Starting phenix.real_space_refine on Sun Sep 29 20:47:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/09_2024/6umm_20820.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/09_2024/6umm_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/09_2024/6umm_20820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/09_2024/6umm_20820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/09_2024/6umm_20820.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/09_2024/6umm_20820.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 15.52, per 1000 atoms: 0.66 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: 6.27 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.44 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: 8.14 Time building geometry restraints manager: 7.25 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: 3.480 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: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 54.340 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.510 ------------------------------------------------------------------------------- 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= 0.429 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (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 TRP 0.020 0.002 TRP H 293 HIS 0.008 0.002 HIS J 239 PHE 0.020 0.002 PHE I 88 TYR 0.027 0.002 TYR F 96 ARG 0.007 0.001 ARG J 198 *********************** 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 fitting. rotamer outliers: 4 poor density : 599 time to evaluate : 2.694 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: 0.3229 time to fit residues: 308.9798 Evaluate side-chains 368 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 367 time to evaluate : 2.655 ------------------------------------------------------------------------------- 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 266 optimal weight: 7.9990 chunk 239 optimal weight: 0.0570 chunk 132 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 95 optimal weight: 0.0980 chunk 150 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 overall best weight: 4.0304 ------------------------------------------------------------------------------- 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 154 HIS B 408 GLN C 154 HIS C 216 ASN C 328 GLN C 330 HIS E 130 HIS E 187 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** ** I 37 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24141 Z= 0.269 Angle : 0.744 9.312 33101 Z= 0.367 Chirality : 0.045 0.342 4059 Planarity : 0.005 0.042 4231 Dihedral : 4.957 73.712 3456 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.06 % Allowed : 17.55 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3148 helix: 0.60 (0.12), residues: 1763 sheet: -1.92 (0.27), residues: 290 loop : -1.45 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 231 HIS 0.008 0.001 HIS G 389 PHE 0.027 0.002 PHE G 165 TYR 0.024 0.002 TYR F 96 ARG 0.011 0.001 ARG A 52 *********************** 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 469 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 395 time to evaluate : 2.870 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: E 228 ILE cc_start: 0.8524 (mt) cc_final: 0.8083 (mm) outliers start: 74 outliers final: 32 residues processed: 437 average time/residue: 0.2946 time to fit residues: 211.8763 Evaluate side-chains 362 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 330 time to evaluate : 2.457 ------------------------------------------------------------------------------- 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 217 VAL Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 373 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 60 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 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 243 VAL 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 50 SER Chi-restraints excluded: chain J residue 105 LEU 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 159 optimal weight: 40.0000 chunk 89 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 195 optimal weight: 30.0000 chunk 79 optimal weight: 4.9990 chunk 287 optimal weight: 4.9990 chunk 310 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 230 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 408 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24141 Z= 0.260 Angle : 0.748 12.053 33101 Z= 0.359 Chirality : 0.044 0.316 4059 Planarity : 0.005 0.110 4231 Dihedral : 4.717 71.046 3452 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.73 % Allowed : 19.04 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3148 helix: 0.93 (0.12), residues: 1770 sheet: -1.75 (0.27), residues: 296 loop : -1.10 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 231 HIS 0.011 0.001 HIS F 74 PHE 0.034 0.002 PHE C 244 TYR 0.023 0.002 TYR F 96 ARG 0.011 0.000 ARG A 141 *********************** 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 445 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 355 time to evaluate : 2.623 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: E 164 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6302 (t70) REVERT: E 271 ASN cc_start: 0.7907 (p0) cc_final: 0.7671 (p0) REVERT: G 195 THR cc_start: 0.7806 (p) cc_final: 0.7541 (t) outliers start: 90 outliers final: 45 residues processed: 406 average time/residue: 0.2812 time to fit residues: 192.6953 Evaluate side-chains 365 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 319 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 414 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 C residue 414 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 85 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 164 ASP 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 12 VAL 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 43 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 282 VAL 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 130 THR 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 67 GLN 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 284 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 288 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 273 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 HIS ** 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** J 392 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 24141 Z= 0.325 Angle : 0.780 13.239 33101 Z= 0.383 Chirality : 0.044 0.306 4059 Planarity : 0.005 0.062 4231 Dihedral : 4.761 65.977 3452 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.97 % Allowed : 20.82 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3148 helix: 1.13 (0.12), residues: 1768 sheet: -1.74 (0.26), residues: 298 loop : -0.84 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 231 HIS 0.008 0.002 HIS G 389 PHE 0.015 0.002 PHE G 165 TYR 0.020 0.002 TYR F 96 ARG 0.010 0.001 ARG A 52 *********************** 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 fitting. rotamer outliers: 96 poor density : 334 time to evaluate : 3.199 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: E 164 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6642 (t70) outliers start: 96 outliers final: 63 residues processed: 389 average time/residue: 0.2956 time to fit residues: 196.3426 Evaluate side-chains 369 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 305 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 194 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 308 THR 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 45 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 85 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 164 ASP 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 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 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 H residue 118 ILE 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 198 VAL Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain J residue 16 THR 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 246 VAL Chi-restraints excluded: chain J residue 269 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 254 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 227 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 260 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 155 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 126 GLN C 126 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 HIS H 330 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.4246 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= 0.215 Angle : 0.755 14.034 33101 Z= 0.354 Chirality : 0.046 0.384 4059 Planarity : 0.005 0.061 4231 Dihedral : 4.616 62.727 3452 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.15 % Allowed : 23.14 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3148 helix: 1.25 (0.12), residues: 1778 sheet: -1.66 (0.27), residues: 292 loop : -0.71 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 231 HIS 0.006 0.001 HIS H 131 PHE 0.015 0.001 PHE G 165 TYR 0.017 0.002 TYR F 96 ARG 0.005 0.000 ARG B 125 *********************** 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 417 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 341 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 414 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8190 (tt) REVERT: E 164 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6357 (t70) outliers start: 76 outliers final: 49 residues processed: 393 average time/residue: 0.2833 time to fit residues: 189.7102 Evaluate side-chains 358 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 307 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 395 VAL Chi-restraints excluded: chain B residue 398 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 282 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 164 ASP 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 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 43 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 331 GLN Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain H residue 125 ARG 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 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 54 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 305 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 0.2980 chunk 160 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 331 GLN ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** 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 74 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 HIS J 114 ASN ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.4490 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= 0.216 Angle : 0.777 13.419 33101 Z= 0.361 Chirality : 0.046 0.389 4059 Planarity : 0.004 0.050 4231 Dihedral : 4.540 59.007 3452 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.27 % Allowed : 23.63 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3148 helix: 1.29 (0.12), residues: 1776 sheet: -1.59 (0.27), residues: 292 loop : -0.62 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP E 231 HIS 0.003 0.001 HIS H 389 PHE 0.028 0.001 PHE B 401 TYR 0.018 0.002 TYR E 104 ARG 0.006 0.000 ARG E 191 *********************** 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 fitting. rotamer outliers: 79 poor density : 326 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 414 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8183 (tt) REVERT: E 164 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6369 (t70) outliers start: 79 outliers final: 57 residues processed: 378 average time/residue: 0.3262 time to fit residues: 210.3689 Evaluate side-chains 364 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 305 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 203 ASP 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 B residue 414 LEU Chi-restraints excluded: chain C residue 37 GLU 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 217 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 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 26 VAL Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 74 HIS 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 43 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 331 GLN 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 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 H residue 393 LEU Chi-restraints excluded: chain I residue 54 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 171 LEU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 269 VAL 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 294 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 190 optimal weight: 0.0470 chunk 185 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 overall best weight: 5.2086 ------------------------------------------------------------------------------- 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 328 GLN ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** 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 74 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 HIS ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 HIS ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24141 Z= 0.293 Angle : 0.816 15.396 33101 Z= 0.387 Chirality : 0.047 0.403 4059 Planarity : 0.005 0.046 4231 Dihedral : 4.579 56.401 3452 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.23 % Allowed : 25.87 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3148 helix: 1.34 (0.12), residues: 1772 sheet: -1.62 (0.26), residues: 292 loop : -0.55 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 231 HIS 0.022 0.001 HIS F 74 PHE 0.048 0.002 PHE C 401 TYR 0.028 0.002 TYR D 28 ARG 0.011 0.000 ARG F 75 *********************** 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 391 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 313 time to evaluate : 3.005 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: 0.7199 (mmt) cc_final: 0.6760 (mmm) REVERT: B 414 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8204 (tt) REVERT: E 164 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6506 (t70) outliers start: 78 outliers final: 60 residues processed: 366 average time/residue: 0.2803 time to fit residues: 175.7986 Evaluate side-chains 358 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 296 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 203 ASP 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 B residue 414 LEU Chi-restraints excluded: chain C residue 37 GLU 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 217 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 414 LEU 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 C residue 469 PHE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 317 VAL 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 43 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 331 GLN 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 96 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 356 SER 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 54 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 16 THR Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 269 VAL 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 188 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 181 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 193 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 277 optimal weight: 1.9990 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 ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24141 Z= 0.243 Angle : 0.818 14.161 33101 Z= 0.381 Chirality : 0.048 0.431 4059 Planarity : 0.005 0.050 4231 Dihedral : 4.541 54.209 3452 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.98 % Allowed : 26.08 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3148 helix: 1.36 (0.12), residues: 1770 sheet: -1.60 (0.26), residues: 296 loop : -0.51 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 231 HIS 0.009 0.001 HIS C 330 PHE 0.020 0.001 PHE C 165 TYR 0.020 0.002 TYR D 28 ARG 0.007 0.000 ARG E 191 *********************** 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 383 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 311 time to evaluate : 2.663 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: A 59 MET cc_start: 0.7148 (mmt) cc_final: 0.6685 (mmm) REVERT: E 164 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6436 (t70) outliers start: 72 outliers final: 57 residues processed: 361 average time/residue: 0.2745 time to fit residues: 170.3308 Evaluate side-chains 356 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 298 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 37 GLU 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 282 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 414 LEU 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 C residue 469 PHE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 74 HIS 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 43 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 331 GLN 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 130 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 356 SER 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 52 VAL Chi-restraints excluded: chain I residue 54 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 0.8980 chunk 266 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 222 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 chunk 282 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 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 74 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.5093 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= 0.196 Angle : 0.854 17.591 33101 Z= 0.387 Chirality : 0.049 0.456 4059 Planarity : 0.005 0.051 4231 Dihedral : 4.507 49.180 3452 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.32 % Allowed : 26.90 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3148 helix: 1.38 (0.12), residues: 1766 sheet: -1.49 (0.27), residues: 296 loop : -0.47 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 231 HIS 0.006 0.001 HIS C 330 PHE 0.032 0.002 PHE C 244 TYR 0.016 0.002 TYR A 96 ARG 0.006 0.000 ARG E 191 *********************** 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 383 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 327 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.7104 (mmt) cc_final: 0.6622 (mmm) REVERT: B 7 MET cc_start: 0.7391 (mmm) cc_final: 0.5993 (mmt) REVERT: B 232 MET cc_start: 0.7303 (tmm) cc_final: 0.7059 (tmm) REVERT: E 164 ASP cc_start: 0.6793 (OUTLIER) cc_final: 0.6315 (t70) outliers start: 56 outliers final: 45 residues processed: 367 average time/residue: 0.2851 time to fit residues: 179.7930 Evaluate side-chains 348 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 302 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 130 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 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 45 MET Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 331 GLN 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 39 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 392 LEU 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 207 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 362 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 314 optimal weight: 5.9990 chunk 289 optimal weight: 0.0970 chunk 250 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 193 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 199 optimal weight: 0.6980 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN E 187 HIS ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24141 Z= 0.244 Angle : 0.861 16.481 33101 Z= 0.397 Chirality : 0.050 0.452 4059 Planarity : 0.005 0.053 4231 Dihedral : 4.465 44.890 3452 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.24 % Allowed : 27.48 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3148 helix: 1.36 (0.12), residues: 1753 sheet: -1.40 (0.27), residues: 294 loop : -0.41 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP C 227 HIS 0.004 0.001 HIS C 330 PHE 0.019 0.001 PHE C 296 TYR 0.021 0.002 TYR A 96 ARG 0.010 0.000 ARG E 191 ********************** 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 352 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 298 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.7168 (mmt) cc_final: 0.6683 (mmm) REVERT: B 7 MET cc_start: 0.7581 (mmm) cc_final: 0.6224 (mmt) REVERT: B 232 MET cc_start: 0.7351 (tmm) cc_final: 0.7094 (tmm) REVERT: E 164 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6454 (t70) outliers start: 54 outliers final: 50 residues processed: 336 average time/residue: 0.2747 time to fit residues: 159.1886 Evaluate side-chains 341 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 290 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 411 LEU Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 455 ASP Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 331 GLN 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 39 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain H residue 360 TRP Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 54 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 171 LEU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 362 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** 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 = 0.3168 r_free = 0.3168 target = 0.044620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.037690 restraints weight = 237769.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.038367 restraints weight = 158900.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.038857 restraints weight = 120631.563| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24141 Z= 0.247 Angle : 0.873 15.858 33101 Z= 0.402 Chirality : 0.050 0.453 4059 Planarity : 0.005 0.053 4231 Dihedral : 4.458 42.399 3452 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.28 % Allowed : 27.73 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3148 helix: 1.33 (0.12), residues: 1755 sheet: -1.36 (0.27), residues: 294 loop : -0.36 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 227 HIS 0.015 0.001 HIS E 187 PHE 0.018 0.002 PHE C 296 TYR 0.029 0.002 TYR A 96 ARG 0.019 0.000 ARG C 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4909.81 seconds wall clock time: 88 minutes 15.23 seconds (5295.23 seconds total)