Starting phenix.real_space_refine on Tue Dec 31 07:00:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a11_15065/12_2024/8a11_15065.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a11_15065/12_2024/8a11_15065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a11_15065/12_2024/8a11_15065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a11_15065/12_2024/8a11_15065.map" model { file = "/net/cci-nas-00/data/ceres_data/8a11_15065/12_2024/8a11_15065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a11_15065/12_2024/8a11_15065.cif" } resolution = 3.52 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= 0.050 sd= 0.669 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 72 5.16 5 C 9209 2.51 5 N 2557 2.21 5 O 2782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14630 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3605 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 445} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3639 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 448} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3639 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 448} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3621 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 446} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 9.78, per 1000 atoms: 0.67 Number of scatterers: 14630 At special positions: 0 Unit cell: (123.571, 135.128, 96.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 10 15.00 O 2782 8.00 N 2557 7.00 C 9209 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: 4.10 Conformation dependent library (CDL) restraints added in 1.9 seconds 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 15 sheets defined 54.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 removed outlier: 3.778A pdb=" N LYS A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 31 through 46 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.501A pdb=" N LEU A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.597A pdb=" N GLU A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 161 through 167 removed outlier: 3.528A pdb=" N ILE A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.622A pdb=" N LEU A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.880A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.576A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 321 through 346 removed outlier: 4.249A pdb=" N LYS A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 414 through 440 removed outlier: 3.612A pdb=" N PHE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 453 removed outlier: 4.089A pdb=" N ALA A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 473 removed outlier: 4.431A pdb=" N ALA A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA A 460 " --> pdb=" O LYS A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.702A pdb=" N MET B 21 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.724A pdb=" N LEU B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.970A pdb=" N ASN B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 71 " --> pdb=" O CYS B 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 67 through 71' Processing helix chain 'B' and resid 86 through 104 removed outlier: 4.012A pdb=" N TYR B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.830A pdb=" N HIS B 151 " --> pdb=" O HIS B 148 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 152 " --> pdb=" O LEU B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 152' Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.691A pdb=" N GLU B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.641A pdb=" N LEU B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 243 through 247 removed outlier: 4.004A pdb=" N GLU B 246 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS B 247 " --> pdb=" O PRO B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 247' Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 305 through 320 Processing helix chain 'B' and resid 321 through 345 removed outlier: 4.287A pdb=" N LYS B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.527A pdb=" N GLY B 367 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.678A pdb=" N VAL B 376 " --> pdb=" O ARG B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.396A pdb=" N LEU B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 410 " --> pdb=" O PRO B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 440 Processing helix chain 'B' and resid 444 through 451 Processing helix chain 'B' and resid 454 through 474 removed outlier: 4.215A pdb=" N ALA B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 23 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.687A pdb=" N TYR C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 67 through 71 removed outlier: 4.180A pdb=" N ASN C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 104 removed outlier: 3.980A pdb=" N TYR C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.588A pdb=" N GLY C 152 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 167 Processing helix chain 'C' and resid 183 through 194 removed outlier: 3.601A pdb=" N GLU C 187 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.566A pdb=" N ASN C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 Processing helix chain 'C' and resid 288 through 297 Processing helix chain 'C' and resid 305 through 320 removed outlier: 3.875A pdb=" N ILE C 309 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA C 310 " --> pdb=" O ASN C 306 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 346 removed outlier: 3.762A pdb=" N LYS C 325 " --> pdb=" O THR C 321 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.837A pdb=" N ALA C 373 " --> pdb=" O ASP C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.560A pdb=" N ARG C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 412' Processing helix chain 'C' and resid 414 through 440 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.589A pdb=" N PHE C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 473 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.724A pdb=" N TYR D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.599A pdb=" N LEU D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 86 through 104 removed outlier: 3.834A pdb=" N TYR D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 119 through 132 Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 161 through 167 Processing helix chain 'D' and resid 183 through 194 removed outlier: 3.996A pdb=" N ARG D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 222 Processing helix chain 'D' and resid 232 through 239 removed outlier: 3.566A pdb=" N GLY D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.735A pdb=" N GLU D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS D 247 " --> pdb=" O PRO D 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 247' Processing helix chain 'D' and resid 287 through 297 removed outlier: 4.084A pdb=" N LEU D 291 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 318 Processing helix chain 'D' and resid 321 through 344 removed outlier: 3.913A pdb=" N LYS D 325 " --> pdb=" O THR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.698A pdb=" N ALA D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 removed outlier: 3.635A pdb=" N THR D 409 " --> pdb=" O THR D 405 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 412 " --> pdb=" O LEU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 440 Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 454 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114 removed outlier: 6.316A pdb=" N LEU A 225 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR A 252 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA A 227 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR A 254 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 198 " --> pdb=" O MET A 226 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP A 228 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA A 200 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ARG A 137 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ILE A 199 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET A 139 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 276 removed outlier: 3.738A pdb=" N SER A 275 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 349 removed outlier: 4.427A pdb=" N LYS A 348 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 385 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 49 removed outlier: 7.366A pdb=" N LEU B 48 " --> pdb=" O ALA B 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 169 removed outlier: 7.483A pdb=" N ARG B 137 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ILE B 199 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET B 139 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLY B 201 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE B 198 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASP B 228 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA B 200 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 174 through 175 removed outlier: 3.608A pdb=" N TYR B 180 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 276 removed outlier: 7.068A pdb=" N ILE B 284 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA9, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.011A pdb=" N ILE C 198 " --> pdb=" O MET C 226 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASP C 228 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AB2, first strand: chain 'C' and resid 273 through 276 removed outlier: 6.996A pdb=" N ILE C 284 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 348 through 349 removed outlier: 4.102A pdb=" N LYS C 348 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 361 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 111 through 114 removed outlier: 6.477A pdb=" N LEU D 225 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N THR D 252 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA D 227 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR D 254 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 273 through 276 removed outlier: 6.795A pdb=" N ILE D 284 " --> pdb=" O LYS D 274 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 358 through 362 removed outlier: 3.956A pdb=" N ASN D 385 " --> pdb=" O ARG D 402 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 2001 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.95 Time building geometry restraints manager: 4.62 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: 4751 1.34 - 1.46: 1966 1.46 - 1.57: 8107 1.57 - 1.69: 15 1.69 - 1.81: 104 Bond restraints: 14943 Sorted by residual: bond pdb=" OP4 LLP A 257 " pdb=" P LLP A 257 " ideal model delta sigma weight residual 1.726 1.544 0.182 2.00e-02 2.50e+03 8.25e+01 bond pdb=" OP4 LLP C 257 " pdb=" P LLP C 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" OP4 LLP D 257 " pdb=" P LLP D 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" OP4 LLP B 257 " pdb=" P LLP B 257 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " ideal model delta sigma weight residual 1.273 1.433 -0.160 2.00e-02 2.50e+03 6.40e+01 ... (remaining 14938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 20024 2.14 - 4.29: 163 4.29 - 6.43: 56 6.43 - 8.57: 2 8.57 - 10.72: 12 Bond angle restraints: 20257 Sorted by residual: angle pdb=" NZ LLP B 257 " pdb=" C4' LLP B 257 " pdb=" C4 LLP B 257 " ideal model delta sigma weight residual 120.09 109.37 10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" NZ LLP D 257 " pdb=" C4' LLP D 257 " pdb=" C4 LLP D 257 " ideal model delta sigma weight residual 120.09 109.43 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" NZ LLP C 257 " pdb=" C4' LLP C 257 " pdb=" C4 LLP C 257 " ideal model delta sigma weight residual 120.09 109.43 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CE LLP C 257 " pdb=" NZ LLP C 257 " pdb=" C4' LLP C 257 " ideal model delta sigma weight residual 119.26 109.23 10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " pdb=" C4 LLP A 257 " ideal model delta sigma weight residual 120.09 110.17 9.92 3.00e+00 1.11e-01 1.09e+01 ... (remaining 20252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 8634 22.60 - 45.20: 304 45.20 - 67.80: 15 67.80 - 90.39: 16 90.39 - 112.99: 2 Dihedral angle restraints: 8971 sinusoidal: 3594 harmonic: 5377 Sorted by residual: dihedral pdb=" CD LLP A 257 " pdb=" CE LLP A 257 " pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " ideal model delta sinusoidal sigma weight residual 249.72 136.73 112.99 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" CB GLU C 133 " pdb=" CG GLU C 133 " pdb=" CD GLU C 133 " pdb=" OE1 GLU C 133 " ideal model delta sinusoidal sigma weight residual 0.00 89.19 -89.19 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU C 63 " pdb=" CG GLU C 63 " pdb=" CD GLU C 63 " pdb=" OE1 GLU C 63 " ideal model delta sinusoidal sigma weight residual 0.00 86.71 -86.71 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 8968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1604 0.032 - 0.064: 437 0.064 - 0.096: 142 0.096 - 0.128: 60 0.128 - 0.160: 4 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA ILE D 199 " pdb=" N ILE D 199 " pdb=" C ILE D 199 " pdb=" CB ILE D 199 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA PRO D 134 " pdb=" N PRO D 134 " pdb=" C PRO D 134 " pdb=" CB PRO D 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA PRO C 134 " pdb=" N PRO C 134 " pdb=" C PRO C 134 " pdb=" CB PRO C 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2244 not shown) Planarity restraints: 2621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP D 257 " 0.162 2.00e-02 2.50e+03 2.80e-01 7.83e+02 pdb=" NZ LLP D 257 " -0.380 2.00e-02 2.50e+03 pdb=" C4 LLP D 257 " -0.134 2.00e-02 2.50e+03 pdb=" C4' LLP D 257 " 0.353 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 257 " -0.159 2.00e-02 2.50e+03 2.77e-01 7.67e+02 pdb=" NZ LLP A 257 " 0.374 2.00e-02 2.50e+03 pdb=" C4 LLP A 257 " 0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 257 " -0.351 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP C 257 " -0.152 2.00e-02 2.50e+03 2.47e-01 6.12e+02 pdb=" NZ LLP C 257 " 0.329 2.00e-02 2.50e+03 pdb=" C4 LLP C 257 " 0.133 2.00e-02 2.50e+03 pdb=" C4' LLP C 257 " -0.310 2.00e-02 2.50e+03 ... (remaining 2618 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1834 2.75 - 3.29: 14271 3.29 - 3.83: 24043 3.83 - 4.36: 27429 4.36 - 4.90: 47827 Nonbonded interactions: 115404 Sorted by model distance: nonbonded pdb=" OG1 THR C 155 " pdb=" O LYS C 158 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 354 " pdb=" OD1 ASN B 356 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR C 327 " pdb=" O PRO C 406 " model vdw 2.261 3.040 nonbonded pdb=" OD2 ASP B 438 " pdb=" OH TYR B 457 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR C 77 " pdb=" O ASN C 293 " model vdw 2.266 3.040 ... (remaining 115399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 16 through 482) selection = (chain 'C' and resid 16 through 482) selection = (chain 'D' and (resid 16 through 278 or (resid 279 and (name N or name CA or nam \ e C or name O or name CB )) or resid 280 through 482)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 36.410 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 0.182 14943 Z= 0.376 Angle : 0.597 10.717 20257 Z= 0.311 Chirality : 0.036 0.160 2247 Planarity : 0.010 0.280 2621 Dihedral : 11.178 112.994 5541 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.20 (0.17), residues: 1855 helix: -0.37 (0.16), residues: 884 sheet: -1.45 (0.35), residues: 192 loop : -2.76 (0.18), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 111 HIS 0.002 0.000 HIS D 135 PHE 0.010 0.001 PHE A 418 TYR 0.005 0.000 TYR D 457 ARG 0.002 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7599 (ptm) cc_final: 0.7075 (ttp) REVERT: A 191 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.8016 (ttp80) REVERT: A 287 ASN cc_start: 0.7847 (t0) cc_final: 0.7569 (t0) REVERT: C 142 ASP cc_start: 0.8375 (t0) cc_final: 0.8149 (t0) REVERT: C 229 MET cc_start: 0.7628 (ptm) cc_final: 0.7419 (ptm) REVERT: D 447 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8236 (tm-30) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2644 time to fit residues: 62.0122 Evaluate side-chains 94 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 44 GLN B 109 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS C 307 HIS C 385 ASN D 44 GLN D 70 ASN D 221 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14943 Z= 0.198 Angle : 0.508 6.099 20257 Z= 0.255 Chirality : 0.038 0.131 2247 Planarity : 0.003 0.042 2621 Dihedral : 7.049 95.217 2151 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.98 % Allowed : 7.25 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.70 (0.19), residues: 1855 helix: 0.97 (0.18), residues: 886 sheet: -0.95 (0.35), residues: 208 loop : -2.09 (0.20), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 111 HIS 0.005 0.001 HIS C 18 PHE 0.016 0.001 PHE D 268 TYR 0.010 0.001 TYR A 269 ARG 0.005 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.814 Fit side-chains revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8165 (t0) cc_final: 0.7897 (t0) outliers start: 15 outliers final: 13 residues processed: 109 average time/residue: 0.2548 time to fit residues: 44.1388 Evaluate side-chains 96 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 231 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14943 Z= 0.189 Angle : 0.498 7.991 20257 Z= 0.250 Chirality : 0.038 0.139 2247 Planarity : 0.003 0.046 2621 Dihedral : 7.155 94.319 2151 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.17 % Allowed : 9.27 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.19 (0.20), residues: 1855 helix: 1.43 (0.18), residues: 887 sheet: -1.08 (0.38), residues: 185 loop : -1.76 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 111 HIS 0.019 0.001 HIS C 231 PHE 0.015 0.001 PHE D 268 TYR 0.009 0.001 TYR C 183 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.760 Fit side-chains revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7650 (mtm180) REVERT: A 287 ASN cc_start: 0.8255 (t0) cc_final: 0.7988 (t0) outliers start: 18 outliers final: 11 residues processed: 102 average time/residue: 0.2350 time to fit residues: 38.7438 Evaluate side-chains 94 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 ASN ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14943 Z= 0.178 Angle : 0.494 9.386 20257 Z= 0.246 Chirality : 0.037 0.132 2247 Planarity : 0.003 0.047 2621 Dihedral : 7.204 93.456 2151 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.44 % Allowed : 10.51 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.14 (0.20), residues: 1855 helix: 1.64 (0.18), residues: 893 sheet: -0.72 (0.37), residues: 193 loop : -1.60 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 15 HIS 0.003 0.001 HIS D 249 PHE 0.013 0.001 PHE D 268 TYR 0.008 0.001 TYR A 172 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.6827 (mtt) cc_final: 0.6623 (mtm) REVERT: A 213 ARG cc_start: 0.8208 (ptm-80) cc_final: 0.7998 (ptm-80) REVERT: A 287 ASN cc_start: 0.8308 (t0) cc_final: 0.8027 (t0) REVERT: D 229 MET cc_start: 0.8052 (ppp) cc_final: 0.7699 (ppp) outliers start: 22 outliers final: 16 residues processed: 103 average time/residue: 0.2404 time to fit residues: 39.9849 Evaluate side-chains 97 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 0.0370 chunk 153 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 45 optimal weight: 0.0970 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS D 70 ASN ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14943 Z= 0.180 Angle : 0.491 7.949 20257 Z= 0.246 Chirality : 0.037 0.132 2247 Planarity : 0.003 0.049 2621 Dihedral : 7.215 91.834 2151 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.24 % Allowed : 11.16 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.43 (0.20), residues: 1855 helix: 1.88 (0.18), residues: 889 sheet: -0.64 (0.37), residues: 193 loop : -1.43 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 15 HIS 0.003 0.001 HIS D 249 PHE 0.014 0.001 PHE D 268 TYR 0.008 0.001 TYR D 172 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 1.548 Fit side-chains revert: symmetry clash REVERT: A 226 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8122 (ttm) REVERT: A 287 ASN cc_start: 0.8351 (t0) cc_final: 0.8069 (t0) REVERT: A 358 LEU cc_start: 0.8427 (pp) cc_final: 0.8179 (pp) REVERT: D 229 MET cc_start: 0.8166 (ppp) cc_final: 0.7795 (ppp) outliers start: 19 outliers final: 17 residues processed: 99 average time/residue: 0.2416 time to fit residues: 38.3295 Evaluate side-chains 97 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.0000 chunk 161 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 0.0770 chunk 44 optimal weight: 8.9990 chunk 179 optimal weight: 0.9990 chunk 149 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.0470 chunk 94 optimal weight: 4.9990 overall best weight: 0.2640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 256 HIS A 306 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14943 Z= 0.115 Angle : 0.458 8.640 20257 Z= 0.227 Chirality : 0.037 0.131 2247 Planarity : 0.003 0.047 2621 Dihedral : 7.107 90.925 2151 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.91 % Allowed : 11.81 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.61 (0.20), residues: 1855 helix: 1.98 (0.18), residues: 895 sheet: -0.47 (0.38), residues: 194 loop : -1.32 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 15 HIS 0.003 0.000 HIS A 256 PHE 0.008 0.001 PHE A 418 TYR 0.007 0.001 TYR A 172 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8268 (mtm180) cc_final: 0.7919 (mtm-85) REVERT: A 213 ARG cc_start: 0.8138 (ptm-80) cc_final: 0.7886 (ptm-80) REVERT: A 287 ASN cc_start: 0.8322 (t0) cc_final: 0.8070 (t0) REVERT: D 229 MET cc_start: 0.8266 (ppp) cc_final: 0.7992 (ppp) REVERT: D 320 MET cc_start: 0.8067 (mmt) cc_final: 0.7853 (mmt) outliers start: 14 outliers final: 11 residues processed: 103 average time/residue: 0.2544 time to fit residues: 41.5050 Evaluate side-chains 95 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 0.3980 chunk 100 optimal weight: 0.0270 chunk 179 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14943 Z= 0.131 Angle : 0.465 9.198 20257 Z= 0.230 Chirality : 0.037 0.130 2247 Planarity : 0.003 0.047 2621 Dihedral : 7.093 90.058 2151 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.98 % Allowed : 11.88 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.79 (0.20), residues: 1855 helix: 2.13 (0.18), residues: 889 sheet: -0.36 (0.38), residues: 193 loop : -1.20 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 15 HIS 0.006 0.000 HIS A 231 PHE 0.009 0.001 PHE D 268 TYR 0.007 0.001 TYR A 172 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8213 (mtm180) cc_final: 0.7998 (mtm180) REVERT: A 213 ARG cc_start: 0.8185 (ptm-80) cc_final: 0.7770 (ttp80) REVERT: A 287 ASN cc_start: 0.8329 (t0) cc_final: 0.8063 (t0) REVERT: D 229 MET cc_start: 0.8297 (ppp) cc_final: 0.8000 (ppp) REVERT: D 320 MET cc_start: 0.8099 (mmt) cc_final: 0.7877 (mmt) outliers start: 15 outliers final: 14 residues processed: 97 average time/residue: 0.2496 time to fit residues: 38.0854 Evaluate side-chains 97 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 0.0030 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14943 Z= 0.142 Angle : 0.474 9.464 20257 Z= 0.235 Chirality : 0.037 0.134 2247 Planarity : 0.003 0.046 2621 Dihedral : 7.105 89.610 2151 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.11 % Allowed : 12.01 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1855 helix: 2.14 (0.18), residues: 892 sheet: -0.39 (0.38), residues: 193 loop : -1.15 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 15 HIS 0.003 0.000 HIS A 256 PHE 0.009 0.001 PHE D 268 TYR 0.007 0.001 TYR D 172 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8223 (mtm180) cc_final: 0.7886 (mtm180) REVERT: A 213 ARG cc_start: 0.8208 (ptm-80) cc_final: 0.7786 (ttp80) REVERT: A 287 ASN cc_start: 0.8325 (t0) cc_final: 0.8074 (t0) REVERT: A 358 LEU cc_start: 0.8344 (pp) cc_final: 0.8080 (pp) REVERT: D 229 MET cc_start: 0.8302 (ppp) cc_final: 0.8043 (ppp) outliers start: 17 outliers final: 17 residues processed: 96 average time/residue: 0.2428 time to fit residues: 37.7641 Evaluate side-chains 100 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 0.0870 chunk 166 optimal weight: 7.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14943 Z= 0.147 Angle : 0.480 10.149 20257 Z= 0.237 Chirality : 0.037 0.136 2247 Planarity : 0.003 0.046 2621 Dihedral : 7.117 89.140 2151 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.17 % Allowed : 12.14 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.89 (0.20), residues: 1855 helix: 2.18 (0.18), residues: 892 sheet: -0.40 (0.38), residues: 195 loop : -1.09 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 15 HIS 0.002 0.000 HIS A 256 PHE 0.010 0.001 PHE D 268 TYR 0.007 0.001 TYR D 172 ARG 0.004 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8221 (mtm180) cc_final: 0.7492 (mtm180) REVERT: A 213 ARG cc_start: 0.8221 (ptm-80) cc_final: 0.7873 (ttp80) REVERT: A 287 ASN cc_start: 0.8350 (t0) cc_final: 0.8110 (t0) REVERT: A 358 LEU cc_start: 0.8361 (pp) cc_final: 0.8107 (pp) REVERT: D 229 MET cc_start: 0.8257 (ppp) cc_final: 0.8003 (ppp) outliers start: 18 outliers final: 17 residues processed: 96 average time/residue: 0.2361 time to fit residues: 36.7193 Evaluate side-chains 100 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 170 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 0.0980 chunk 90 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14943 Z= 0.156 Angle : 0.487 10.317 20257 Z= 0.241 Chirality : 0.037 0.139 2247 Planarity : 0.003 0.046 2621 Dihedral : 7.129 88.754 2151 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.17 % Allowed : 12.21 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.92 (0.20), residues: 1855 helix: 2.19 (0.18), residues: 892 sheet: -0.39 (0.38), residues: 195 loop : -1.06 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 15 HIS 0.007 0.001 HIS A 231 PHE 0.010 0.001 PHE D 268 TYR 0.008 0.001 TYR D 172 ARG 0.003 0.000 ARG A 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: A 191 ARG cc_start: 0.7962 (mtm180) cc_final: 0.7690 (mtm-85) REVERT: A 213 ARG cc_start: 0.8223 (ptm-80) cc_final: 0.7874 (ttp80) REVERT: A 287 ASN cc_start: 0.8339 (t0) cc_final: 0.8105 (t0) REVERT: A 358 LEU cc_start: 0.8365 (pp) cc_final: 0.8108 (pp) REVERT: D 229 MET cc_start: 0.8264 (ppp) cc_final: 0.8010 (ppp) outliers start: 18 outliers final: 18 residues processed: 97 average time/residue: 0.2446 time to fit residues: 38.2998 Evaluate side-chains 101 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 136 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.081508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.062158 restraints weight = 63020.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064026 restraints weight = 35912.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.065273 restraints weight = 25441.762| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14943 Z= 0.139 Angle : 0.486 10.602 20257 Z= 0.240 Chirality : 0.037 0.138 2247 Planarity : 0.003 0.047 2621 Dihedral : 7.122 88.356 2151 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.24 % Allowed : 12.27 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.98 (0.20), residues: 1855 helix: 2.24 (0.18), residues: 886 sheet: -0.37 (0.37), residues: 195 loop : -1.00 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 15 HIS 0.003 0.000 HIS A 231 PHE 0.009 0.001 PHE D 268 TYR 0.007 0.001 TYR A 183 ARG 0.004 0.000 ARG A 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2672.48 seconds wall clock time: 51 minutes 9.76 seconds (3069.76 seconds total)