1675 " --> pdb=" O UNK Y1671 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 128 removed outlier: 4.464A pdb=" N UNK X 111 " --> pdb=" O UNK X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 137 through 167 Processing helix chain 'X' and resid 177 through 206 Processing helix chain 'M' and resid 72 through 127 removed outlier: 3.799A pdb=" N UNK M 76 " --> pdb=" O UNK M 72 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N UNK M 78 " --> pdb=" O UNK M 74 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N UNK M 82 " --> pdb=" O UNK M 78 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N UNK M 103 " --> pdb=" O UNK M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 164 removed outlier: 5.227A pdb=" N UNK M 156 " --> pdb=" O UNK M 152 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N UNK M 159 " --> pdb=" O UNK M 155 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N UNK M 160 " --> pdb=" O UNK M 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 23 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 77 removed outlier: 4.675A pdb=" N MET B 85 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP B 112 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 38 removed outlier: 3.804A pdb=" N GLN B 36 " --> pdb=" O ARG B 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.546A pdb=" N TYR B 148 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 209 through 210 removed outlier: 3.532A pdb=" N THR B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.691A pdb=" N TYR C 221 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 298 through 299 removed outlier: 3.667A pdb=" N PHE C 308 " --> pdb=" O VAL C 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 108 through 109 removed outlier: 4.537A pdb=" N ARG E 198 " --> pdb=" O GLN E 160 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN E 160 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 397 through 403 removed outlier: 3.671A pdb=" N ILE E 442 " --> pdb=" O THR E 388 " (cutoff:3.500A) 1125 hydrogen bonds defined for protein. 3327 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4018 1.33 - 1.45: 3185 1.45 - 1.57: 9177 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 16460 Sorted by residual: bond pdb=" CB TRP E 106 " pdb=" CG TRP E 106 " ideal model delta sigma weight residual 1.498 1.371 0.127 3.10e-02 1.04e+03 1.68e+01 bond pdb=" C TYR D 187 " pdb=" N LYS D 188 " ideal model delta sigma weight residual 1.333 1.279 0.054 1.34e-02 5.57e+03 1.65e+01 bond pdb=" CA ASN E 277 " pdb=" C ASN E 277 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.34e-02 5.57e+03 1.46e+01 bond pdb=" N PRO E 260 " pdb=" CD PRO E 260 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.46e+01 bond pdb=" CA HIS E 284 " pdb=" CB HIS E 284 " ideal model delta sigma weight residual 1.535 1.478 0.057 1.69e-02 3.50e+03 1.13e+01 ... (remaining 16455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 21194 2.90 - 5.80: 954 5.80 - 8.70: 168 8.70 - 11.60: 33 11.60 - 14.51: 13 Bond angle restraints: 22362 Sorted by residual: angle pdb=" CA PRO E 260 " pdb=" N PRO E 260 " pdb=" CD PRO E 260 " ideal model delta sigma weight residual 112.00 99.54 12.46 1.40e+00 5.10e-01 7.92e+01 angle pdb=" C LEU E 283 " pdb=" N HIS E 284 " pdb=" CA HIS E 284 " ideal model delta sigma weight residual 122.56 110.10 12.46 1.50e+00 4.44e-01 6.90e+01 angle pdb=" N PRO J 129 " pdb=" CA PRO J 129 " pdb=" CB PRO J 129 " ideal model delta sigma weight residual 103.25 111.85 -8.60 1.05e+00 9.07e-01 6.71e+01 angle pdb=" N PRO H 184 " pdb=" CA PRO H 184 " pdb=" CB PRO H 184 " ideal model delta sigma weight residual 103.25 111.11 -7.86 1.05e+00 9.07e-01 5.60e+01 angle pdb=" N PRO H 104 " pdb=" CA PRO H 104 " pdb=" CB PRO H 104 " ideal model delta sigma weight residual 103.00 110.54 -7.54 1.10e+00 8.26e-01 4.70e+01 ... (remaining 22357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 9020 16.47 - 32.93: 756 32.93 - 49.40: 183 49.40 - 65.86: 32 65.86 - 82.33: 14 Dihedral angle restraints: 10005 sinusoidal: 3073 harmonic: 6932 Sorted by residual: dihedral pdb=" CA ASN D 149 " pdb=" C ASN D 149 " pdb=" N MET D 150 " pdb=" CA MET D 150 " ideal model delta harmonic sigma weight residual -180.00 -120.99 -59.01 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA VAL E 29 " pdb=" C VAL E 29 " pdb=" N THR E 30 " pdb=" CA THR E 30 " ideal model delta harmonic sigma weight residual -180.00 -128.68 -51.32 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA LYS G 90 " pdb=" C LYS G 90 " pdb=" N TYR G 91 " pdb=" CA TYR G 91 " ideal model delta harmonic sigma weight residual 180.00 -134.61 -45.39 0 5.00e+00 4.00e-02 8.24e+01 ... (remaining 10002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2330 0.097 - 0.194: 335 0.194 - 0.292: 61 0.292 - 0.389: 5 0.389 - 0.486: 2 Chirality restraints: 2733 Sorted by residual: chirality pdb=" CB ILE H 57 " pdb=" CA ILE H 57 " pdb=" CG1 ILE H 57 " pdb=" CG2 ILE H 57 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" CB VAL E 120 " pdb=" CA VAL E 120 " pdb=" CG1 VAL E 120 " pdb=" CG2 VAL E 120 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CB ILE E 251 " pdb=" CA ILE E 251 " pdb=" CG1 ILE E 251 " pdb=" CG2 ILE E 251 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 2730 not shown) Planarity restraints: 2919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 149 " 0.096 5.00e-02 4.00e+02 1.46e-01 3.43e+01 pdb=" N PRO E 150 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO E 150 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO E 150 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 268 " 0.080 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO E 269 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO E 269 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 269 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 106 " 0.036 2.00e-02 2.50e+03 2.99e-02 2.24e+01 pdb=" CG TRP E 106 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP E 106 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP E 106 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 106 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 106 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 106 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 106 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 106 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP E 106 " -0.006 2.00e-02 2.50e+03 ... (remaining 2916 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 8 1.96 - 2.69: 835 2.69 - 3.43: 25435 3.43 - 4.16: 37680 4.16 - 4.90: 63092 Nonbonded interactions: 127050 Sorted by model distance: nonbonded pdb=" CB PHE C 209 " pdb=" OE1 GLN D 238 " model vdw 1.219 3.440 nonbonded pdb=" OE2 GLU C 302 " pdb=" CG ASN E 207 " model vdw 1.757 3.270 nonbonded pdb=" OD1 ASP C 300 " pdb=" O MET C 305 " model vdw 1.839 3.040 nonbonded pdb=" OD2 ASP C 300 " pdb=" N MET C 305 " model vdw 1.853 3.120 nonbonded pdb=" C THR D 234 " pdb=" NH1 ARG D 235 " model vdw 1.903 3.350 ... (remaining 127045 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.97 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: 1.760 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.600 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.012 0.127 16460 Z= 0.577 Angle : 1.448 14.505 22362 Z= 0.808 Chirality : 0.074 0.486 2733 Planarity : 0.009 0.146 2919 Dihedral : 14.250 82.328 5435 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.79 % Allowed : 15.22 % Favored : 83.98 % Rotamer: Outliers : 6.01 % Allowed : 12.10 % Favored : 81.89 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 4.55 % Twisted General : 0.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.70 (0.15), residues: 2023 helix: -2.32 (0.11), residues: 1191 sheet: -4.41 (0.34), residues: 139 loop : -4.05 (0.20), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG E 158 TYR 0.050 0.005 TYR C 163 PHE 0.058 0.006 PHE E 240 TRP 0.082 0.006 TRP E 106 HIS 0.023 0.005 HIS J 8 Details of bonding type rmsd covalent geometry : bond 0.01190 (16460) covalent geometry : angle 1.44837 (22362) hydrogen bonds : bond 0.12187 ( 1125) hydrogen bonds : angle 7.20741 ( 3327) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 359 time to evaluate : 0.382 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: B 164 GLU cc_start: 0.8085 (tt0) cc_final: 0.7877 (tm-30) REVERT: C 170 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: C 277 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8327 (pp20) REVERT: C 309 PHE cc_start: 0.8385 (m-10) cc_final: 0.8109 (m-80) REVERT: C 313 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7473 (pp) REVERT: C 343 LYS cc_start: 0.7432 (mtpp) cc_final: 0.7069 (tttt) REVERT: C 344 TRP cc_start: 0.8591 (m-90) cc_final: 0.7927 (m100) REVERT: C 345 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: C 348 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8364 (mm) REVERT: D 136 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7986 (mmtp) REVERT: D 142 TYR cc_start: 0.7976 (p90) cc_final: 0.7515 (p90) REVERT: D 150 MET cc_start: 0.8112 (mpp) cc_final: 0.7879 (pmm) REVERT: D 152 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8202 (tm) REVERT: D 180 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.8845 (mm) REVERT: D 303 THR cc_start: 0.8635 (p) cc_final: 0.8240 (p) REVERT: D 313 ASN cc_start: 0.8080 (m110) cc_final: 0.7702 (p0) REVERT: D 314 CYS cc_start: 0.7877 (p) cc_final: 0.7675 (p) REVERT: E 39 TRP cc_start: 0.8248 (t-100) cc_final: 0.8016 (t-100) REVERT: E 96 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8487 (tp) REVERT: E 98 ILE cc_start: 0.9228 (pp) cc_final: 0.8922 (mm) REVERT: E 106 TRP cc_start: 0.8663 (OUTLIER) cc_final: 0.6566 (m-10) REVERT: E 133 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8440 (tm-30) REVERT: E 160 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8345 (tm-30) REVERT: E 212 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7889 (p90) REVERT: E 226 GLN cc_start: 0.8948 (tp40) cc_final: 0.8344 (tm-30) REVERT: E 328 LYS cc_start: 0.9310 (mtpt) cc_final: 0.8936 (mtmm) REVERT: E 425 ASP cc_start: 0.8247 (p0) cc_final: 0.7858 (p0) REVERT: E 431 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8997 (pp) REVERT: F 237 ILE cc_start: 0.8011 (mm) cc_final: 0.7782 (mm) REVERT: F 239 SER cc_start: 0.8549 (m) cc_final: 0.7587 (p) REVERT: F 247 ARG cc_start: 0.9208 (tpt170) cc_final: 0.8711 (mmm160) REVERT: F 250 GLN cc_start: 0.8553 (mp-120) cc_final: 0.8311 (mm-40) REVERT: F 254 ASN cc_start: 0.8796 (m-40) cc_final: 0.8356 (m110) REVERT: F 335 MET cc_start: 0.8696 (mmm) cc_final: 0.8331 (mmm) REVERT: G 51 LYS cc_start: 0.9372 (mttt) cc_final: 0.9019 (mtmt) REVERT: G 97 LEU cc_start: 0.9576 (pt) cc_final: 0.9370 (pt) REVERT: G 99 ASN cc_start: 0.8067 (t0) cc_final: 0.7738 (t0) REVERT: I 185 MET cc_start: 0.9360 (ttt) cc_final: 0.8936 (ptt) REVERT: I 202 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8468 (pp) REVERT: I 237 HIS cc_start: 0.7800 (m90) cc_final: 0.7435 (p-80) REVERT: I 255 ARG cc_start: 0.8855 (mmm160) cc_final: 0.8499 (mmm-85) REVERT: I 268 GLU cc_start: 0.5752 (mt-10) cc_final: 0.5474 (mm-30) REVERT: I 296 VAL cc_start: 0.8801 (t) cc_final: 0.8340 (p) REVERT: I 299 MET cc_start: 0.8247 (ptt) cc_final: 0.7825 (tmm) REVERT: H 46 GLN cc_start: 0.8754 (mt0) cc_final: 0.8285 (mm-40) REVERT: H 135 ILE cc_start: 0.9005 (mm) cc_final: 0.8778 (mt) REVERT: H 139 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8198 (mt) REVERT: J 5 GLN cc_start: 0.8846 (mm110) cc_final: 0.8324 (mm-40) REVERT: J 27 GLN cc_start: 0.3735 (tp-100) cc_final: 0.2999 (mp10) REVERT: J 38 GLN cc_start: 0.8863 (pm20) cc_final: 0.8604 (pm20) REVERT: J 44 GLU cc_start: 0.9264 (tp30) cc_final: 0.8986 (pp20) REVERT: J 45 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7004 (tp) REVERT: J 53 VAL cc_start: 0.8790 (t) cc_final: 0.8542 (t) REVERT: J 62 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8772 (mttt) REVERT: J 63 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8480 (tp40) outliers start: 79 outliers final: 24 residues processed: 413 average time/residue: 0.1294 time to fit residues: 77.3828 Evaluate side-chains 301 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 283 GLN D 186 ASN D 259 GLN D 313 ASN E 23 GLN E 95 HIS E 133 GLN E 143 HIS E 149 HIS E 207 ASN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN F 250 GLN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 HIS I 205 GLN I 228 GLN I 294 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.097010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.074532 restraints weight = 68489.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.074352 restraints weight = 53589.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074085 restraints weight = 40750.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.074362 restraints weight = 36363.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.075728 restraints weight = 31016.359| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16460 Z= 0.239 Angle : 0.853 11.386 22362 Z= 0.453 Chirality : 0.047 0.269 2733 Planarity : 0.006 0.120 2919 Dihedral : 7.194 47.676 2440 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.86 % Favored : 87.94 % Rotamer: Outliers : 0.84 % Allowed : 8.07 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.17), residues: 2023 helix: -0.75 (0.14), residues: 1203 sheet: -3.60 (0.38), residues: 130 loop : -4.03 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 176 TYR 0.025 0.002 TYR C 163 PHE 0.039 0.003 PHE J 65 TRP 0.022 0.002 TRP H 140 HIS 0.016 0.002 HIS E 149 Details of bonding type rmsd covalent geometry : bond 0.00489 (16460) covalent geometry : angle 0.85333 (22362) hydrogen bonds : bond 0.04878 ( 1125) hydrogen bonds : angle 5.64277 ( 3327) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 372 time to evaluate : 0.616 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: B 76 LEU cc_start: 0.9268 (tt) cc_final: 0.8974 (tt) REVERT: B 162 SER cc_start: 0.9302 (m) cc_final: 0.9014 (p) REVERT: B 164 GLU cc_start: 0.8273 (tt0) cc_final: 0.7889 (tm-30) REVERT: B 237 LEU cc_start: 0.9437 (tt) cc_final: 0.9169 (tt) REVERT: C 209 PHE cc_start: 0.8330 (t80) cc_final: 0.7823 (t80) REVERT: C 343 LYS cc_start: 0.7330 (mtpp) cc_final: 0.7061 (tttt) REVERT: C 344 TRP cc_start: 0.8870 (m-90) cc_final: 0.8048 (m100) REVERT: D 131 LEU cc_start: 0.8449 (tp) cc_final: 0.8064 (tt) REVERT: D 148 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7225 (mm) REVERT: D 150 MET cc_start: 0.8103 (mpp) cc_final: 0.7685 (mpp) REVERT: E 133 GLN cc_start: 0.8855 (tm130) cc_final: 0.8586 (tm-30) REVERT: E 226 GLN cc_start: 0.8935 (tp40) cc_final: 0.8398 (tm-30) REVERT: E 425 ASP cc_start: 0.8420 (p0) cc_final: 0.8027 (p0) REVERT: F 237 ILE cc_start: 0.7902 (mm) cc_final: 0.7614 (mm) REVERT: F 239 SER cc_start: 0.8198 (m) cc_final: 0.7757 (p) REVERT: F 247 ARG cc_start: 0.9360 (tpt170) cc_final: 0.8772 (mmm160) REVERT: F 250 GLN cc_start: 0.8749 (mp10) cc_final: 0.8400 (mm-40) REVERT: F 254 ASN cc_start: 0.8702 (m-40) cc_final: 0.8331 (m-40) REVERT: F 255 ASN cc_start: 0.9079 (m-40) cc_final: 0.8792 (t0) REVERT: F 333 ASN cc_start: 0.8917 (t0) cc_final: 0.7970 (t0) REVERT: F 363 TYR cc_start: 0.8878 (m-80) cc_final: 0.8638 (m-80) REVERT: G 42 LEU cc_start: 0.8900 (mm) cc_final: 0.8419 (tp) REVERT: G 99 ASN cc_start: 0.7801 (t0) cc_final: 0.7545 (t0) REVERT: G 106 GLN cc_start: 0.9196 (tp40) cc_final: 0.8861 (tp-100) REVERT: I 185 MET cc_start: 0.9448 (ttt) cc_final: 0.9081 (ptt) REVERT: I 216 LEU cc_start: 0.9044 (mm) cc_final: 0.8684 (mm) REVERT: I 237 HIS cc_start: 0.7607 (m90) cc_final: 0.7388 (p-80) REVERT: I 255 ARG cc_start: 0.8506 (mmm160) cc_final: 0.8084 (mmm-85) REVERT: I 299 MET cc_start: 0.8384 (ptt) cc_final: 0.8088 (tmm) REVERT: H 46 GLN cc_start: 0.8877 (mt0) cc_final: 0.8334 (mm-40) REVERT: H 135 ILE cc_start: 0.8930 (mm) cc_final: 0.8690 (mt) REVERT: J 5 GLN cc_start: 0.8402 (mm110) cc_final: 0.8179 (mm-40) REVERT: J 38 GLN cc_start: 0.9144 (pm20) cc_final: 0.8734 (pm20) REVERT: J 44 GLU cc_start: 0.9410 (tp30) cc_final: 0.8938 (pp20) REVERT: J 50 ASP cc_start: 0.9418 (p0) cc_final: 0.9029 (p0) REVERT: J 54 THR cc_start: 0.9195 (p) cc_final: 0.8777 (p) REVERT: J 58 GLU cc_start: 0.9354 (mt-10) cc_final: 0.8615 (mp0) REVERT: J 63 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8604 (tp40) outliers start: 11 outliers final: 3 residues processed: 378 average time/residue: 0.1366 time to fit residues: 74.9435 Evaluate side-chains 296 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 292 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 43 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 170 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 119 optimal weight: 30.0000 chunk 225 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN E 23 GLN E 133 GLN E 143 HIS ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS F 376 GLN H 87 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.100319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078180 restraints weight = 70940.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.078588 restraints weight = 42049.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.078717 restraints weight = 36731.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078838 restraints weight = 30585.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.078955 restraints weight = 26851.881| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16460 Z= 0.152 Angle : 0.760 8.949 22362 Z= 0.391 Chirality : 0.045 0.227 2733 Planarity : 0.005 0.111 2919 Dihedral : 6.307 41.159 2440 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.83 % Favored : 88.98 % Rotamer: Outliers : 0.30 % Allowed : 7.08 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.19), residues: 2023 helix: 0.15 (0.15), residues: 1223 sheet: -3.29 (0.42), residues: 119 loop : -3.86 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 158 TYR 0.018 0.002 TYR D 162 PHE 0.032 0.002 PHE J 65 TRP 0.023 0.002 TRP E 39 HIS 0.009 0.002 HIS J 8 Details of bonding type rmsd covalent geometry : bond 0.00315 (16460) covalent geometry : angle 0.75966 (22362) hydrogen bonds : bond 0.04263 ( 1125) hydrogen bonds : angle 5.11654 ( 3327) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 393 time to evaluate : 0.616 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: B 85 MET cc_start: 0.7924 (mtp) cc_final: 0.7598 (mtt) REVERT: B 160 GLN cc_start: 0.8307 (tt0) cc_final: 0.7916 (tm-30) REVERT: B 164 GLU cc_start: 0.8298 (tt0) cc_final: 0.7881 (tm-30) REVERT: C 163 TYR cc_start: 0.8744 (m-80) cc_final: 0.8345 (m-80) REVERT: C 167 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8381 (tm-30) REVERT: C 206 LEU cc_start: 0.9018 (mm) cc_final: 0.8624 (mm) REVERT: C 277 GLU cc_start: 0.8167 (pp20) cc_final: 0.7701 (tm-30) REVERT: C 283 GLN cc_start: 0.8843 (tt0) cc_final: 0.8635 (tt0) REVERT: C 343 LYS cc_start: 0.7210 (mtpp) cc_final: 0.6684 (tttt) REVERT: C 344 TRP cc_start: 0.8705 (m-90) cc_final: 0.7961 (m100) REVERT: D 148 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7628 (mm) REVERT: E 77 TYR cc_start: 0.9229 (m-10) cc_final: 0.8726 (m-80) REVERT: E 133 GLN cc_start: 0.9103 (tp-100) cc_final: 0.8715 (tm-30) REVERT: E 226 GLN cc_start: 0.8579 (tp40) cc_final: 0.8344 (tm-30) REVERT: E 267 MET cc_start: 0.8556 (pmm) cc_final: 0.8311 (pmm) REVERT: E 327 GLU cc_start: 0.8445 (tp30) cc_final: 0.8182 (tp30) REVERT: E 425 ASP cc_start: 0.8022 (p0) cc_final: 0.7326 (p0) REVERT: F 241 ARG cc_start: 0.8867 (tmm160) cc_final: 0.8507 (ptm-80) REVERT: F 247 ARG cc_start: 0.9389 (tpt170) cc_final: 0.8792 (mmm160) REVERT: F 250 GLN cc_start: 0.8568 (mp10) cc_final: 0.8325 (mm-40) REVERT: F 254 ASN cc_start: 0.8636 (m-40) cc_final: 0.8092 (m-40) REVERT: F 255 ASN cc_start: 0.9094 (m-40) cc_final: 0.8786 (t0) REVERT: F 376 GLN cc_start: 0.9152 (mp10) cc_final: 0.8790 (pm20) REVERT: F 377 MET cc_start: 0.7432 (mmm) cc_final: 0.7171 (mmm) REVERT: G 42 LEU cc_start: 0.8959 (mm) cc_final: 0.8518 (tp) REVERT: G 98 ARG cc_start: 0.8356 (mtt180) cc_final: 0.8010 (mtt-85) REVERT: G 106 GLN cc_start: 0.8963 (tp40) cc_final: 0.8590 (tp-100) REVERT: G 112 ARG cc_start: 0.8872 (tmm160) cc_final: 0.8533 (tmm160) REVERT: G 113 LEU cc_start: 0.8627 (mm) cc_final: 0.8312 (mm) REVERT: I 185 MET cc_start: 0.9429 (ttt) cc_final: 0.9082 (ptt) REVERT: I 216 LEU cc_start: 0.8969 (mm) cc_final: 0.8630 (mm) REVERT: I 299 MET cc_start: 0.8378 (ptt) cc_final: 0.8000 (tmm) REVERT: H 46 GLN cc_start: 0.8933 (mt0) cc_final: 0.8406 (mm-40) REVERT: H 135 ILE cc_start: 0.8981 (mm) cc_final: 0.8742 (mt) REVERT: J 27 GLN cc_start: 0.4943 (tp-100) cc_final: 0.3507 (mp10) outliers start: 4 outliers final: 1 residues processed: 396 average time/residue: 0.1304 time to fit residues: 75.3975 Evaluate side-chains 304 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 302 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 228 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 175 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B -1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 283 GLN C 295 HIS ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN E 23 GLN E 143 HIS ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN H 44 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.096942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.075091 restraints weight = 71273.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.074125 restraints weight = 52707.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.074124 restraints weight = 49004.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074553 restraints weight = 38432.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.075342 restraints weight = 31170.154| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16460 Z= 0.251 Angle : 0.804 10.036 22362 Z= 0.422 Chirality : 0.046 0.207 2733 Planarity : 0.006 0.111 2919 Dihedral : 6.229 38.357 2440 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.65 % Favored : 87.15 % Rotamer: Outliers : 0.38 % Allowed : 6.47 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.19), residues: 2023 helix: 0.47 (0.15), residues: 1207 sheet: -2.91 (0.42), residues: 129 loop : -3.86 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 158 TYR 0.021 0.002 TYR D 187 PHE 0.033 0.003 PHE I 295 TRP 0.022 0.002 TRP E 39 HIS 0.011 0.002 HIS H 138 Details of bonding type rmsd covalent geometry : bond 0.00527 (16460) covalent geometry : angle 0.80390 (22362) hydrogen bonds : bond 0.04468 ( 1125) hydrogen bonds : angle 5.22730 ( 3327) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 348 time to evaluate : 0.428 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: B 76 LEU cc_start: 0.9444 (tt) cc_final: 0.9141 (tt) REVERT: B 85 MET cc_start: 0.8342 (mtp) cc_final: 0.7994 (mtt) REVERT: B 164 GLU cc_start: 0.8399 (tt0) cc_final: 0.8004 (tm-30) REVERT: C 163 TYR cc_start: 0.8855 (m-80) cc_final: 0.8448 (m-80) REVERT: C 207 GLU cc_start: 0.7385 (mp0) cc_final: 0.7079 (mp0) REVERT: C 209 PHE cc_start: 0.8011 (t80) cc_final: 0.7582 (t80) REVERT: C 277 GLU cc_start: 0.8378 (pp20) cc_final: 0.7840 (tm-30) REVERT: C 343 LYS cc_start: 0.7114 (mtpp) cc_final: 0.6862 (tttt) REVERT: C 344 TRP cc_start: 0.8821 (m-90) cc_final: 0.7749 (m100) REVERT: D 147 LEU cc_start: 0.9010 (tp) cc_final: 0.8627 (tp) REVERT: D 148 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7503 (mm) REVERT: E 77 TYR cc_start: 0.9271 (m-10) cc_final: 0.8723 (m-80) REVERT: E 106 TRP cc_start: 0.7992 (OUTLIER) cc_final: 0.6413 (m-10) REVERT: E 133 GLN cc_start: 0.9167 (tp-100) cc_final: 0.8821 (tp-100) REVERT: E 226 GLN cc_start: 0.8768 (tp40) cc_final: 0.8505 (tm-30) REVERT: E 267 MET cc_start: 0.8757 (pmm) cc_final: 0.8343 (pmm) REVERT: E 327 GLU cc_start: 0.8571 (tp30) cc_final: 0.8325 (tp30) REVERT: E 425 ASP cc_start: 0.8347 (p0) cc_final: 0.7909 (p0) REVERT: F 247 ARG cc_start: 0.9483 (tpt170) cc_final: 0.8912 (mmm160) REVERT: F 254 ASN cc_start: 0.8490 (m-40) cc_final: 0.8186 (m-40) REVERT: F 255 ASN cc_start: 0.9085 (m-40) cc_final: 0.8742 (t0) REVERT: F 265 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8581 (tt0) REVERT: F 376 GLN cc_start: 0.9128 (mp10) cc_final: 0.8741 (pm20) REVERT: F 377 MET cc_start: 0.7464 (mmm) cc_final: 0.7171 (mmm) REVERT: G 42 LEU cc_start: 0.8960 (mm) cc_final: 0.8490 (tp) REVERT: I 176 ARG cc_start: 0.9231 (tmm160) cc_final: 0.9002 (tmm160) REVERT: I 185 MET cc_start: 0.9409 (ttt) cc_final: 0.9145 (ptt) REVERT: I 216 LEU cc_start: 0.8938 (mm) cc_final: 0.8636 (mm) REVERT: I 299 MET cc_start: 0.8487 (ptt) cc_final: 0.8072 (tmm) REVERT: H 46 GLN cc_start: 0.8894 (mt0) cc_final: 0.8452 (mm-40) REVERT: H 60 THR cc_start: 0.8644 (t) cc_final: 0.8306 (p) REVERT: H 135 ILE cc_start: 0.8957 (mm) cc_final: 0.8730 (mt) REVERT: J 27 GLN cc_start: 0.5355 (tp-100) cc_final: 0.3890 (mp10) REVERT: J 50 ASP cc_start: 0.9334 (p0) cc_final: 0.8988 (p0) REVERT: J 58 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8544 (mp0) REVERT: J 64 PHE cc_start: 0.9236 (m-80) cc_final: 0.8995 (m-80) outliers start: 5 outliers final: 0 residues processed: 353 average time/residue: 0.1289 time to fit residues: 66.2830 Evaluate side-chains 278 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 173 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN D 259 GLN E 23 GLN E 143 HIS ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.099122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.077591 restraints weight = 69441.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.078047 restraints weight = 42890.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077958 restraints weight = 36875.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.078022 restraints weight = 31016.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.078168 restraints weight = 27380.364| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16460 Z= 0.165 Angle : 0.768 15.029 22362 Z= 0.390 Chirality : 0.045 0.314 2733 Planarity : 0.005 0.117 2919 Dihedral : 5.903 34.108 2440 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.92 % Favored : 88.93 % Rotamer: Outliers : 0.15 % Allowed : 5.71 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 2023 helix: 0.81 (0.15), residues: 1220 sheet: -2.81 (0.41), residues: 134 loop : -3.69 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 212 TYR 0.023 0.002 TYR J 10 PHE 0.027 0.002 PHE E 240 TRP 0.024 0.002 TRP E 39 HIS 0.009 0.002 HIS H 138 Details of bonding type rmsd covalent geometry : bond 0.00347 (16460) covalent geometry : angle 0.76819 (22362) hydrogen bonds : bond 0.04130 ( 1125) hydrogen bonds : angle 4.91442 ( 3327) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 360 time to evaluate : 0.613 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: B 1 MET cc_start: 0.6209 (mtt) cc_final: 0.5825 (mtm) REVERT: B 76 LEU cc_start: 0.9334 (tt) cc_final: 0.9085 (tt) REVERT: B 85 MET cc_start: 0.8420 (mtp) cc_final: 0.8094 (mtt) REVERT: B 164 GLU cc_start: 0.8467 (tt0) cc_final: 0.8004 (tm-30) REVERT: C 163 TYR cc_start: 0.8780 (m-80) cc_final: 0.8415 (m-80) REVERT: C 206 LEU cc_start: 0.9039 (mm) cc_final: 0.8746 (mm) REVERT: C 209 PHE cc_start: 0.7948 (t80) cc_final: 0.7741 (t80) REVERT: C 274 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8406 (tp-100) REVERT: C 277 GLU cc_start: 0.8275 (pp20) cc_final: 0.7865 (tm-30) REVERT: C 343 LYS cc_start: 0.6868 (mtpp) cc_final: 0.6615 (tttt) REVERT: C 344 TRP cc_start: 0.8466 (m-90) cc_final: 0.7894 (m100) REVERT: D 144 THR cc_start: 0.8945 (t) cc_final: 0.7302 (p) REVERT: D 237 PHE cc_start: 0.8254 (p90) cc_final: 0.7607 (p90) REVERT: E 77 TYR cc_start: 0.9170 (m-10) cc_final: 0.8615 (m-80) REVERT: E 133 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8714 (tm-30) REVERT: E 226 GLN cc_start: 0.8745 (tp40) cc_final: 0.8467 (tm-30) REVERT: E 238 ILE cc_start: 0.8271 (mp) cc_final: 0.7583 (pt) REVERT: E 267 MET cc_start: 0.8435 (pmm) cc_final: 0.8186 (pmm) REVERT: E 327 GLU cc_start: 0.8601 (tp30) cc_final: 0.8352 (tp30) REVERT: E 425 ASP cc_start: 0.8081 (p0) cc_final: 0.7609 (p0) REVERT: F 241 ARG cc_start: 0.8934 (tmm160) cc_final: 0.8660 (tmm-80) REVERT: F 247 ARG cc_start: 0.9383 (tpt170) cc_final: 0.8795 (mmm160) REVERT: F 250 GLN cc_start: 0.8606 (mp-120) cc_final: 0.8386 (mm-40) REVERT: F 254 ASN cc_start: 0.8506 (m-40) cc_final: 0.8225 (m-40) REVERT: F 265 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8605 (tt0) REVERT: F 363 TYR cc_start: 0.8898 (m-80) cc_final: 0.8472 (m-80) REVERT: F 376 GLN cc_start: 0.9147 (mp10) cc_final: 0.8706 (pm20) REVERT: G 42 LEU cc_start: 0.8865 (mm) cc_final: 0.8460 (tp) REVERT: G 106 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8946 (tp40) REVERT: I 176 ARG cc_start: 0.9229 (tmm160) cc_final: 0.8959 (tmm160) REVERT: I 185 MET cc_start: 0.9423 (ttt) cc_final: 0.9122 (ptt) REVERT: I 296 VAL cc_start: 0.8531 (m) cc_final: 0.8321 (m) REVERT: I 299 MET cc_start: 0.8474 (ptt) cc_final: 0.8021 (tmm) REVERT: H 46 GLN cc_start: 0.8925 (mt0) cc_final: 0.8440 (mm-40) REVERT: H 60 THR cc_start: 0.8566 (t) cc_final: 0.8288 (p) REVERT: H 135 ILE cc_start: 0.8862 (mm) cc_final: 0.8635 (mt) REVERT: J 20 ILE cc_start: 0.7908 (mm) cc_final: 0.7649 (mm) REVERT: J 25 PHE cc_start: 0.7590 (m-80) cc_final: 0.7374 (m-80) REVERT: J 27 GLN cc_start: 0.5496 (tp-100) cc_final: 0.3512 (mp10) REVERT: J 38 GLN cc_start: 0.8891 (pm20) cc_final: 0.8285 (pm20) REVERT: J 42 TRP cc_start: 0.7500 (m-10) cc_final: 0.7020 (m-10) REVERT: J 64 PHE cc_start: 0.9217 (m-80) cc_final: 0.8949 (m-80) outliers start: 2 outliers final: 0 residues processed: 362 average time/residue: 0.1275 time to fit residues: 67.9488 Evaluate side-chains 288 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 207 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 196 optimal weight: 0.0470 chunk 217 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 ASN C 215 GLN ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN E 23 GLN E 143 HIS E 284 HIS F 250 GLN ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.100208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.078532 restraints weight = 69726.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078193 restraints weight = 44372.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.078500 restraints weight = 37776.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.078683 restraints weight = 31580.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.078770 restraints weight = 28478.436| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16460 Z= 0.152 Angle : 0.763 11.331 22362 Z= 0.387 Chirality : 0.045 0.327 2733 Planarity : 0.005 0.118 2919 Dihedral : 5.662 29.268 2440 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.07 % Favored : 88.78 % Rotamer: Outliers : 0.15 % Allowed : 4.34 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.20), residues: 2023 helix: 1.01 (0.16), residues: 1233 sheet: -2.84 (0.41), residues: 127 loop : -3.68 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 176 TYR 0.033 0.002 TYR F 238 PHE 0.032 0.002 PHE E 240 TRP 0.030 0.002 TRP E 270 HIS 0.013 0.002 HIS H 138 Details of bonding type rmsd covalent geometry : bond 0.00325 (16460) covalent geometry : angle 0.76294 (22362) hydrogen bonds : bond 0.04043 ( 1125) hydrogen bonds : angle 4.86768 ( 3327) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 355 time to evaluate : 0.393 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: B 1 MET cc_start: 0.5959 (mtt) cc_final: 0.5731 (mtt) REVERT: B 76 LEU cc_start: 0.9372 (tt) cc_final: 0.9143 (tt) REVERT: B 85 MET cc_start: 0.8552 (mtp) cc_final: 0.8275 (mtt) REVERT: B 154 GLN cc_start: 0.8647 (pt0) cc_final: 0.8260 (pt0) REVERT: B 164 GLU cc_start: 0.8486 (tt0) cc_final: 0.7906 (tm-30) REVERT: C 163 TYR cc_start: 0.8818 (m-80) cc_final: 0.8409 (m-80) REVERT: C 215 GLN cc_start: 0.8870 (mt0) cc_final: 0.8666 (mm110) REVERT: C 277 GLU cc_start: 0.8179 (pp20) cc_final: 0.7723 (tm-30) REVERT: E 39 TRP cc_start: 0.8235 (t-100) cc_final: 0.7730 (t60) REVERT: E 77 TYR cc_start: 0.9208 (m-10) cc_final: 0.8694 (m-80) REVERT: E 117 LYS cc_start: 0.8823 (mttm) cc_final: 0.8287 (mtpt) REVERT: E 133 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8744 (tm-30) REVERT: E 226 GLN cc_start: 0.8806 (tp40) cc_final: 0.8551 (tm-30) REVERT: E 267 MET cc_start: 0.8310 (pmm) cc_final: 0.8021 (pmm) REVERT: E 327 GLU cc_start: 0.8490 (tp30) cc_final: 0.8245 (tp30) REVERT: E 425 ASP cc_start: 0.8127 (p0) cc_final: 0.7676 (p0) REVERT: F 241 ARG cc_start: 0.8835 (tmm160) cc_final: 0.8573 (ptm-80) REVERT: F 247 ARG cc_start: 0.9417 (tpt170) cc_final: 0.8790 (mmm160) REVERT: F 265 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8578 (tt0) REVERT: F 363 TYR cc_start: 0.8995 (m-80) cc_final: 0.8569 (m-80) REVERT: F 376 GLN cc_start: 0.9168 (mp10) cc_final: 0.8747 (pm20) REVERT: G 42 LEU cc_start: 0.8833 (mm) cc_final: 0.8421 (tp) REVERT: G 106 GLN cc_start: 0.9123 (tp-100) cc_final: 0.8811 (tp-100) REVERT: I 185 MET cc_start: 0.9309 (ttt) cc_final: 0.9029 (ptt) REVERT: I 216 LEU cc_start: 0.8849 (mm) cc_final: 0.8547 (mm) REVERT: I 299 MET cc_start: 0.8494 (ptt) cc_final: 0.7983 (tmm) REVERT: H 46 GLN cc_start: 0.8961 (mt0) cc_final: 0.8535 (mm-40) REVERT: H 50 ARG cc_start: 0.8997 (mtt180) cc_final: 0.8602 (tpt-90) REVERT: H 57 ILE cc_start: 0.7326 (mm) cc_final: 0.7018 (mm) REVERT: H 60 THR cc_start: 0.8708 (t) cc_final: 0.8456 (p) REVERT: H 85 ILE cc_start: 0.7641 (mp) cc_final: 0.7172 (tp) REVERT: H 135 ILE cc_start: 0.8804 (mm) cc_final: 0.8586 (mt) REVERT: J 20 ILE cc_start: 0.7961 (mm) cc_final: 0.7757 (mm) REVERT: J 25 PHE cc_start: 0.7583 (m-80) cc_final: 0.7292 (m-80) REVERT: J 27 GLN cc_start: 0.5306 (tp-100) cc_final: 0.3388 (mp10) REVERT: J 38 GLN cc_start: 0.8912 (pm20) cc_final: 0.8302 (pm20) REVERT: J 42 TRP cc_start: 0.7521 (m-10) cc_final: 0.7164 (m-10) REVERT: J 50 ASP cc_start: 0.9271 (p0) cc_final: 0.8952 (p0) REVERT: J 64 PHE cc_start: 0.9226 (m-80) cc_final: 0.8948 (m-80) REVERT: J 69 ARG cc_start: 0.8469 (mtt180) cc_final: 0.8223 (mtt180) outliers start: 2 outliers final: 1 residues processed: 357 average time/residue: 0.1260 time to fit residues: 66.1396 Evaluate side-chains 284 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 129 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 295 HIS D 230 GLN D 259 GLN D 260 ASN E 23 GLN E 143 HIS ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.100351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.078873 restraints weight = 69586.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.078575 restraints weight = 42258.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.078812 restraints weight = 40440.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.078875 restraints weight = 31482.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.079121 restraints weight = 27743.243| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16460 Z= 0.153 Angle : 0.766 14.271 22362 Z= 0.385 Chirality : 0.045 0.332 2733 Planarity : 0.005 0.101 2919 Dihedral : 5.496 29.536 2440 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.02 % Favored : 88.83 % Rotamer: Outliers : 0.15 % Allowed : 3.42 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.20), residues: 2023 helix: 1.27 (0.16), residues: 1216 sheet: -2.50 (0.42), residues: 141 loop : -3.60 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 212 TYR 0.025 0.002 TYR J 10 PHE 0.033 0.002 PHE I 178 TRP 0.021 0.002 TRP E 106 HIS 0.014 0.002 HIS J 8 Details of bonding type rmsd covalent geometry : bond 0.00331 (16460) covalent geometry : angle 0.76585 (22362) hydrogen bonds : bond 0.03947 ( 1125) hydrogen bonds : angle 4.70755 ( 3327) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 355 time to evaluate : 0.595 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: B 76 LEU cc_start: 0.9333 (tt) cc_final: 0.9114 (tt) REVERT: B 85 MET cc_start: 0.8460 (mtp) cc_final: 0.8167 (mtt) REVERT: B 154 GLN cc_start: 0.8666 (pt0) cc_final: 0.8271 (pt0) REVERT: B 164 GLU cc_start: 0.8488 (tt0) cc_final: 0.7922 (tm-30) REVERT: C 163 TYR cc_start: 0.8842 (m-80) cc_final: 0.8424 (m-80) REVERT: C 182 ASP cc_start: 0.8808 (p0) cc_final: 0.8376 (p0) REVERT: C 207 GLU cc_start: 0.7390 (mp0) cc_final: 0.6865 (mp0) REVERT: C 215 GLN cc_start: 0.8786 (mt0) cc_final: 0.8419 (mm-40) REVERT: C 274 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8281 (tp-100) REVERT: C 344 TRP cc_start: 0.8735 (m-90) cc_final: 0.7903 (m100) REVERT: E 39 TRP cc_start: 0.8244 (t-100) cc_final: 0.7692 (t60) REVERT: E 77 TYR cc_start: 0.9180 (m-10) cc_final: 0.8641 (m-80) REVERT: E 117 LYS cc_start: 0.8832 (mttm) cc_final: 0.8332 (mtpt) REVERT: E 132 LEU cc_start: 0.8896 (pp) cc_final: 0.8691 (mt) REVERT: E 133 GLN cc_start: 0.9123 (tp-100) cc_final: 0.8481 (tm-30) REVERT: E 238 ILE cc_start: 0.8276 (mp) cc_final: 0.7875 (pt) REVERT: E 267 MET cc_start: 0.8268 (pmm) cc_final: 0.7846 (pmm) REVERT: E 327 GLU cc_start: 0.8454 (tp30) cc_final: 0.8251 (tp30) REVERT: E 418 ASP cc_start: 0.8356 (m-30) cc_final: 0.8108 (m-30) REVERT: E 425 ASP cc_start: 0.8117 (p0) cc_final: 0.7657 (p0) REVERT: E 439 SER cc_start: 0.8731 (m) cc_final: 0.8527 (m) REVERT: F 247 ARG cc_start: 0.9413 (tpt170) cc_final: 0.8761 (mmm160) REVERT: F 265 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8589 (tt0) REVERT: F 349 ASP cc_start: 0.8662 (p0) cc_final: 0.8460 (p0) REVERT: F 363 TYR cc_start: 0.9033 (m-80) cc_final: 0.8636 (m-80) REVERT: F 376 GLN cc_start: 0.9216 (mp10) cc_final: 0.8700 (pm20) REVERT: G 42 LEU cc_start: 0.8784 (mm) cc_final: 0.8354 (tp) REVERT: G 61 LEU cc_start: 0.8966 (mt) cc_final: 0.8761 (mt) REVERT: G 78 SER cc_start: 0.8243 (p) cc_final: 0.7929 (p) REVERT: G 106 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8848 (tp40) REVERT: I 185 MET cc_start: 0.9298 (ttt) cc_final: 0.9023 (ptt) REVERT: I 212 ARG cc_start: 0.8750 (tpt90) cc_final: 0.8543 (mmm160) REVERT: I 215 ASP cc_start: 0.8772 (t0) cc_final: 0.8445 (t0) REVERT: I 299 MET cc_start: 0.8503 (ptt) cc_final: 0.8008 (tmm) REVERT: H 46 GLN cc_start: 0.8869 (mt0) cc_final: 0.8460 (mm-40) REVERT: H 50 ARG cc_start: 0.9008 (mtt180) cc_final: 0.8607 (ttt90) REVERT: H 85 ILE cc_start: 0.7200 (mp) cc_final: 0.6807 (tp) REVERT: H 135 ILE cc_start: 0.8707 (mm) cc_final: 0.8487 (mt) REVERT: J 25 PHE cc_start: 0.7627 (m-80) cc_final: 0.7287 (m-80) REVERT: J 27 GLN cc_start: 0.5054 (tp-100) cc_final: 0.3420 (mp10) REVERT: J 38 GLN cc_start: 0.8895 (pm20) cc_final: 0.8305 (pm20) REVERT: J 42 TRP cc_start: 0.7476 (m-10) cc_final: 0.7121 (m-10) REVERT: J 50 ASP cc_start: 0.9262 (p0) cc_final: 0.8925 (p0) REVERT: J 64 PHE cc_start: 0.9247 (m-80) cc_final: 0.8934 (m-80) outliers start: 2 outliers final: 0 residues processed: 357 average time/residue: 0.1239 time to fit residues: 64.8684 Evaluate side-chains 283 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 98 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 160 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 42 optimal weight: 0.0770 chunk 119 optimal weight: 0.0870 chunk 162 optimal weight: 9.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 295 HIS C 340 ASN D 259 GLN E 23 GLN E 143 HIS ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.100838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.079517 restraints weight = 69890.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.078831 restraints weight = 51260.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.079574 restraints weight = 44613.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079713 restraints weight = 34303.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.079961 restraints weight = 30324.733| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16460 Z= 0.146 Angle : 0.772 18.263 22362 Z= 0.385 Chirality : 0.045 0.527 2733 Planarity : 0.005 0.100 2919 Dihedral : 5.366 29.299 2440 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.87 % Favored : 88.98 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 2023 helix: 1.41 (0.16), residues: 1218 sheet: -2.44 (0.44), residues: 127 loop : -3.54 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 158 TYR 0.025 0.001 TYR J 10 PHE 0.031 0.002 PHE I 178 TRP 0.032 0.002 TRP E 106 HIS 0.015 0.002 HIS J 8 Details of bonding type rmsd covalent geometry : bond 0.00315 (16460) covalent geometry : angle 0.77249 (22362) hydrogen bonds : bond 0.03859 ( 1125) hydrogen bonds : angle 4.62048 ( 3327) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.510 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: B 76 LEU cc_start: 0.9365 (tt) cc_final: 0.9137 (tt) REVERT: B 85 MET cc_start: 0.8432 (mtp) cc_final: 0.8221 (mtt) REVERT: B 154 GLN cc_start: 0.8641 (pt0) cc_final: 0.8284 (pt0) REVERT: B 164 GLU cc_start: 0.8496 (tt0) cc_final: 0.8008 (tm-30) REVERT: C 163 TYR cc_start: 0.8738 (m-80) cc_final: 0.8366 (m-80) REVERT: C 274 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8174 (tp-100) REVERT: C 343 LYS cc_start: 0.7048 (tttt) cc_final: 0.6605 (tttt) REVERT: E 39 TRP cc_start: 0.8256 (t-100) cc_final: 0.7839 (t60) REVERT: E 77 TYR cc_start: 0.9117 (m-10) cc_final: 0.8593 (m-80) REVERT: E 117 LYS cc_start: 0.8785 (mttm) cc_final: 0.8338 (mtpt) REVERT: E 132 LEU cc_start: 0.8817 (pp) cc_final: 0.8588 (mt) REVERT: E 133 GLN cc_start: 0.9137 (tp-100) cc_final: 0.8515 (tm-30) REVERT: E 238 ILE cc_start: 0.8306 (mp) cc_final: 0.7955 (pt) REVERT: E 267 MET cc_start: 0.8445 (pmm) cc_final: 0.7922 (pmm) REVERT: E 425 ASP cc_start: 0.8150 (p0) cc_final: 0.7685 (p0) REVERT: F 241 ARG cc_start: 0.9000 (tmm160) cc_final: 0.8669 (ptm-80) REVERT: F 247 ARG cc_start: 0.9359 (tpt170) cc_final: 0.8814 (mmm160) REVERT: F 252 LEU cc_start: 0.9305 (mm) cc_final: 0.9096 (mp) REVERT: F 265 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8556 (tt0) REVERT: F 363 TYR cc_start: 0.9010 (m-80) cc_final: 0.8620 (m-80) REVERT: F 376 GLN cc_start: 0.9155 (mp10) cc_final: 0.8592 (pm20) REVERT: G 42 LEU cc_start: 0.8779 (mm) cc_final: 0.8323 (tp) REVERT: G 106 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8787 (tp40) REVERT: G 112 ARG cc_start: 0.8690 (pmt-80) cc_final: 0.8486 (pmt-80) REVERT: I 185 MET cc_start: 0.9312 (ttt) cc_final: 0.9017 (ptt) REVERT: I 299 MET cc_start: 0.8480 (ptt) cc_final: 0.8011 (tmm) REVERT: H 46 GLN cc_start: 0.8829 (mt0) cc_final: 0.8434 (mm-40) REVERT: H 50 ARG cc_start: 0.8991 (mtt180) cc_final: 0.8654 (tpt-90) REVERT: H 135 ILE cc_start: 0.8730 (mm) cc_final: 0.8494 (mt) REVERT: J 5 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8621 (mm-40) REVERT: J 8 HIS cc_start: 0.7901 (p90) cc_final: 0.7529 (p90) REVERT: J 25 PHE cc_start: 0.7559 (m-80) cc_final: 0.7177 (m-80) REVERT: J 38 GLN cc_start: 0.8888 (pm20) cc_final: 0.8172 (pm20) REVERT: J 42 TRP cc_start: 0.7477 (m-10) cc_final: 0.7173 (m-10) REVERT: J 50 ASP cc_start: 0.9262 (p0) cc_final: 0.8863 (p0) REVERT: J 64 PHE cc_start: 0.9207 (m-80) cc_final: 0.8154 (m-80) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.1228 time to fit residues: 65.1175 Evaluate side-chains 288 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 65 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 118 optimal weight: 40.0000 chunk 24 optimal weight: 3.9990 chunk 173 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 32 optimal weight: 0.0270 chunk 3 optimal weight: 2.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 283 GLN C 295 HIS C 340 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN E 23 GLN ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.098929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.077390 restraints weight = 70365.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.077007 restraints weight = 44088.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.077505 restraints weight = 40129.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.077535 restraints weight = 32234.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.077727 restraints weight = 28909.734| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16460 Z= 0.190 Angle : 0.801 16.399 22362 Z= 0.408 Chirality : 0.046 0.577 2733 Planarity : 0.005 0.100 2919 Dihedral : 5.466 29.142 2440 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.06 % Favored : 87.79 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 2023 helix: 1.41 (0.16), residues: 1221 sheet: -2.35 (0.43), residues: 139 loop : -3.68 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 158 TYR 0.025 0.002 TYR J 10 PHE 0.034 0.002 PHE E 240 TRP 0.038 0.002 TRP E 106 HIS 0.013 0.002 HIS J 8 Details of bonding type rmsd covalent geometry : bond 0.00410 (16460) covalent geometry : angle 0.80122 (22362) hydrogen bonds : bond 0.04026 ( 1125) hydrogen bonds : angle 4.76564 ( 3327) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.605 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: B 85 MET cc_start: 0.8569 (mtp) cc_final: 0.8342 (mtt) REVERT: B 154 GLN cc_start: 0.8698 (pt0) cc_final: 0.8394 (pt0) REVERT: B 164 GLU cc_start: 0.8481 (tt0) cc_final: 0.7914 (tm-30) REVERT: C 163 TYR cc_start: 0.8854 (m-80) cc_final: 0.8447 (m-80) REVERT: C 207 GLU cc_start: 0.7466 (mp0) cc_final: 0.7018 (mp0) REVERT: C 225 LYS cc_start: 0.8039 (tmtt) cc_final: 0.7784 (tmtt) REVERT: C 274 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8371 (tp-100) REVERT: C 283 GLN cc_start: 0.8765 (tt0) cc_final: 0.8207 (tp40) REVERT: D 313 ASN cc_start: 0.9241 (p0) cc_final: 0.9001 (p0) REVERT: E 23 GLN cc_start: 0.9392 (mp10) cc_final: 0.9188 (mp10) REVERT: E 77 TYR cc_start: 0.9148 (m-10) cc_final: 0.8614 (m-80) REVERT: E 133 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8480 (tm-30) REVERT: E 267 MET cc_start: 0.8370 (pmm) cc_final: 0.7960 (pmm) REVERT: E 383 GLU cc_start: 0.7845 (tt0) cc_final: 0.7598 (tm-30) REVERT: E 425 ASP cc_start: 0.8237 (p0) cc_final: 0.7943 (p0) REVERT: E 439 SER cc_start: 0.8701 (m) cc_final: 0.8489 (m) REVERT: F 241 ARG cc_start: 0.8744 (tmm160) cc_final: 0.8359 (ttp80) REVERT: F 247 ARG cc_start: 0.9392 (tpt170) cc_final: 0.8797 (mmm160) REVERT: F 265 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8614 (tt0) REVERT: F 363 TYR cc_start: 0.8996 (m-80) cc_final: 0.8566 (m-80) REVERT: F 376 GLN cc_start: 0.9148 (mp10) cc_final: 0.8619 (pm20) REVERT: G 42 LEU cc_start: 0.8782 (mm) cc_final: 0.8327 (tp) REVERT: G 70 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8242 (mp0) REVERT: I 185 MET cc_start: 0.9280 (ttt) cc_final: 0.9022 (ptt) REVERT: I 216 LEU cc_start: 0.8703 (mm) cc_final: 0.8425 (mm) REVERT: I 274 MET cc_start: 0.3617 (tpp) cc_final: 0.2907 (tpt) REVERT: I 299 MET cc_start: 0.8517 (ptt) cc_final: 0.8060 (tmm) REVERT: H 46 GLN cc_start: 0.8892 (mt0) cc_final: 0.8423 (mm-40) REVERT: H 135 ILE cc_start: 0.8719 (mm) cc_final: 0.8502 (mt) REVERT: J 5 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8466 (mm-40) REVERT: J 8 HIS cc_start: 0.7788 (p90) cc_final: 0.7413 (p-80) REVERT: J 25 PHE cc_start: 0.7381 (m-80) cc_final: 0.6974 (m-80) REVERT: J 38 GLN cc_start: 0.8904 (pm20) cc_final: 0.8619 (pm20) REVERT: J 50 ASP cc_start: 0.9242 (p0) cc_final: 0.8911 (p0) REVERT: J 60 ARG cc_start: 0.8415 (tpt170) cc_final: 0.8038 (tpp80) REVERT: J 62 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8311 (mmtt) REVERT: J 64 PHE cc_start: 0.8907 (m-80) cc_final: 0.8190 (m-80) REVERT: J 69 ARG cc_start: 0.8679 (mtt180) cc_final: 0.8397 (mtt180) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.1263 time to fit residues: 63.3088 Evaluate side-chains 280 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 192 optimal weight: 30.0000 chunk 145 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 152 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN E 143 HIS E 207 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.100346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.078793 restraints weight = 69963.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.078646 restraints weight = 46387.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.078920 restraints weight = 42876.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.079008 restraints weight = 34490.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.079106 restraints weight = 30378.278| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16460 Z= 0.154 Angle : 0.800 18.730 22362 Z= 0.401 Chirality : 0.046 0.535 2733 Planarity : 0.005 0.099 2919 Dihedral : 5.350 29.835 2440 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.92 % Favored : 88.93 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 2023 helix: 1.47 (0.16), residues: 1218 sheet: -2.38 (0.46), residues: 125 loop : -3.58 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 158 TYR 0.026 0.001 TYR J 10 PHE 0.031 0.002 PHE E 240 TRP 0.030 0.002 TRP E 106 HIS 0.013 0.002 HIS J 8 Details of bonding type rmsd covalent geometry : bond 0.00334 (16460) covalent geometry : angle 0.80030 (22362) hydrogen bonds : bond 0.03929 ( 1125) hydrogen bonds : angle 4.69414 ( 3327) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.426 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: B 1 MET cc_start: 0.6075 (mtt) cc_final: 0.5306 (mtt) REVERT: B 10 ILE cc_start: 0.8653 (mp) cc_final: 0.8257 (mp) REVERT: B 85 MET cc_start: 0.8573 (mtp) cc_final: 0.8059 (mtp) REVERT: B 154 GLN cc_start: 0.8665 (pt0) cc_final: 0.8385 (pt0) REVERT: B 157 ASN cc_start: 0.9301 (m-40) cc_final: 0.8911 (m-40) REVERT: B 164 GLU cc_start: 0.8385 (tt0) cc_final: 0.7990 (tm-30) REVERT: B 203 LEU cc_start: 0.9416 (mm) cc_final: 0.8967 (tt) REVERT: C 163 TYR cc_start: 0.8781 (m-80) cc_final: 0.8394 (m-80) REVERT: C 207 GLU cc_start: 0.7431 (mp0) cc_final: 0.6967 (mp0) REVERT: C 269 LYS cc_start: 0.9446 (ptmt) cc_final: 0.9115 (ptmt) REVERT: C 274 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8204 (tp-100) REVERT: D 258 PHE cc_start: 0.8779 (m-10) cc_final: 0.8565 (m-80) REVERT: E 39 TRP cc_start: 0.8316 (t-100) cc_final: 0.8026 (t60) REVERT: E 77 TYR cc_start: 0.9156 (m-10) cc_final: 0.8615 (m-80) REVERT: E 117 LYS cc_start: 0.8797 (mttm) cc_final: 0.8331 (mtpt) REVERT: E 238 ILE cc_start: 0.7713 (pt) cc_final: 0.7389 (pt) REVERT: E 267 MET cc_start: 0.8525 (pmm) cc_final: 0.8155 (pmm) REVERT: E 383 GLU cc_start: 0.7801 (tt0) cc_final: 0.7387 (tm-30) REVERT: E 425 ASP cc_start: 0.8140 (p0) cc_final: 0.7756 (p0) REVERT: F 241 ARG cc_start: 0.8947 (tmm160) cc_final: 0.8671 (ptm-80) REVERT: F 247 ARG cc_start: 0.9394 (tpt170) cc_final: 0.8706 (mmm160) REVERT: F 265 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8627 (tt0) REVERT: F 363 TYR cc_start: 0.8977 (m-80) cc_final: 0.8524 (m-80) REVERT: F 376 GLN cc_start: 0.9195 (mp10) cc_final: 0.8717 (pm20) REVERT: G 42 LEU cc_start: 0.8771 (mm) cc_final: 0.8345 (tp) REVERT: G 106 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8660 (tp-100) REVERT: G 112 ARG cc_start: 0.8654 (pmt-80) cc_final: 0.8432 (pmt-80) REVERT: I 185 MET cc_start: 0.9281 (ttt) cc_final: 0.9017 (ptt) REVERT: I 299 MET cc_start: 0.8535 (ptt) cc_final: 0.8042 (tmm) REVERT: H 46 GLN cc_start: 0.8798 (mt0) cc_final: 0.8401 (mm-40) REVERT: H 50 ARG cc_start: 0.8992 (mtt180) cc_final: 0.8673 (tpt-90) REVERT: H 85 ILE cc_start: 0.7203 (mp) cc_final: 0.6926 (tp) REVERT: H 135 ILE cc_start: 0.8722 (mm) cc_final: 0.8515 (mt) REVERT: J 5 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8482 (mm-40) REVERT: J 8 HIS cc_start: 0.7855 (p90) cc_final: 0.7466 (p-80) REVERT: J 25 PHE cc_start: 0.7513 (m-80) cc_final: 0.7037 (m-80) REVERT: J 41 HIS cc_start: 0.9078 (m90) cc_final: 0.8324 (m-70) REVERT: J 50 ASP cc_start: 0.9179 (p0) cc_final: 0.8815 (p0) REVERT: J 58 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8594 (mp0) REVERT: J 60 ARG cc_start: 0.8500 (tpt170) cc_final: 0.8115 (tpp80) REVERT: J 64 PHE cc_start: 0.8940 (m-80) cc_final: 0.8186 (m-80) REVERT: J 69 ARG cc_start: 0.8684 (mtt180) cc_final: 0.8372 (mtt180) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1184 time to fit residues: 60.0459 Evaluate side-chains 285 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 187 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 152 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B -1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN E 23 GLN ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS E 207 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.095994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.074145 restraints weight = 70577.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.073145 restraints weight = 56816.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.073526 restraints weight = 50628.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.073596 restraints weight = 41155.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.073755 restraints weight = 35087.688| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 16460 Z= 0.315 Angle : 0.914 16.494 22362 Z= 0.474 Chirality : 0.051 0.639 2733 Planarity : 0.006 0.111 2919 Dihedral : 5.912 30.912 2440 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.49 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.20), residues: 2023 helix: 1.02 (0.15), residues: 1215 sheet: -2.46 (0.46), residues: 141 loop : -3.70 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 158 TYR 0.026 0.003 TYR E 200 PHE 0.040 0.003 PHE E 240 TRP 0.044 0.003 TRP E 106 HIS 0.012 0.002 HIS J 8 Details of bonding type rmsd covalent geometry : bond 0.00664 (16460) covalent geometry : angle 0.91400 (22362) hydrogen bonds : bond 0.04603 ( 1125) hydrogen bonds : angle 5.23771 ( 3327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2745.02 seconds wall clock time: 48 minutes 6.15 seconds (2886.15 seconds total)