Starting phenix.real_space_refine on Fri Sep 19 05:28:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6umm_20820/09_2025/6umm_20820.cif Found real_map, /net/cci-nas-00/data/ceres_data/6umm_20820/09_2025/6umm_20820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6umm_20820/09_2025/6umm_20820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6umm_20820/09_2025/6umm_20820.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6umm_20820/09_2025/6umm_20820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6umm_20820/09_2025/6umm_20820.map" } resolution = 3.7 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= 0.001 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 60 5.16 5 C 15131 2.51 5 N 4240 2.21 5 O 4227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 185 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23658 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2169 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 268} Chain: "B" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3162 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 415} Chain breaks: 2 Chain: "C" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3238 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 422} Chain breaks: 1 Chain: "D" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 644 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "E" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2698 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 313} Chain breaks: 1 Chain: "F" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2169 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 268} Chain: "G" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3162 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 415} Chain breaks: 2 Chain: "H" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3238 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 422} Chain breaks: 1 Chain: "I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "J" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2698 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 313} Chain breaks: 1 Time building chain proxies: 5.54, per 1000 atoms: 0.23 Number of scatterers: 23658 At special positions: 0 Unit cell: (188.6, 141.86, 154.98, 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 60 16.00 O 4227 8.00 N 4240 7.00 C 15131 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: 1.74 Conformation dependent library (CDL) restraints added in 791.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5908 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 19 sheets defined 58.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 Processing helix chain 'A' and resid 23 through 41 Processing helix chain 'A' and resid 48 through 65 Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.671A pdb=" N VAL A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.793A pdb=" N LEU A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 163 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 263 through 270 Processing helix chain 'B' and resid 34 through 47 removed outlier: 3.796A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 111 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 127 through 159 removed outlier: 3.803A pdb=" N HIS B 131 " --> pdb=" O TRP B 127 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 181 removed outlier: 3.675A pdb=" N LEU B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 213 through 234 removed outlier: 3.553A pdb=" N GLY B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 264 Processing helix chain 'B' and resid 267 through 285 removed outlier: 3.556A pdb=" N ILE B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 319 through 351 Processing helix chain 'B' and resid 356 through 374 removed outlier: 3.556A pdb=" N TRP B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 removed outlier: 4.396A pdb=" N SER B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 430 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 436 through 439 removed outlier: 3.540A pdb=" N TYR B 439 " --> pdb=" O PRO B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 436 through 439' Processing helix chain 'B' and resid 440 through 455 Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.984A pdb=" N VAL B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'C' and resid 34 through 47 Proline residue: C 40 - end of helix Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 115 through 123 removed outlier: 3.926A pdb=" N ARG C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 158 Processing helix chain 'C' and resid 161 through 182 Processing helix chain 'C' and resid 185 through 196 removed outlier: 3.543A pdb=" N ALA C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 208 removed outlier: 3.889A pdb=" N LEU C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 removed outlier: 3.587A pdb=" N VAL C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 264 removed outlier: 3.753A pdb=" N VAL C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 285 Processing helix chain 'C' and resid 285 through 294 Processing helix chain 'C' and resid 313 through 351 removed outlier: 3.667A pdb=" N LEU C 317 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Proline residue: C 321 - end of helix Processing helix chain 'C' and resid 356 through 373 Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 379 through 404 removed outlier: 4.648A pdb=" N SER C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 430 Processing helix chain 'C' and resid 435 through 439 Processing helix chain 'C' and resid 440 through 466 removed outlier: 4.443A pdb=" N ILE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) Proline residue: C 460 - end of helix Processing helix chain 'C' and resid 467 through 474 Processing helix chain 'D' and resid 34 through 54 Processing helix chain 'D' and resid 62 through 92 Processing helix chain 'E' and resid 95 through 130 Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.540A pdb=" N ILE E 139 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 197 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 220 through 237 Processing helix chain 'E' and resid 258 through 264 Processing helix chain 'E' and resid 285 through 298 Proline residue: E 295 - end of helix Processing helix chain 'E' and resid 386 through 399 removed outlier: 3.953A pdb=" N ARG E 399 " --> pdb=" O ARG E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 17 Processing helix chain 'F' and resid 23 through 41 Processing helix chain 'F' and resid 48 through 65 Processing helix chain 'F' and resid 89 through 96 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 143 through 163 Processing helix chain 'F' and resid 204 through 215 removed outlier: 3.638A pdb=" N VAL F 208 " --> pdb=" O ARG F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 271 Processing helix chain 'G' and resid 34 through 37 Processing helix chain 'G' and resid 38 through 47 Processing helix chain 'G' and resid 112 through 121 removed outlier: 3.585A pdb=" N GLU G 121 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 159 Processing helix chain 'G' and resid 161 through 181 removed outlier: 3.805A pdb=" N PHE G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 208 removed outlier: 3.664A pdb=" N ALA G 189 " --> pdb=" O SER G 185 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL G 198 " --> pdb=" O VAL G 194 " (cutoff:3.500A) Proline residue: G 199 - end of helix removed outlier: 3.993A pdb=" N VAL G 208 " --> pdb=" O PHE G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 235 removed outlier: 3.616A pdb=" N VAL G 217 " --> pdb=" O GLY G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 264 Processing helix chain 'G' and resid 267 through 285 removed outlier: 3.501A pdb=" N ILE G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 294 Processing helix chain 'G' and resid 319 through 349 Processing helix chain 'G' and resid 356 through 374 Processing helix chain 'G' and resid 379 through 404 removed outlier: 3.518A pdb=" N TRP G 385 " --> pdb=" O ALA G 381 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER G 390 " --> pdb=" O LEU G 386 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR G 391 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 430 removed outlier: 3.552A pdb=" N ALA G 410 " --> pdb=" O ARG G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 435 removed outlier: 3.634A pdb=" N ALA G 434 " --> pdb=" O ASN G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 466 removed outlier: 5.280A pdb=" N ILE G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) Proline residue: G 460 - end of helix Processing helix chain 'G' and resid 469 through 474 Processing helix chain 'H' and resid 34 through 47 removed outlier: 3.980A pdb=" N ILE H 38 " --> pdb=" O PRO H 34 " (cutoff:3.500A) Proline residue: H 40 - end of helix removed outlier: 3.518A pdb=" N GLN H 47 " --> pdb=" O GLN H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 115 through 123 Processing helix chain 'H' and resid 128 through 158 Processing helix chain 'H' and resid 160 through 181 removed outlier: 4.408A pdb=" N GLN H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 186 through 196 Processing helix chain 'H' and resid 196 through 206 Processing helix chain 'H' and resid 213 through 233 removed outlier: 4.021A pdb=" N VAL H 217 " --> pdb=" O GLY H 213 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 264 removed outlier: 3.534A pdb=" N TRP H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 285 removed outlier: 3.527A pdb=" N ILE H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 285 " --> pdb=" O ILE H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 294 Processing helix chain 'H' and resid 313 through 351 removed outlier: 3.531A pdb=" N LEU H 317 " --> pdb=" O PRO H 313 " (cutoff:3.500A) Proline residue: H 321 - end of helix Processing helix chain 'H' and resid 356 through 373 Processing helix chain 'H' and resid 380 through 404 removed outlier: 3.846A pdb=" N ALA H 384 " --> pdb=" O ALA H 380 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER H 390 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR H 391 " --> pdb=" O LEU H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 430 Processing helix chain 'H' and resid 435 through 439 Processing helix chain 'H' and resid 440 through 466 removed outlier: 4.331A pdb=" N ILE H 459 " --> pdb=" O ASP H 455 " (cutoff:3.500A) Proline residue: H 460 - end of helix Processing helix chain 'H' and resid 468 through 475 Processing helix chain 'I' and resid 34 through 51 Processing helix chain 'I' and resid 62 through 92 Processing helix chain 'J' and resid 95 through 130 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'J' and resid 183 through 197 Processing helix chain 'J' and resid 210 through 212 No H-bonds generated for 'chain 'J' and resid 210 through 212' Processing helix chain 'J' and resid 220 through 237 Processing helix chain 'J' and resid 255 through 260 removed outlier: 4.226A pdb=" N TRP J 260 " --> pdb=" O GLY J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 263 No H-bonds generated for 'chain 'J' and resid 261 through 263' Processing helix chain 'J' and resid 285 through 294 Processing helix chain 'J' and resid 295 through 297 No H-bonds generated for 'chain 'J' and resid 295 through 297' Processing helix chain 'J' and resid 324 through 328 removed outlier: 3.623A pdb=" N ILE J 328 " --> pdb=" O PRO J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 398 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 169 removed outlier: 4.401A pdb=" N VAL A 79 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A 120 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.305A pdb=" N ASP A 105 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY A 228 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 219 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL A 237 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 199 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 181 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.647A pdb=" N LYS A 181 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 169 removed outlier: 4.401A pdb=" N VAL A 79 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP A 127 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS A 104 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP A 105 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY A 228 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 219 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL A 237 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 199 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 67 through 71 removed outlier: 8.836A pdb=" N LEU B 94 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 13 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU B 96 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU B 15 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N ALA B 98 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 14 Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AA8, first strand: chain 'E' and resid 22 through 24 removed outlier: 6.039A pdb=" N ILE E 22 " --> pdb=" O LYS E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 157 through 166 removed outlier: 6.793A pdb=" N VAL E 157 " --> pdb=" O ASP E 208 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP E 208 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG E 159 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY E 206 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY E 161 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N HIS E 163 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 202 " --> pdb=" O HIS E 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 246 through 249 removed outlier: 6.225A pdb=" N ALA E 247 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL E 316 " --> pdb=" O ILE E 340 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG E 342 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU E 318 " --> pdb=" O ARG E 342 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU E 360 " --> pdb=" O ARG E 214 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR E 216 " --> pdb=" O LEU E 360 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL E 362 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE E 218 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE E 359 " --> pdb=" O TRP E 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 166 through 168 removed outlier: 3.868A pdb=" N SER F 120 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS F 106 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER F 229 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL F 237 " --> pdb=" O VAL F 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 98 through 99 Processing sheet with id=AB4, first strand: chain 'F' and resid 181 through 182 Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 71 removed outlier: 8.471A pdb=" N LEU G 94 " --> pdb=" O ARG G 11 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA G 13 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU G 96 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU G 15 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N ALA G 98 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG G 23 " --> pdb=" O ALA G 16 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 24 through 30 removed outlier: 3.918A pdb=" N LEU H 96 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=AB8, first strand: chain 'J' and resid 157 through 163 removed outlier: 6.938A pdb=" N THR J 205 " --> pdb=" O ALA J 160 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG J 162 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ALA J 203 " --> pdb=" O ARG J 162 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 216 through 219 removed outlier: 5.824A pdb=" N THR J 216 " --> pdb=" O LEU J 360 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL J 362 " --> pdb=" O THR J 216 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE J 218 " --> pdb=" O VAL J 362 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE J 359 " --> pdb=" O TRP J 370 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 246 through 248 removed outlier: 6.429A pdb=" N ALA J 247 " --> pdb=" O VAL J 317 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU J 314 " --> pdb=" O THR J 338 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE J 340 " --> pdb=" O LEU J 314 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL J 316 " --> pdb=" O ILE J 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 1531 hydrogen bonds defined for protein. 4485 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: 4.30 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7885 1.34 - 1.45: 3036 1.45 - 1.57: 13116 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 24141 Sorted by residual: bond pdb=" C LEU A 270 " pdb=" N ASN A 271 " ideal model delta sigma weight residual 1.327 1.246 0.081 2.31e-02 1.87e+03 1.23e+01 bond pdb=" N VAL G 350 " pdb=" CA VAL G 350 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.92e+00 bond pdb=" N LEU G 349 " pdb=" CA LEU G 349 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.90e+00 bond pdb=" N ARG C 312 " pdb=" CA ARG C 312 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.41e-02 5.03e+03 6.75e+00 bond pdb=" N SER G 351 " pdb=" CA SER G 351 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.22e-02 6.72e+03 6.00e+00 ... (remaining 24136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 32641 2.73 - 5.46: 431 5.46 - 8.18: 26 8.18 - 10.91: 2 10.91 - 13.64: 1 Bond angle restraints: 33101 Sorted by residual: angle pdb=" N ILE E 328 " pdb=" CA ILE E 328 " pdb=" C ILE E 328 " ideal model delta sigma weight residual 113.71 107.40 6.31 9.50e-01 1.11e+00 4.41e+01 angle pdb=" N ARG J 151 " pdb=" CA ARG J 151 " pdb=" C ARG J 151 " ideal model delta sigma weight residual 114.64 105.58 9.06 1.52e+00 4.33e-01 3.55e+01 angle pdb=" N ILE J 328 " pdb=" CA ILE J 328 " pdb=" C ILE J 328 " ideal model delta sigma weight residual 111.62 108.19 3.43 7.90e-01 1.60e+00 1.88e+01 angle pdb=" N ASP H 19 " pdb=" CA ASP H 19 " pdb=" C ASP H 19 " ideal model delta sigma weight residual 114.39 108.40 5.99 1.45e+00 4.76e-01 1.71e+01 angle pdb=" N TRP E 258 " pdb=" CA TRP E 258 " pdb=" C TRP E 258 " ideal model delta sigma weight residual 114.64 108.46 6.18 1.52e+00 4.33e-01 1.66e+01 ... (remaining 33096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13337 17.86 - 35.71: 913 35.71 - 53.57: 130 53.57 - 71.43: 43 71.43 - 89.28: 24 Dihedral angle restraints: 14447 sinusoidal: 5342 harmonic: 9105 Sorted by residual: dihedral pdb=" CA SER D 15 " pdb=" C SER D 15 " pdb=" N ARG D 16 " pdb=" CA ARG D 16 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ARG E 349 " pdb=" C ARG E 349 " pdb=" N GLU E 350 " pdb=" CA GLU E 350 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP E 364 " pdb=" C ASP E 364 " pdb=" N GLY E 365 " pdb=" CA GLY E 365 " ideal model delta harmonic sigma weight residual 180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 14444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3260 0.053 - 0.106: 689 0.106 - 0.159: 104 0.159 - 0.212: 5 0.212 - 0.265: 1 Chirality restraints: 4059 Sorted by residual: chirality pdb=" CB ILE H 459 " pdb=" CA ILE H 459 " pdb=" CG1 ILE H 459 " pdb=" CG2 ILE H 459 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE J 180 " pdb=" CA ILE J 180 " pdb=" CG1 ILE J 180 " pdb=" CG2 ILE J 180 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL C 167 " pdb=" CA VAL C 167 " pdb=" CG1 VAL C 167 " pdb=" CG2 VAL C 167 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 4056 not shown) Planarity restraints: 4231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 200 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.47e+00 pdb=" C VAL E 200 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL E 200 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG E 201 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 435 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO H 436 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 436 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 436 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 441 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO C 442 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 442 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 442 " -0.026 5.00e-02 4.00e+02 ... (remaining 4228 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3222 2.74 - 3.28: 24920 3.28 - 3.82: 39502 3.82 - 4.36: 44139 4.36 - 4.90: 76758 Nonbonded interactions: 188541 Sorted by model distance: nonbonded pdb=" OG SER C 352 " pdb=" OD1 ASN C 354 " model vdw 2.203 3.040 nonbonded pdb=" O THR C 82 " pdb=" OG1 THR C 85 " model vdw 2.227 3.040 nonbonded pdb=" NH1 ARG J 225 " pdb=" OD2 ASP J 257 " model vdw 2.230 3.120 nonbonded pdb=" OG SER G 31 " pdb=" OD1 ASP G 84 " model vdw 2.231 3.040 nonbonded pdb=" NE ARG A 138 " pdb=" OE2 GLU C 110 " model vdw 2.237 3.120 ... (remaining 188536 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = (chain 'B' and (resid 7 through 49 or resid 67 through 475)) selection = (chain 'C' and (resid 7 through 295 or resid 313 through 475)) selection = (chain 'G' and (resid 7 through 49 or resid 67 through 475)) selection = (chain 'H' and (resid 7 through 295 or resid 313 through 475)) } ncs_group { reference = chain 'E' selection = chain 'J' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.630 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.670 Find NCS groups from input model: 0.370 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 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 : 0.006 0.081 24141 Z= 0.300 Angle : 0.793 13.638 33101 Z= 0.455 Chirality : 0.043 0.265 4059 Planarity : 0.005 0.046 4231 Dihedral : 13.227 89.283 8539 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.17 % Allowed : 7.66 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.13), residues: 3148 helix: -0.54 (0.11), residues: 1748 sheet: -2.31 (0.25), residues: 283 loop : -2.33 (0.16), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 198 TYR 0.027 0.002 TYR F 96 PHE 0.020 0.002 PHE I 88 TRP 0.020 0.002 TRP H 293 HIS 0.008 0.002 HIS J 239 Details of bonding type rmsd covalent geometry : bond 0.00647 (24141) covalent geometry : angle 0.79290 (33101) hydrogen bonds : bond 0.11859 ( 1496) hydrogen bonds : angle 5.46079 ( 4485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 599 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 289 LEU cc_start: 0.8386 (mt) cc_final: 0.8043 (mt) REVERT: C 288 GLN cc_start: 0.7078 (pt0) cc_final: 0.6671 (pt0) REVERT: E 228 ILE cc_start: 0.8167 (mt) cc_final: 0.7855 (mm) REVERT: H 461 VAL cc_start: 0.7424 (t) cc_final: 0.7064 (t) outliers start: 4 outliers final: 1 residues processed: 600 average time/residue: 0.1429 time to fit residues: 137.5398 Evaluate side-chains 368 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 201 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 89 GLN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 HIS B 408 GLN C 154 HIS C 216 ASN C 328 GLN C 330 HIS E 130 HIS ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 313 HIS F 74 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 271 ASN G 47 GLN G 328 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 GLN ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 313 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.055481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.047137 restraints weight = 152736.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.047615 restraints weight = 127366.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.047845 restraints weight = 109972.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.048131 restraints weight = 101143.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.048129 restraints weight = 91250.939| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24141 Z= 0.163 Angle : 0.745 10.005 33101 Z= 0.362 Chirality : 0.046 0.388 4059 Planarity : 0.005 0.044 4231 Dihedral : 4.962 74.301 3456 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.02 % Allowed : 17.09 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3148 helix: 0.54 (0.12), residues: 1761 sheet: -1.94 (0.27), residues: 294 loop : -1.49 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 153 TYR 0.025 0.002 TYR F 96 PHE 0.028 0.002 PHE G 165 TRP 0.023 0.001 TRP E 231 HIS 0.007 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00348 (24141) covalent geometry : angle 0.74455 (33101) hydrogen bonds : bond 0.04308 ( 1496) hydrogen bonds : angle 4.55366 ( 4485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 407 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 MET cc_start: 0.8294 (tmm) cc_final: 0.8082 (tmm) REVERT: B 378 ASP cc_start: 0.9567 (p0) cc_final: 0.9117 (p0) REVERT: B 401 PHE cc_start: 0.9472 (m-10) cc_final: 0.9138 (m-10) REVERT: B 446 MET cc_start: 0.9354 (mmp) cc_final: 0.9128 (mmp) REVERT: C 126 GLN cc_start: 0.9382 (pm20) cc_final: 0.8481 (pp30) REVERT: C 218 LEU cc_start: 0.9740 (mt) cc_final: 0.9510 (mt) REVERT: C 244 PHE cc_start: 0.8894 (m-80) cc_final: 0.8543 (m-80) REVERT: C 255 LEU cc_start: 0.9536 (mt) cc_final: 0.9211 (mt) REVERT: C 285 GLN cc_start: 0.9286 (mm-40) cc_final: 0.8426 (tp-100) REVERT: C 288 GLN cc_start: 0.9316 (pt0) cc_final: 0.8938 (pm20) REVERT: C 292 MET cc_start: 0.9095 (ppp) cc_final: 0.8891 (ppp) REVERT: C 377 TRP cc_start: 0.9358 (m-90) cc_final: 0.9011 (m-90) REVERT: C 401 PHE cc_start: 0.9613 (m-80) cc_final: 0.9309 (m-80) REVERT: C 446 MET cc_start: 0.9503 (mmp) cc_final: 0.9300 (mmt) REVERT: D 28 TYR cc_start: 0.7563 (m-80) cc_final: 0.6993 (m-10) REVERT: D 45 MET cc_start: 0.9563 (tpp) cc_final: 0.9051 (mpp) REVERT: E 1 MET cc_start: 0.3251 (mtt) cc_final: 0.2216 (ptp) REVERT: E 197 GLN cc_start: 0.9677 (mm-40) cc_final: 0.9445 (mp10) REVERT: E 202 ASP cc_start: 0.9184 (t0) cc_final: 0.8575 (t0) REVERT: E 228 ILE cc_start: 0.9923 (mt) cc_final: 0.9691 (mm) REVERT: G 229 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9437 (mm) REVERT: G 391 TYR cc_start: 0.8842 (t80) cc_final: 0.8603 (t80) REVERT: G 458 LEU cc_start: 0.9594 (mm) cc_final: 0.9363 (mm) REVERT: G 462 MET cc_start: 0.9577 (ttm) cc_final: 0.9158 (tmm) REVERT: H 232 MET cc_start: 0.9198 (ttm) cc_final: 0.8540 (mtp) REVERT: H 331 GLN cc_start: 0.9508 (tp40) cc_final: 0.9042 (tp40) REVERT: H 361 TYR cc_start: 0.9041 (t80) cc_final: 0.8524 (t80) REVERT: H 382 CYS cc_start: 0.9622 (m) cc_final: 0.9361 (p) REVERT: I 54 LEU cc_start: 0.9660 (mm) cc_final: 0.9454 (mm) REVERT: J 243 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7928 (ptp) outliers start: 73 outliers final: 29 residues processed: 446 average time/residue: 0.1358 time to fit residues: 99.1316 Evaluate side-chains 374 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 343 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 243 MET Chi-restraints excluded: chain J residue 317 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 133 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 270 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 143 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 6 optimal weight: 0.0470 chunk 24 optimal weight: 9.9990 chunk 82 optimal weight: 0.3980 overall best weight: 2.0884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.056979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.048420 restraints weight = 132964.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.048421 restraints weight = 118285.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.048421 restraints weight = 118256.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.048421 restraints weight = 118256.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.048421 restraints weight = 118256.786| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24141 Z= 0.144 Angle : 0.733 12.199 33101 Z= 0.345 Chirality : 0.044 0.376 4059 Planarity : 0.005 0.113 4231 Dihedral : 4.657 72.823 3452 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.19 % Allowed : 18.87 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.15), residues: 3148 helix: 0.87 (0.12), residues: 1763 sheet: -1.65 (0.27), residues: 294 loop : -1.16 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 141 TYR 0.022 0.002 TYR F 96 PHE 0.030 0.002 PHE C 119 TRP 0.042 0.001 TRP E 231 HIS 0.006 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00316 (24141) covalent geometry : angle 0.73260 (33101) hydrogen bonds : bond 0.04031 ( 1496) hydrogen bonds : angle 4.38692 ( 4485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 370 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 LEU cc_start: 0.9401 (mt) cc_final: 0.9142 (mt) REVERT: B 292 MET cc_start: 0.8348 (tmm) cc_final: 0.8145 (tmm) REVERT: B 372 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8859 (mm) REVERT: C 244 PHE cc_start: 0.8993 (m-80) cc_final: 0.8638 (m-80) REVERT: C 255 LEU cc_start: 0.9493 (mt) cc_final: 0.9168 (mt) REVERT: C 285 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8366 (tp-100) REVERT: C 288 GLN cc_start: 0.9380 (pt0) cc_final: 0.8962 (pm20) REVERT: C 292 MET cc_start: 0.9097 (ppp) cc_final: 0.8894 (ppp) REVERT: C 401 PHE cc_start: 0.9566 (m-80) cc_final: 0.9166 (m-80) REVERT: D 45 MET cc_start: 0.9639 (tpp) cc_final: 0.9206 (mpp) REVERT: E 1 MET cc_start: 0.3624 (mtt) cc_final: 0.2460 (ptp) REVERT: E 164 ASP cc_start: 0.9612 (OUTLIER) cc_final: 0.9331 (t0) REVERT: E 197 GLN cc_start: 0.9720 (mm-40) cc_final: 0.9372 (mp10) REVERT: E 202 ASP cc_start: 0.9233 (t0) cc_final: 0.8651 (t0) REVERT: E 248 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8393 (tp) REVERT: G 391 TYR cc_start: 0.8815 (t80) cc_final: 0.8561 (t80) REVERT: G 458 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9334 (mm) REVERT: G 462 MET cc_start: 0.9542 (ttm) cc_final: 0.9106 (tmm) REVERT: H 232 MET cc_start: 0.9285 (ttm) cc_final: 0.8759 (mtp) REVERT: H 331 GLN cc_start: 0.9585 (tp40) cc_final: 0.9188 (tp40) REVERT: H 361 TYR cc_start: 0.9117 (t80) cc_final: 0.8641 (t80) REVERT: H 455 ASP cc_start: 0.9464 (m-30) cc_final: 0.8907 (m-30) REVERT: I 59 MET cc_start: 0.8559 (mmm) cc_final: 0.8289 (mmm) REVERT: J 1 MET cc_start: 0.8482 (ptt) cc_final: 0.7279 (ppp) REVERT: J 19 LYS cc_start: 0.9313 (tptt) cc_final: 0.9102 (tptp) REVERT: J 105 LEU cc_start: 0.9853 (OUTLIER) cc_final: 0.9610 (mt) REVERT: J 243 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8096 (ptp) outliers start: 77 outliers final: 37 residues processed: 413 average time/residue: 0.1336 time to fit residues: 92.9350 Evaluate side-chains 376 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 333 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 243 MET Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 362 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 277 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 312 optimal weight: 8.9990 chunk 227 optimal weight: 0.8980 chunk 135 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 305 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 331 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 HIS ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.047155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.039786 restraints weight = 225470.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.040522 restraints weight = 149954.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.041039 restraints weight = 113928.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.041419 restraints weight = 93682.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041676 restraints weight = 81175.924| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24141 Z= 0.167 Angle : 0.732 13.400 33101 Z= 0.347 Chirality : 0.044 0.343 4059 Planarity : 0.005 0.053 4231 Dihedral : 4.534 69.856 3452 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.35 % Allowed : 20.90 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.15), residues: 3148 helix: 1.19 (0.12), residues: 1770 sheet: -1.59 (0.27), residues: 296 loop : -0.91 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 153 TYR 0.025 0.002 TYR D 28 PHE 0.015 0.001 PHE G 165 TRP 0.054 0.001 TRP E 231 HIS 0.007 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00353 (24141) covalent geometry : angle 0.73215 (33101) hydrogen bonds : bond 0.03869 ( 1496) hydrogen bonds : angle 4.38732 ( 4485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 349 time to evaluate : 0.849 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: A 59 MET cc_start: 0.8971 (tpp) cc_final: 0.8674 (tpp) REVERT: A 96 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: B 289 LEU cc_start: 0.9425 (mt) cc_final: 0.9205 (mt) REVERT: B 446 MET cc_start: 0.9343 (mmp) cc_final: 0.9094 (mmp) REVERT: C 10 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8721 (t) REVERT: C 232 MET cc_start: 0.9018 (ppp) cc_final: 0.8693 (ppp) REVERT: C 244 PHE cc_start: 0.9131 (m-80) cc_final: 0.8870 (m-80) REVERT: C 285 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8354 (tp-100) REVERT: C 288 GLN cc_start: 0.9379 (pt0) cc_final: 0.8973 (pm20) REVERT: C 401 PHE cc_start: 0.9664 (m-80) cc_final: 0.9232 (m-80) REVERT: C 424 TRP cc_start: 0.9581 (m100) cc_final: 0.9315 (m100) REVERT: C 443 MET cc_start: 0.9251 (ptp) cc_final: 0.8945 (ptt) REVERT: D 45 MET cc_start: 0.9610 (tpp) cc_final: 0.9199 (mpp) REVERT: D 64 LEU cc_start: 0.9617 (pp) cc_final: 0.9363 (pp) REVERT: E 1 MET cc_start: 0.2934 (mtt) cc_final: 0.1972 (ptp) REVERT: E 164 ASP cc_start: 0.9320 (OUTLIER) cc_final: 0.8958 (t0) REVERT: E 197 GLN cc_start: 0.9658 (mm-40) cc_final: 0.9308 (mp10) REVERT: E 248 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8574 (tp) REVERT: F 10 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9180 (mm) REVERT: G 143 LEU cc_start: 0.9830 (tt) cc_final: 0.9555 (tp) REVERT: G 362 ILE cc_start: 0.9588 (mt) cc_final: 0.9344 (mt) REVERT: G 391 TYR cc_start: 0.8757 (t80) cc_final: 0.8552 (t80) REVERT: G 458 LEU cc_start: 0.9720 (mm) cc_final: 0.9389 (mm) REVERT: G 462 MET cc_start: 0.9625 (ttm) cc_final: 0.9277 (tmm) REVERT: H 232 MET cc_start: 0.9216 (ttm) cc_final: 0.8162 (tpp) REVERT: H 331 GLN cc_start: 0.9444 (tp40) cc_final: 0.8948 (tp40) REVERT: H 361 TYR cc_start: 0.9244 (t80) cc_final: 0.8715 (t80) REVERT: H 382 CYS cc_start: 0.9711 (m) cc_final: 0.9448 (p) REVERT: H 455 ASP cc_start: 0.9486 (m-30) cc_final: 0.9205 (t0) REVERT: I 59 MET cc_start: 0.8668 (mmm) cc_final: 0.8387 (mmm) REVERT: J 1 MET cc_start: 0.7081 (ptt) cc_final: 0.6223 (ppp) REVERT: J 96 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: J 105 LEU cc_start: 0.9803 (OUTLIER) cc_final: 0.9539 (mt) REVERT: J 243 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8193 (ptp) REVERT: J 348 ASN cc_start: 0.9572 (t0) cc_final: 0.9341 (m-40) outliers start: 81 outliers final: 46 residues processed: 395 average time/residue: 0.1285 time to fit residues: 85.5785 Evaluate side-chains 373 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 319 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 85 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 243 MET Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 322 ASP Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 362 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 192 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 80 optimal weight: 0.0980 chunk 168 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.053695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.045833 restraints weight = 162792.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.046204 restraints weight = 132712.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046561 restraints weight = 116589.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.046687 restraints weight = 104993.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.046955 restraints weight = 100257.414| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24141 Z= 0.129 Angle : 0.743 13.375 33101 Z= 0.341 Chirality : 0.045 0.423 4059 Planarity : 0.004 0.053 4231 Dihedral : 4.409 67.616 3452 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.06 % Allowed : 22.60 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.15), residues: 3148 helix: 1.25 (0.12), residues: 1780 sheet: -1.52 (0.27), residues: 292 loop : -0.79 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 162 TYR 0.023 0.002 TYR D 28 PHE 0.014 0.001 PHE G 165 TRP 0.036 0.001 TRP E 231 HIS 0.005 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00282 (24141) covalent geometry : angle 0.74314 (33101) hydrogen bonds : bond 0.03765 ( 1496) hydrogen bonds : angle 4.31474 ( 4485) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 353 time to evaluate : 0.769 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: A 59 MET cc_start: 0.9073 (tpp) cc_final: 0.8814 (tpp) REVERT: A 96 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: B 289 LEU cc_start: 0.9446 (mt) cc_final: 0.9228 (mt) REVERT: B 351 SER cc_start: 0.9042 (t) cc_final: 0.8691 (p) REVERT: B 446 MET cc_start: 0.9354 (mmp) cc_final: 0.9094 (mmp) REVERT: C 121 GLU cc_start: 0.9540 (mm-30) cc_final: 0.9333 (mm-30) REVERT: C 244 PHE cc_start: 0.9043 (m-80) cc_final: 0.8756 (m-80) REVERT: C 255 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9243 (mt) REVERT: C 285 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8266 (tp-100) REVERT: C 288 GLN cc_start: 0.9422 (pt0) cc_final: 0.8951 (pm20) REVERT: C 401 PHE cc_start: 0.9637 (m-80) cc_final: 0.9172 (m-80) REVERT: C 424 TRP cc_start: 0.9460 (m100) cc_final: 0.9167 (m100) REVERT: C 454 LEU cc_start: 0.9778 (mt) cc_final: 0.9389 (tp) REVERT: D 21 GLU cc_start: 0.9052 (mp0) cc_final: 0.8839 (pm20) REVERT: D 45 MET cc_start: 0.9522 (tpp) cc_final: 0.9225 (mpp) REVERT: E 1 MET cc_start: 0.3210 (mtt) cc_final: 0.2962 (mtt) REVERT: E 248 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8463 (tp) REVERT: F 10 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9210 (mm) REVERT: G 143 LEU cc_start: 0.9845 (tt) cc_final: 0.9623 (tp) REVERT: G 393 LEU cc_start: 0.9650 (tt) cc_final: 0.9325 (mt) REVERT: G 443 MET cc_start: 0.9072 (mpp) cc_final: 0.8167 (mpp) REVERT: G 458 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9170 (mt) REVERT: G 462 MET cc_start: 0.9517 (ttm) cc_final: 0.9080 (tmm) REVERT: H 227 TRP cc_start: 0.9282 (t-100) cc_final: 0.8908 (t-100) REVERT: H 232 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8287 (tpp) REVERT: H 331 GLN cc_start: 0.9379 (tp40) cc_final: 0.9040 (tp40) REVERT: H 361 TYR cc_start: 0.9339 (t80) cc_final: 0.8874 (t80) REVERT: H 455 ASP cc_start: 0.9360 (m-30) cc_final: 0.9104 (t0) REVERT: H 458 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9467 (mt) REVERT: I 59 MET cc_start: 0.8593 (mmm) cc_final: 0.8233 (mmm) REVERT: J 1 MET cc_start: 0.8313 (ptt) cc_final: 0.6994 (ppp) REVERT: J 96 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: J 105 LEU cc_start: 0.9872 (OUTLIER) cc_final: 0.9607 (mt) REVERT: J 243 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8273 (ptm) REVERT: J 348 ASN cc_start: 0.9531 (t0) cc_final: 0.9292 (m-40) outliers start: 74 outliers final: 39 residues processed: 397 average time/residue: 0.1235 time to fit residues: 83.0840 Evaluate side-chains 367 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 318 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 243 MET Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 362 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 296 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 195 optimal weight: 0.0060 chunk 258 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 overall best weight: 2.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 ASN ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.046872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039491 restraints weight = 229779.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.040234 restraints weight = 152603.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.040757 restraints weight = 116285.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.041125 restraints weight = 95645.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.041378 restraints weight = 83248.294| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24141 Z= 0.147 Angle : 0.752 13.718 33101 Z= 0.349 Chirality : 0.045 0.403 4059 Planarity : 0.004 0.058 4231 Dihedral : 4.351 63.915 3452 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.35 % Allowed : 23.22 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.15), residues: 3148 helix: 1.32 (0.12), residues: 1784 sheet: -1.39 (0.27), residues: 288 loop : -0.68 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 44 TYR 0.014 0.002 TYR F 96 PHE 0.014 0.001 PHE C 296 TRP 0.029 0.001 TRP E 231 HIS 0.006 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00315 (24141) covalent geometry : angle 0.75223 (33101) hydrogen bonds : bond 0.03752 ( 1496) hydrogen bonds : angle 4.38683 ( 4485) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 324 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8787 (ppp) cc_final: 0.8568 (tmm) REVERT: A 59 MET cc_start: 0.8947 (tpp) cc_final: 0.8603 (tpp) REVERT: A 96 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: B 289 LEU cc_start: 0.9477 (mt) cc_final: 0.9214 (mt) REVERT: B 378 ASP cc_start: 0.9417 (p0) cc_final: 0.9198 (p0) REVERT: B 446 MET cc_start: 0.9335 (mmp) cc_final: 0.9090 (mmp) REVERT: C 121 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9161 (mm-30) REVERT: C 232 MET cc_start: 0.9032 (ppp) cc_final: 0.8693 (ppp) REVERT: C 244 PHE cc_start: 0.9189 (m-80) cc_final: 0.8932 (m-80) REVERT: C 255 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9242 (mt) REVERT: C 285 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8381 (tp40) REVERT: C 288 GLN cc_start: 0.9476 (pt0) cc_final: 0.9051 (tm-30) REVERT: C 401 PHE cc_start: 0.9663 (m-10) cc_final: 0.9306 (m-80) REVERT: C 424 TRP cc_start: 0.9613 (m100) cc_final: 0.9334 (m100) REVERT: C 454 LEU cc_start: 0.9835 (mt) cc_final: 0.9455 (tp) REVERT: D 45 MET cc_start: 0.9580 (tpp) cc_final: 0.9347 (mpp) REVERT: E 1 MET cc_start: 0.2798 (mtt) cc_final: 0.2559 (mtt) REVERT: E 248 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8509 (tp) REVERT: F 10 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9172 (mm) REVERT: G 362 ILE cc_start: 0.9593 (mt) cc_final: 0.9314 (mt) REVERT: G 393 LEU cc_start: 0.9624 (tt) cc_final: 0.9268 (mt) REVERT: G 458 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9227 (mt) REVERT: G 462 MET cc_start: 0.9599 (ttm) cc_final: 0.9275 (tmm) REVERT: H 227 TRP cc_start: 0.9301 (t-100) cc_final: 0.8934 (t-100) REVERT: H 232 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8212 (tpp) REVERT: H 331 GLN cc_start: 0.9200 (tp40) cc_final: 0.8933 (tp40) REVERT: H 361 TYR cc_start: 0.9402 (t80) cc_final: 0.8970 (t80) REVERT: H 455 ASP cc_start: 0.9442 (m-30) cc_final: 0.9213 (t0) REVERT: H 458 LEU cc_start: 0.9777 (tp) cc_final: 0.9537 (mt) REVERT: I 72 LEU cc_start: 0.9591 (mt) cc_final: 0.9349 (pp) REVERT: J 1 MET cc_start: 0.6950 (ptt) cc_final: 0.6229 (ppp) REVERT: J 105 LEU cc_start: 0.9803 (OUTLIER) cc_final: 0.9553 (mt) REVERT: J 348 ASN cc_start: 0.9577 (t0) cc_final: 0.9323 (m-40) outliers start: 81 outliers final: 46 residues processed: 380 average time/residue: 0.1207 time to fit residues: 78.5873 Evaluate side-chains 365 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 322 ASP Chi-restraints excluded: chain J residue 362 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 47 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.052517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.044676 restraints weight = 164416.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.044997 restraints weight = 137550.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.045248 restraints weight = 122603.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045415 restraints weight = 110878.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.045421 restraints weight = 105438.790| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24141 Z= 0.157 Angle : 0.765 13.831 33101 Z= 0.355 Chirality : 0.045 0.432 4059 Planarity : 0.004 0.050 4231 Dihedral : 4.316 59.703 3452 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.69 % Allowed : 24.50 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.15), residues: 3148 helix: 1.36 (0.12), residues: 1779 sheet: -1.38 (0.27), residues: 287 loop : -0.62 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 65 TYR 0.013 0.002 TYR F 96 PHE 0.012 0.001 PHE F 11 TRP 0.025 0.001 TRP E 231 HIS 0.005 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00339 (24141) covalent geometry : angle 0.76539 (33101) hydrogen bonds : bond 0.03742 ( 1496) hydrogen bonds : angle 4.43974 ( 4485) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 315 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.9056 (tpp) cc_final: 0.8774 (tpp) REVERT: A 96 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: B 289 LEU cc_start: 0.9451 (mt) cc_final: 0.9194 (mt) REVERT: B 378 ASP cc_start: 0.9538 (p0) cc_final: 0.9285 (p0) REVERT: B 446 MET cc_start: 0.9327 (mmp) cc_final: 0.9055 (mmt) REVERT: C 121 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9360 (mm-30) REVERT: C 165 PHE cc_start: 0.9228 (m-10) cc_final: 0.8975 (m-80) REVERT: C 232 MET cc_start: 0.8935 (ppp) cc_final: 0.8541 (ppp) REVERT: C 244 PHE cc_start: 0.9095 (m-80) cc_final: 0.8808 (m-80) REVERT: C 255 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9223 (mt) REVERT: C 401 PHE cc_start: 0.9584 (m-10) cc_final: 0.9291 (m-80) REVERT: C 424 TRP cc_start: 0.9478 (m100) cc_final: 0.9157 (m100) REVERT: C 454 LEU cc_start: 0.9793 (mt) cc_final: 0.9431 (tp) REVERT: E 1 MET cc_start: 0.2920 (mtt) cc_final: 0.2660 (mtt) REVERT: E 248 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8477 (tp) REVERT: F 10 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9188 (mm) REVERT: G 362 ILE cc_start: 0.9578 (mt) cc_final: 0.9325 (mt) REVERT: G 393 LEU cc_start: 0.9660 (tt) cc_final: 0.9308 (mt) REVERT: G 458 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9187 (mt) REVERT: G 462 MET cc_start: 0.9489 (ttm) cc_final: 0.9145 (tmm) REVERT: H 227 TRP cc_start: 0.9334 (t-100) cc_final: 0.9008 (t-100) REVERT: H 232 MET cc_start: 0.9322 (ttm) cc_final: 0.8368 (tpp) REVERT: H 331 GLN cc_start: 0.9263 (tp40) cc_final: 0.8974 (tp40) REVERT: H 361 TYR cc_start: 0.9466 (t80) cc_final: 0.9022 (t80) REVERT: H 458 LEU cc_start: 0.9776 (tp) cc_final: 0.9564 (mt) REVERT: I 59 MET cc_start: 0.8796 (mmm) cc_final: 0.8463 (mmm) REVERT: J 1 MET cc_start: 0.8303 (ptt) cc_final: 0.7075 (ppp) REVERT: J 96 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: J 105 LEU cc_start: 0.9855 (OUTLIER) cc_final: 0.9606 (mt) REVERT: J 348 ASN cc_start: 0.9563 (t0) cc_final: 0.9323 (m-40) outliers start: 65 outliers final: 46 residues processed: 360 average time/residue: 0.1270 time to fit residues: 78.2446 Evaluate side-chains 353 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 430 ASN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 322 ASP Chi-restraints excluded: chain J residue 362 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 61 optimal weight: 9.9990 chunk 167 optimal weight: 0.5980 chunk 305 optimal weight: 7.9990 chunk 223 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.046518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039209 restraints weight = 228488.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.039932 restraints weight = 151568.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.040440 restraints weight = 116188.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.040794 restraints weight = 96059.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.041057 restraints weight = 84001.848| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24141 Z= 0.134 Angle : 0.784 14.180 33101 Z= 0.359 Chirality : 0.047 0.476 4059 Planarity : 0.004 0.049 4231 Dihedral : 4.268 55.534 3452 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.32 % Allowed : 24.83 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.15), residues: 3148 helix: 1.31 (0.12), residues: 1771 sheet: -1.17 (0.28), residues: 281 loop : -0.52 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 162 TYR 0.015 0.001 TYR F 96 PHE 0.018 0.001 PHE C 296 TRP 0.067 0.001 TRP E 231 HIS 0.004 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00294 (24141) covalent geometry : angle 0.78449 (33101) hydrogen bonds : bond 0.03737 ( 1496) hydrogen bonds : angle 4.40600 ( 4485) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 325 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: B 289 LEU cc_start: 0.9502 (mt) cc_final: 0.9264 (mt) REVERT: B 378 ASP cc_start: 0.9456 (p0) cc_final: 0.9172 (p0) REVERT: B 397 LEU cc_start: 0.9888 (OUTLIER) cc_final: 0.9687 (mm) REVERT: B 446 MET cc_start: 0.9308 (mmp) cc_final: 0.9059 (mmp) REVERT: C 121 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9147 (mm-30) REVERT: C 165 PHE cc_start: 0.9217 (m-10) cc_final: 0.8933 (m-80) REVERT: C 244 PHE cc_start: 0.9242 (m-80) cc_final: 0.8956 (m-80) REVERT: C 255 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9216 (mt) REVERT: C 285 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8204 (tp-100) REVERT: C 288 GLN cc_start: 0.9449 (pt0) cc_final: 0.9064 (pm20) REVERT: C 401 PHE cc_start: 0.9597 (m-10) cc_final: 0.9282 (m-80) REVERT: C 424 TRP cc_start: 0.9654 (m100) cc_final: 0.9337 (m100) REVERT: C 454 LEU cc_start: 0.9839 (mt) cc_final: 0.9471 (tp) REVERT: D 32 PHE cc_start: 0.7965 (m-80) cc_final: 0.7648 (m-10) REVERT: D 45 MET cc_start: 0.9474 (tpp) cc_final: 0.8865 (mpp) REVERT: E 1 MET cc_start: 0.2315 (mtt) cc_final: 0.2099 (mtt) REVERT: E 248 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8522 (tp) REVERT: E 385 MET cc_start: 0.9088 (ppp) cc_final: 0.8772 (ppp) REVERT: F 10 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9156 (mm) REVERT: G 362 ILE cc_start: 0.9565 (mt) cc_final: 0.9263 (mt) REVERT: G 387 LEU cc_start: 0.9573 (mt) cc_final: 0.9301 (mt) REVERT: G 393 LEU cc_start: 0.9603 (tt) cc_final: 0.9225 (mt) REVERT: G 458 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9232 (mt) REVERT: G 462 MET cc_start: 0.9601 (ttm) cc_final: 0.9312 (tmm) REVERT: H 232 MET cc_start: 0.9241 (ttm) cc_final: 0.8264 (tpp) REVERT: H 331 GLN cc_start: 0.9174 (tp40) cc_final: 0.8869 (tp40) REVERT: H 361 TYR cc_start: 0.9448 (t80) cc_final: 0.8981 (t80) REVERT: H 458 LEU cc_start: 0.9790 (tp) cc_final: 0.9509 (mt) REVERT: I 59 MET cc_start: 0.8775 (mmm) cc_final: 0.8421 (mmm) REVERT: I 72 LEU cc_start: 0.9559 (mt) cc_final: 0.9294 (pp) REVERT: J 1 MET cc_start: 0.6986 (ptt) cc_final: 0.6240 (ppp) REVERT: J 96 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: J 243 MET cc_start: 0.8886 (ptp) cc_final: 0.8674 (mpp) REVERT: J 348 ASN cc_start: 0.9593 (t0) cc_final: 0.9339 (m-40) outliers start: 56 outliers final: 38 residues processed: 363 average time/residue: 0.1130 time to fit residues: 70.6765 Evaluate side-chains 353 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 308 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 239 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.046609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039247 restraints weight = 228922.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.039988 restraints weight = 152194.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.040511 restraints weight = 115974.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.040866 restraints weight = 95721.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.041135 restraints weight = 83468.381| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24141 Z= 0.133 Angle : 0.809 14.911 33101 Z= 0.365 Chirality : 0.048 0.429 4059 Planarity : 0.004 0.048 4231 Dihedral : 4.230 51.433 3452 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.15 % Allowed : 25.29 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.15), residues: 3148 helix: 1.31 (0.12), residues: 1769 sheet: -1.10 (0.28), residues: 285 loop : -0.49 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 55 TYR 0.015 0.001 TYR F 96 PHE 0.016 0.001 PHE H 296 TRP 0.071 0.001 TRP E 231 HIS 0.004 0.001 HIS G 389 Details of bonding type rmsd covalent geometry : bond 0.00295 (24141) covalent geometry : angle 0.80924 (33101) hydrogen bonds : bond 0.03731 ( 1496) hydrogen bonds : angle 4.44652 ( 4485) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 320 time to evaluate : 0.668 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: A 59 MET cc_start: 0.9254 (mmm) cc_final: 0.9036 (mmt) REVERT: A 96 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: B 289 LEU cc_start: 0.9518 (mt) cc_final: 0.9277 (mt) REVERT: B 378 ASP cc_start: 0.9449 (p0) cc_final: 0.9147 (p0) REVERT: B 397 LEU cc_start: 0.9877 (OUTLIER) cc_final: 0.9674 (mm) REVERT: B 446 MET cc_start: 0.9361 (mmp) cc_final: 0.9061 (mmp) REVERT: C 121 GLU cc_start: 0.9381 (mm-30) cc_final: 0.9143 (mm-30) REVERT: C 165 PHE cc_start: 0.9200 (m-10) cc_final: 0.8919 (m-80) REVERT: C 244 PHE cc_start: 0.9265 (m-80) cc_final: 0.8988 (m-80) REVERT: C 255 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9233 (mt) REVERT: C 285 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8104 (tp-100) REVERT: C 288 GLN cc_start: 0.9472 (pt0) cc_final: 0.9073 (pm20) REVERT: C 354 ASN cc_start: 0.9330 (t0) cc_final: 0.8933 (p0) REVERT: C 401 PHE cc_start: 0.9595 (m-10) cc_final: 0.9249 (m-80) REVERT: C 424 TRP cc_start: 0.9674 (m100) cc_final: 0.9344 (m100) REVERT: C 454 LEU cc_start: 0.9843 (mt) cc_final: 0.9488 (tp) REVERT: D 32 PHE cc_start: 0.7867 (m-80) cc_final: 0.7610 (m-10) REVERT: D 45 MET cc_start: 0.9458 (tpp) cc_final: 0.8955 (mpp) REVERT: E 248 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8465 (tp) REVERT: F 10 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9155 (mm) REVERT: G 362 ILE cc_start: 0.9565 (mt) cc_final: 0.9274 (mt) REVERT: G 387 LEU cc_start: 0.9533 (mt) cc_final: 0.9255 (mt) REVERT: G 393 LEU cc_start: 0.9597 (tt) cc_final: 0.9221 (mt) REVERT: G 458 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9237 (mt) REVERT: G 462 MET cc_start: 0.9586 (ttm) cc_final: 0.9299 (tmm) REVERT: H 232 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8776 (mmm) REVERT: H 331 GLN cc_start: 0.9206 (tp40) cc_final: 0.8900 (tp40) REVERT: H 361 TYR cc_start: 0.9479 (t80) cc_final: 0.9026 (t80) REVERT: H 458 LEU cc_start: 0.9795 (tp) cc_final: 0.9502 (mt) REVERT: I 59 MET cc_start: 0.8787 (mmm) cc_final: 0.8444 (mmm) REVERT: I 72 LEU cc_start: 0.9520 (mt) cc_final: 0.9254 (pp) REVERT: J 1 MET cc_start: 0.6815 (ptt) cc_final: 0.6127 (ppp) REVERT: J 243 MET cc_start: 0.8825 (ptp) cc_final: 0.8609 (mpp) REVERT: J 348 ASN cc_start: 0.9574 (t0) cc_final: 0.9330 (m-40) outliers start: 52 outliers final: 40 residues processed: 355 average time/residue: 0.1200 time to fit residues: 72.7957 Evaluate side-chains 358 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 311 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 430 ASN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 68 optimal weight: 20.0000 chunk 241 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 297 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 235 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.046292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.039003 restraints weight = 230541.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.039728 restraints weight = 154484.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.040229 restraints weight = 117727.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.040605 restraints weight = 97333.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.040867 restraints weight = 84372.626| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24141 Z= 0.142 Angle : 0.821 14.898 33101 Z= 0.375 Chirality : 0.048 0.490 4059 Planarity : 0.004 0.047 4231 Dihedral : 4.187 47.959 3452 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.24 % Allowed : 25.17 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.15), residues: 3148 helix: 1.40 (0.12), residues: 1752 sheet: -1.06 (0.28), residues: 292 loop : -0.45 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 11 TYR 0.014 0.001 TYR F 96 PHE 0.029 0.001 PHE C 296 TRP 0.065 0.001 TRP E 231 HIS 0.013 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00316 (24141) covalent geometry : angle 0.82139 (33101) hydrogen bonds : bond 0.03707 ( 1496) hydrogen bonds : angle 4.47968 ( 4485) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 313 time to evaluate : 0.627 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: A 96 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: B 289 LEU cc_start: 0.9529 (mt) cc_final: 0.9264 (mt) REVERT: B 378 ASP cc_start: 0.9481 (p0) cc_final: 0.9182 (p0) REVERT: B 397 LEU cc_start: 0.9873 (OUTLIER) cc_final: 0.9661 (mm) REVERT: B 446 MET cc_start: 0.9356 (mmp) cc_final: 0.9079 (mmp) REVERT: C 121 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9155 (mm-30) REVERT: C 165 PHE cc_start: 0.9205 (m-10) cc_final: 0.8929 (m-80) REVERT: C 244 PHE cc_start: 0.9291 (m-80) cc_final: 0.8999 (m-80) REVERT: C 255 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9230 (mt) REVERT: C 285 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8129 (tp-100) REVERT: C 288 GLN cc_start: 0.9492 (pt0) cc_final: 0.9084 (pm20) REVERT: C 354 ASN cc_start: 0.9356 (t0) cc_final: 0.8964 (p0) REVERT: C 401 PHE cc_start: 0.9603 (m-10) cc_final: 0.9269 (m-80) REVERT: C 424 TRP cc_start: 0.9667 (m100) cc_final: 0.9352 (m100) REVERT: C 454 LEU cc_start: 0.9839 (mt) cc_final: 0.9494 (tp) REVERT: D 32 PHE cc_start: 0.7859 (m-80) cc_final: 0.7592 (m-10) REVERT: D 45 MET cc_start: 0.9484 (tpp) cc_final: 0.8980 (mpp) REVERT: E 1 MET cc_start: 0.4092 (mtt) cc_final: 0.3728 (ptp) REVERT: E 248 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8540 (tp) REVERT: E 385 MET cc_start: 0.9191 (ppp) cc_final: 0.8642 (ppp) REVERT: G 362 ILE cc_start: 0.9564 (mt) cc_final: 0.9270 (mt) REVERT: G 387 LEU cc_start: 0.9526 (mt) cc_final: 0.9245 (mt) REVERT: G 393 LEU cc_start: 0.9594 (tt) cc_final: 0.9221 (mt) REVERT: G 458 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9229 (mt) REVERT: G 462 MET cc_start: 0.9595 (ttm) cc_final: 0.9306 (tmm) REVERT: H 232 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8813 (mmm) REVERT: H 331 GLN cc_start: 0.9185 (tp40) cc_final: 0.8876 (tp40) REVERT: H 361 TYR cc_start: 0.9478 (t80) cc_final: 0.9019 (t80) REVERT: H 458 LEU cc_start: 0.9771 (tp) cc_final: 0.9477 (mt) REVERT: I 59 MET cc_start: 0.8771 (mmm) cc_final: 0.8428 (mmm) REVERT: J 1 MET cc_start: 0.6970 (ptt) cc_final: 0.6275 (ppp) REVERT: J 243 MET cc_start: 0.8877 (ptp) cc_final: 0.8633 (mpp) REVERT: J 348 ASN cc_start: 0.9607 (t0) cc_final: 0.9366 (m-40) outliers start: 54 outliers final: 47 residues processed: 349 average time/residue: 0.1183 time to fit residues: 70.9074 Evaluate side-chains 362 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 309 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 430 ASN Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 129 optimal weight: 8.9990 chunk 236 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 302 optimal weight: 0.0670 chunk 181 optimal weight: 10.0000 chunk 253 optimal weight: 0.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.046556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039299 restraints weight = 234863.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.040055 restraints weight = 155932.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.040600 restraints weight = 117246.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.040975 restraints weight = 95521.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041266 restraints weight = 82523.279| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24141 Z= 0.131 Angle : 0.825 15.615 33101 Z= 0.372 Chirality : 0.048 0.477 4059 Planarity : 0.005 0.082 4231 Dihedral : 4.146 43.721 3452 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.19 % Allowed : 25.41 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.15), residues: 3148 helix: 1.36 (0.12), residues: 1750 sheet: -0.81 (0.29), residues: 268 loop : -0.36 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 44 TYR 0.014 0.001 TYR F 96 PHE 0.023 0.001 PHE C 296 TRP 0.063 0.001 TRP E 231 HIS 0.012 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00292 (24141) covalent geometry : angle 0.82539 (33101) hydrogen bonds : bond 0.03706 ( 1496) hydrogen bonds : angle 4.44471 ( 4485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4312.35 seconds wall clock time: 74 minutes 59.34 seconds (4499.34 seconds total)