Starting phenix.real_space_refine on Fri Jun 13 14:18:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a11_15065/06_2025/8a11_15065.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a11_15065/06_2025/8a11_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_15065/06_2025/8a11_15065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a11_15065/06_2025/8a11_15065.map" model { file = "/net/cci-nas-00/data/ceres_data/8a11_15065/06_2025/8a11_15065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a11_15065/06_2025/8a11_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.85, per 1000 atoms: 0.74 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: 4.00 Conformation dependent library (CDL) restraints added in 2.1 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: 1.68 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: 4.47 Time building geometry restraints manager: 4.61 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: 4.270 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: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.190 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.850 ------------------------------------------------------------------------------- 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= 0.290 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 Details of bonding type rmsd hydrogen bonds : bond 0.15815 ( 694) hydrogen bonds : angle 5.31832 ( 2001) covalent geometry : bond 0.00572 (14943) covalent geometry : angle 0.59744 (20257) *********************** 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 : 1.739 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: 0.2605 time to fit residues: 61.7197 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 : 1.772 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.082284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063180 restraints weight = 63209.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.065032 restraints weight = 35576.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.065907 restraints weight = 24982.346| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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= 0.134 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 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 694) hydrogen bonds : angle 3.86708 ( 2001) covalent geometry : bond 0.00301 (14943) covalent geometry : angle 0.50837 (20257) *********************** 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 : 1.593 Fit side-chains revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.8338 (mtm-85) REVERT: A 287 ASN cc_start: 0.8214 (t0) cc_final: 0.7939 (t0) outliers start: 15 outliers final: 13 residues processed: 109 average time/residue: 0.2341 time to fit residues: 40.3745 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 : 1.575 ------------------------------------------------------------------------------- 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 70 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 D 70 ASN ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.079443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060197 restraints weight = 62963.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062005 restraints weight = 35284.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.063214 restraints weight = 24843.155| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14943 Z= 0.181 Angle : 0.561 7.118 20257 Z= 0.285 Chirality : 0.039 0.142 2247 Planarity : 0.004 0.045 2621 Dihedral : 7.377 94.234 2151 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.83 % Allowed : 9.79 % Favored : 88.38 % 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: -0.21 (0.20), residues: 1855 helix: 1.37 (0.18), residues: 887 sheet: -0.92 (0.37), residues: 194 loop : -1.77 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.030 0.001 HIS C 231 PHE 0.019 0.002 PHE D 268 TYR 0.011 0.001 TYR B 128 ARG 0.004 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 694) hydrogen bonds : angle 3.97492 ( 2001) covalent geometry : bond 0.00412 (14943) covalent geometry : angle 0.56089 (20257) *********************** 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 113 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8439 (mtm110) REVERT: A 358 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8218 (pp) REVERT: C 142 ASP cc_start: 0.8301 (t0) cc_final: 0.8097 (t0) REVERT: C 231 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7738 (t-90) REVERT: D 229 MET cc_start: 0.8190 (ppp) cc_final: 0.7676 (ppp) outliers start: 28 outliers final: 20 residues processed: 105 average time/residue: 0.2485 time to fit residues: 41.7200 Evaluate side-chains 98 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 B residue 143 LEU 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 135 HIS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 132 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 181 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 306 ASN B 148 HIS C 231 HIS C 385 ASN D 24 GLN D 70 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.076941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057525 restraints weight = 65403.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059294 restraints weight = 37462.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.060483 restraints weight = 26760.029| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 14943 Z= 0.378 Angle : 0.763 8.400 20257 Z= 0.392 Chirality : 0.046 0.175 2247 Planarity : 0.005 0.064 2621 Dihedral : 8.029 93.172 2151 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.15 % Allowed : 11.81 % Favored : 86.03 % 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: -0.57 (0.19), residues: 1855 helix: 1.01 (0.17), residues: 879 sheet: -1.23 (0.36), residues: 201 loop : -1.80 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 111 HIS 0.008 0.002 HIS B 249 PHE 0.022 0.002 PHE D 268 TYR 0.014 0.002 TYR A 224 ARG 0.012 0.001 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 694) hydrogen bonds : angle 4.71276 ( 2001) covalent geometry : bond 0.00857 (14943) covalent geometry : angle 0.76349 (20257) *********************** 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 109 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8299 (ttp80) cc_final: 0.8051 (ptm-80) REVERT: A 229 MET cc_start: 0.8573 (ppp) cc_final: 0.7734 (ppp) REVERT: A 358 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8374 (pp) REVERT: C 109 GLN cc_start: 0.8319 (tm-30) cc_final: 0.8099 (tm-30) outliers start: 33 outliers final: 26 residues processed: 97 average time/residue: 0.2310 time to fit residues: 36.1751 Evaluate side-chains 99 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 300 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 B residue 292 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 150 THR 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 253 THR Chi-restraints excluded: chain D residue 300 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 71 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 138 optimal weight: 0.2980 chunk 132 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 231 HIS A 247 HIS C 231 HIS C 385 ASN D 24 GLN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.079935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.060640 restraints weight = 63760.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.062490 restraints weight = 36117.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.063734 restraints weight = 25473.037| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14943 Z= 0.103 Angle : 0.509 9.217 20257 Z= 0.257 Chirality : 0.038 0.138 2247 Planarity : 0.004 0.050 2621 Dihedral : 7.476 89.878 2151 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.24 % Allowed : 12.86 % Favored : 85.90 % 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: 1.60 (0.18), residues: 891 sheet: -0.77 (0.36), residues: 206 loop : -1.53 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 111 HIS 0.018 0.001 HIS C 231 PHE 0.011 0.001 PHE D 268 TYR 0.010 0.001 TYR C 183 ARG 0.005 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 694) hydrogen bonds : angle 3.92077 ( 2001) covalent geometry : bond 0.00225 (14943) covalent geometry : angle 0.50917 (20257) *********************** 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 102 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 LEU cc_start: 0.8487 (pp) cc_final: 0.8277 (pp) outliers start: 19 outliers final: 14 residues processed: 98 average time/residue: 0.2345 time to fit residues: 37.0993 Evaluate side-chains 88 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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 413 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 233 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 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 273 VAL 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 162 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3752 r_free = 0.3752 target = 0.078989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.059750 restraints weight = 63318.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.061565 restraints weight = 35866.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062756 restraints weight = 25306.171| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14943 Z= 0.155 Angle : 0.548 7.992 20257 Z= 0.276 Chirality : 0.039 0.268 2247 Planarity : 0.004 0.048 2621 Dihedral : 7.471 87.972 2151 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.63 % Allowed : 13.05 % Favored : 85.31 % 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: 0.25 (0.20), residues: 1855 helix: 1.69 (0.18), residues: 891 sheet: -0.64 (0.36), residues: 202 loop : -1.50 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 15 HIS 0.011 0.001 HIS C 231 PHE 0.014 0.001 PHE D 268 TYR 0.013 0.001 TYR A 183 ARG 0.003 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 694) hydrogen bonds : angle 4.00400 ( 2001) covalent geometry : bond 0.00354 (14943) covalent geometry : angle 0.54805 (20257) *********************** 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 101 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 1.577 Fit side-chains REVERT: A 358 LEU cc_start: 0.8481 (pp) cc_final: 0.8241 (pp) REVERT: B 251 VAL cc_start: 0.8871 (t) cc_final: 0.8526 (p) REVERT: B 262 CYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7407 (p) REVERT: C 231 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7760 (t-90) outliers start: 25 outliers final: 18 residues processed: 94 average time/residue: 0.2143 time to fit residues: 33.5206 Evaluate side-chains 93 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 231 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 262 CYS 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 173 LYS Chi-restraints excluded: chain C residue 231 HIS 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 253 THR Chi-restraints excluded: chain D residue 273 VAL 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 143 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 72 optimal weight: 0.0770 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.0000 chunk 75 optimal weight: 0.8980 chunk 6 optimal weight: 0.0370 chunk 13 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.081075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.061730 restraints weight = 63359.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.063632 restraints weight = 35915.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.064867 restraints weight = 25260.889| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14943 Z= 0.088 Angle : 0.494 8.782 20257 Z= 0.245 Chirality : 0.038 0.210 2247 Planarity : 0.003 0.050 2621 Dihedral : 7.236 88.041 2151 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.91 % Allowed : 13.58 % Favored : 85.51 % 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: 0.56 (0.20), residues: 1855 helix: 1.91 (0.18), residues: 891 sheet: -0.56 (0.36), residues: 209 loop : -1.27 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 15 HIS 0.004 0.000 HIS C 231 PHE 0.009 0.001 PHE A 418 TYR 0.010 0.001 TYR A 183 ARG 0.005 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.02731 ( 694) hydrogen bonds : angle 3.71978 ( 2001) covalent geometry : bond 0.00189 (14943) covalent geometry : angle 0.49390 (20257) *********************** 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 100 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 229 MET cc_start: 0.8516 (ppp) cc_final: 0.7546 (ppp) outliers start: 14 outliers final: 13 residues processed: 99 average time/residue: 0.2114 time to fit residues: 34.5089 Evaluate side-chains 95 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain B residue 276 VAL 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 233 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 273 VAL 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 178 optimal weight: 6.9990 chunk 122 optimal weight: 0.0370 chunk 113 optimal weight: 0.4980 chunk 179 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 153 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS A 256 HIS ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3793 r_free = 0.3793 target = 0.080819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.061473 restraints weight = 63066.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063320 restraints weight = 35971.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064550 restraints weight = 25584.802| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14943 Z= 0.094 Angle : 0.504 10.326 20257 Z= 0.247 Chirality : 0.038 0.302 2247 Planarity : 0.003 0.049 2621 Dihedral : 7.164 85.337 2151 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.17 % Allowed : 13.51 % Favored : 85.31 % 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: 0.69 (0.20), residues: 1855 helix: 1.99 (0.18), residues: 890 sheet: -0.44 (0.36), residues: 208 loop : -1.19 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 15 HIS 0.006 0.001 HIS A 231 PHE 0.009 0.001 PHE D 268 TYR 0.012 0.001 TYR A 183 ARG 0.004 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.02762 ( 694) hydrogen bonds : angle 3.66512 ( 2001) covalent geometry : bond 0.00210 (14943) covalent geometry : angle 0.50380 (20257) *********************** 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 100 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8480 (t0) cc_final: 0.8271 (t0) outliers start: 18 outliers final: 18 residues processed: 97 average time/residue: 0.2281 time to fit residues: 35.7876 Evaluate side-chains 100 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 276 VAL 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 233 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 273 VAL 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 54 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 155 optimal weight: 0.0670 chunk 179 optimal weight: 2.9990 chunk 128 optimal weight: 0.0050 chunk 33 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 overall best weight: 0.3290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3811 r_free = 0.3811 target = 0.081549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.062219 restraints weight = 62900.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.064093 restraints weight = 35781.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065321 restraints weight = 25278.609| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3182 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= 0.086 Angle : 0.495 10.043 20257 Z= 0.242 Chirality : 0.037 0.286 2247 Planarity : 0.003 0.049 2621 Dihedral : 7.088 86.956 2151 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.17 % Allowed : 13.58 % Favored : 85.25 % 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: 0.81 (0.20), residues: 1855 helix: 2.08 (0.18), residues: 889 sheet: -0.41 (0.36), residues: 209 loop : -1.09 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 15 HIS 0.003 0.000 HIS A 256 PHE 0.008 0.001 PHE A 418 TYR 0.011 0.001 TYR A 269 ARG 0.003 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.02555 ( 694) hydrogen bonds : angle 3.57111 ( 2001) covalent geometry : bond 0.00184 (14943) covalent geometry : angle 0.49504 (20257) *********************** 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 107 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8431 (t0) cc_final: 0.8217 (t0) REVERT: C 142 ASP cc_start: 0.8247 (t0) cc_final: 0.8037 (t0) REVERT: D 248 CYS cc_start: 0.7576 (t) cc_final: 0.7328 (t) outliers start: 18 outliers final: 15 residues processed: 106 average time/residue: 0.2241 time to fit residues: 38.5981 Evaluate side-chains 100 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 233 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 273 VAL 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 172 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 45 optimal weight: 0.0370 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.080348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.060801 restraints weight = 63662.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.062644 restraints weight = 36360.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.063836 restraints weight = 25781.588| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3320 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= 0.123 Angle : 0.528 10.868 20257 Z= 0.259 Chirality : 0.038 0.268 2247 Planarity : 0.003 0.048 2621 Dihedral : 7.196 84.856 2151 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.24 % Allowed : 13.64 % Favored : 85.12 % 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: 0.81 (0.20), residues: 1855 helix: 2.09 (0.18), residues: 890 sheet: -0.41 (0.36), residues: 207 loop : -1.11 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 15 HIS 0.005 0.001 HIS A 231 PHE 0.012 0.001 PHE D 268 TYR 0.014 0.001 TYR A 183 ARG 0.004 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 694) hydrogen bonds : angle 3.68051 ( 2001) covalent geometry : bond 0.00280 (14943) covalent geometry : angle 0.52795 (20257) ********************** 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 100 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.636 Fit side-chains REVERT: A 287 ASN cc_start: 0.8402 (t0) cc_final: 0.8183 (t0) outliers start: 19 outliers final: 17 residues processed: 97 average time/residue: 0.2293 time to fit residues: 36.1041 Evaluate side-chains 96 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 B residue 276 VAL 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 233 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 273 VAL 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 129 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 72 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 69 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.081084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.061636 restraints weight = 63572.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.063500 restraints weight = 36066.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.064755 restraints weight = 25562.434| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3284 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= 0.096 Angle : 0.509 10.734 20257 Z= 0.250 Chirality : 0.038 0.257 2247 Planarity : 0.003 0.048 2621 Dihedral : 7.203 87.587 2151 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.17 % Allowed : 13.90 % Favored : 84.92 % 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: 0.88 (0.20), residues: 1855 helix: 2.13 (0.18), residues: 888 sheet: -0.35 (0.36), residues: 207 loop : -1.05 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 15 HIS 0.003 0.000 HIS A 231 PHE 0.009 0.001 PHE D 268 TYR 0.015 0.001 TYR A 183 ARG 0.007 0.000 ARG D 393 Details of bonding type rmsd hydrogen bonds : bond 0.02713 ( 694) hydrogen bonds : angle 3.59501 ( 2001) covalent geometry : bond 0.00214 (14943) covalent geometry : angle 0.50876 (20257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4712.14 seconds wall clock time: 82 minutes 35.37 seconds (4955.37 seconds total)