Starting phenix.real_space_refine on Tue May 20 18:08:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z2f_39744/05_2025/8z2f_39744.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z2f_39744/05_2025/8z2f_39744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z2f_39744/05_2025/8z2f_39744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z2f_39744/05_2025/8z2f_39744.map" model { file = "/net/cci-nas-00/data/ceres_data/8z2f_39744/05_2025/8z2f_39744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z2f_39744/05_2025/8z2f_39744.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 12850 2.51 5 N 3585 2.21 5 O 3902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20404 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3392 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 441} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3450 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 441} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3386 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 16, 'TRANS': 441} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3392 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 441} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3392 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 441} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3392 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 441} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 12.89, per 1000 atoms: 0.63 Number of scatterers: 20404 At special positions: 0 Unit cell: (113.42, 117.7, 123.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 3902 8.00 N 3585 7.00 C 12850 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 3.0 seconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 23 sheets defined 53.9% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 7 through 24 Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 35 through 42 removed outlier: 4.561A pdb=" N VAL A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 106 removed outlier: 4.921A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 158 through 174 removed outlier: 3.549A pdb=" N ILE A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 214 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.996A pdb=" N LEU A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.585A pdb=" N ASP A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 329 through 336 removed outlier: 4.089A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.660A pdb=" N ILE A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.541A pdb=" N ALA A 368 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 396 Processing helix chain 'A' and resid 400 through 426 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 436 through 457 removed outlier: 3.854A pdb=" N SER A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASN A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 23 Processing helix chain 'B' and resid 24 through 30 removed outlier: 4.158A pdb=" N GLN B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 42 removed outlier: 3.595A pdb=" N ALA B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 107 removed outlier: 4.532A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 159 through 174 Processing helix chain 'B' and resid 197 through 214 removed outlier: 4.302A pdb=" N VAL B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR B 203 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 removed outlier: 4.227A pdb=" N LEU B 238 " --> pdb=" O GLN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 281 Processing helix chain 'B' and resid 284 through 290 removed outlier: 3.879A pdb=" N LEU B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 328 through 337 removed outlier: 4.388A pdb=" N ILE B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 380 through 396 Processing helix chain 'B' and resid 400 through 426 Processing helix chain 'B' and resid 437 through 456 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 24 through 30 removed outlier: 3.745A pdb=" N GLN C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 34 Processing helix chain 'C' and resid 35 through 42 removed outlier: 3.995A pdb=" N VAL C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 107 removed outlier: 4.446A pdb=" N PHE C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU C 105 " --> pdb=" O PHE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 141 removed outlier: 4.289A pdb=" N GLU C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS C 141 " --> pdb=" O MET C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 174 removed outlier: 3.514A pdb=" N ILE C 162 " --> pdb=" O THR C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 214 removed outlier: 3.608A pdb=" N VAL C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.927A pdb=" N LEU C 238 " --> pdb=" O GLN C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 326 through 330 removed outlier: 3.639A pdb=" N GLU C 329 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.835A pdb=" N ILE C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 364 removed outlier: 3.828A pdb=" N GLU C 362 " --> pdb=" O GLU C 358 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 396 removed outlier: 4.548A pdb=" N ALA C 378 " --> pdb=" O PRO C 374 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLY C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY C 382 " --> pdb=" O ALA C 378 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL C 383 " --> pdb=" O ASN C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 426 removed outlier: 3.585A pdb=" N GLU C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 456 removed outlier: 3.807A pdb=" N SER C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN C 442 " --> pdb=" O VAL C 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 24 removed outlier: 3.584A pdb=" N SER F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 32 through 35 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 88 through 107 Processing helix chain 'F' and resid 125 through 141 Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 158 through 174 Processing helix chain 'F' and resid 197 through 213 Processing helix chain 'F' and resid 230 through 244 removed outlier: 4.128A pdb=" N LEU F 238 " --> pdb=" O GLN F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 285 through 290 Processing helix chain 'F' and resid 291 through 298 removed outlier: 3.587A pdb=" N LYS F 297 " --> pdb=" O ALA F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 329 through 337 removed outlier: 3.924A pdb=" N ILE F 334 " --> pdb=" O ALA F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 356 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 374 through 378 Processing helix chain 'F' and resid 380 through 396 Processing helix chain 'F' and resid 400 through 427 Processing helix chain 'F' and resid 433 through 435 No H-bonds generated for 'chain 'F' and resid 433 through 435' Processing helix chain 'F' and resid 436 through 457 removed outlier: 4.010A pdb=" N SER F 441 " --> pdb=" O LEU F 437 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN F 442 " --> pdb=" O VAL F 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.634A pdb=" N GLN D 28 " --> pdb=" O SER D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 removed outlier: 3.760A pdb=" N LEU D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 107 removed outlier: 4.812A pdb=" N PHE D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 158 through 174 removed outlier: 4.066A pdb=" N ILE D 162 " --> pdb=" O THR D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 188 removed outlier: 4.146A pdb=" N GLY D 188 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 214 Processing helix chain 'D' and resid 230 through 244 removed outlier: 4.161A pdb=" N LEU D 238 " --> pdb=" O GLN D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 281 removed outlier: 4.393A pdb=" N ASP D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 328 through 337 removed outlier: 5.004A pdb=" N ILE D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 359 removed outlier: 4.262A pdb=" N ALA D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE D 357 " --> pdb=" O ALA D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 379 through 396 removed outlier: 3.830A pdb=" N VAL D 383 " --> pdb=" O ASN D 379 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER D 386 " --> pdb=" O GLY D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 426 removed outlier: 3.609A pdb=" N VAL D 404 " --> pdb=" O THR D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 456 removed outlier: 3.684A pdb=" N ASN D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 24 Processing helix chain 'E' and resid 24 through 29 removed outlier: 3.561A pdb=" N GLN E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 35 through 42 removed outlier: 4.528A pdb=" N VAL E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 107 removed outlier: 3.610A pdb=" N GLU E 98 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY E 107 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 141 removed outlier: 4.092A pdb=" N ALA E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 174 removed outlier: 3.748A pdb=" N ILE E 162 " --> pdb=" O THR E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 213 Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.787A pdb=" N LEU E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 281 removed outlier: 3.942A pdb=" N ILE E 272 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 290 removed outlier: 3.537A pdb=" N VAL E 289 " --> pdb=" O ILE E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.672A pdb=" N VAL E 310 " --> pdb=" O TRP E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 336 removed outlier: 5.091A pdb=" N ILE E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 365 through 369 removed outlier: 3.942A pdb=" N ALA E 368 " --> pdb=" O LYS E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 396 removed outlier: 4.523A pdb=" N SER E 386 " --> pdb=" O GLY E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 426 Processing helix chain 'E' and resid 437 through 457 removed outlier: 3.831A pdb=" N VAL E 449 " --> pdb=" O GLY E 445 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA E 450 " --> pdb=" O PHE E 446 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 3.630A pdb=" N VAL A 51 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS A 78 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLY A 115 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY A 80 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER A 117 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG A 82 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR A 77 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA A 152 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY A 79 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA3, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA4, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.830A pdb=" N ASN B 63 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 65 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY F 112 " --> pdb=" O PHE F 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.830A pdb=" N ASN B 63 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 65 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY F 80 " --> pdb=" O GLY F 115 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N SER F 117 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG F 82 " --> pdb=" O SER F 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 251 Processing sheet with id=AA9, first strand: chain 'B' and resid 340 through 342 removed outlier: 6.461A pdb=" N ILE B 341 " --> pdb=" O ALA B 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 81 removed outlier: 7.133A pdb=" N TYR C 77 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ALA C 152 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY C 79 " --> pdb=" O ALA C 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 246 through 247 removed outlier: 7.264A pdb=" N ARG C 223 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA C 316 " --> pdb=" O ARG C 223 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA C 225 " --> pdb=" O ALA C 316 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 249 through 251 Processing sheet with id=AB6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'F' and resid 246 through 247 removed outlier: 7.292A pdb=" N ARG F 223 " --> pdb=" O VAL F 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 249 through 250 Processing sheet with id=AB9, first strand: chain 'D' and resid 47 through 54 Processing sheet with id=AC1, first strand: chain 'D' and resid 246 through 247 removed outlier: 5.982A pdb=" N ARG D 223 " --> pdb=" O VAL D 313 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'E' and resid 65 through 66 Processing sheet with id=AC4, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.945A pdb=" N GLY E 79 " --> pdb=" O VAL E 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 246 through 249 removed outlier: 7.242A pdb=" N VAL E 224 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG E 223 " --> pdb=" O VAL E 313 " (cutoff:3.500A) 1029 hydrogen bonds defined for protein. 2997 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: 7.25 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.34: 6926 1.34 - 1.66: 13776 1.66 - 1.98: 105 1.98 - 2.29: 0 2.29 - 2.61: 2 Bond restraints: 20809 Sorted by residual: bond pdb=" N PRO C 76 " pdb=" CD PRO C 76 " ideal model delta sigma weight residual 1.473 2.611 -1.138 1.40e-02 5.10e+03 6.60e+03 bond pdb=" CB PRO A 318 " pdb=" CG PRO A 318 " ideal model delta sigma weight residual 1.492 2.480 -0.988 5.00e-02 4.00e+02 3.90e+02 bond pdb=" CG PRO E 31 " pdb=" CD PRO E 31 " ideal model delta sigma weight residual 1.503 1.027 0.476 3.40e-02 8.65e+02 1.96e+02 bond pdb=" CG PRO A 318 " pdb=" CD PRO A 318 " ideal model delta sigma weight residual 1.503 1.035 0.468 3.40e-02 8.65e+02 1.90e+02 bond pdb=" CG PRO C 76 " pdb=" CD PRO C 76 " ideal model delta sigma weight residual 1.503 1.153 0.350 3.40e-02 8.65e+02 1.06e+02 ... (remaining 20804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.22: 28172 21.22 - 42.43: 2 42.43 - 63.65: 0 63.65 - 84.86: 1 84.86 - 106.08: 1 Bond angle restraints: 28176 Sorted by residual: angle pdb=" N PRO C 76 " pdb=" CD PRO C 76 " pdb=" CG PRO C 76 " ideal model delta sigma weight residual 103.20 33.10 70.10 1.50e+00 4.44e-01 2.18e+03 angle pdb=" CB PRO A 318 " pdb=" CG PRO A 318 " pdb=" CD PRO A 318 " ideal model delta sigma weight residual 106.10 0.02 106.08 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO C 76 " pdb=" N PRO C 76 " pdb=" CD PRO C 76 " ideal model delta sigma weight residual 112.00 90.04 21.96 1.40e+00 5.10e-01 2.46e+02 angle pdb=" CA PRO A 318 " pdb=" N PRO A 318 " pdb=" CD PRO A 318 " ideal model delta sigma weight residual 112.00 92.11 19.89 1.40e+00 5.10e-01 2.02e+02 angle pdb=" N PRO A 318 " pdb=" CA PRO A 318 " pdb=" CB PRO A 318 " ideal model delta sigma weight residual 103.25 89.01 14.24 1.05e+00 9.07e-01 1.84e+02 ... (remaining 28171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.79: 10545 19.79 - 39.58: 1315 39.58 - 59.37: 299 59.37 - 79.16: 54 79.16 - 98.95: 24 Dihedral angle restraints: 12237 sinusoidal: 4527 harmonic: 7710 Sorted by residual: dihedral pdb=" N PRO A 318 " pdb=" CG PRO A 318 " pdb=" CD PRO A 318 " pdb=" CB PRO A 318 " ideal model delta sinusoidal sigma weight residual -30.00 -128.95 98.95 1 1.50e+01 4.44e-03 4.93e+01 dihedral pdb=" CA GLN F 351 " pdb=" C GLN F 351 " pdb=" N ALA F 352 " pdb=" CA ALA F 352 " ideal model delta harmonic sigma weight residual 180.00 -151.03 -28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" N PRO A 318 " pdb=" C PRO A 318 " pdb=" CA PRO A 318 " pdb=" CB PRO A 318 " ideal model delta harmonic sigma weight residual 115.10 101.82 13.28 0 2.50e+00 1.60e-01 2.82e+01 ... (remaining 12234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2739 0.074 - 0.148: 298 0.148 - 0.222: 16 0.222 - 0.296: 3 0.296 - 0.370: 1 Chirality restraints: 3057 Sorted by residual: chirality pdb=" CG LEU B 21 " pdb=" CB LEU B 21 " pdb=" CD1 LEU B 21 " pdb=" CD2 LEU B 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CB VAL B 157 " pdb=" CA VAL B 157 " pdb=" CG1 VAL B 157 " pdb=" CG2 VAL B 157 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL B 289 " pdb=" CA VAL B 289 " pdb=" CG1 VAL B 289 " pdb=" CG2 VAL B 289 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3054 not shown) Planarity restraints: 3737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 30 " 0.086 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO E 31 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO E 31 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO E 31 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 21 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C LEU B 21 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU B 21 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU B 22 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 371 " 0.033 2.00e-02 2.50e+03 2.29e-02 1.32e+01 pdb=" CG TRP E 371 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP E 371 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 371 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP E 371 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP E 371 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 371 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 371 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 371 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 371 " 0.027 2.00e-02 2.50e+03 ... (remaining 3734 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 108 2.38 - 3.01: 13428 3.01 - 3.64: 35251 3.64 - 4.27: 52114 4.27 - 4.90: 82745 Nonbonded interactions: 183646 Sorted by model distance: nonbonded pdb=" NH2 ARG F 305 " pdb=" OG1 THR F 321 " model vdw 1.753 3.120 nonbonded pdb=" CE MET E 137 " pdb=" O LEU E 165 " model vdw 1.816 3.460 nonbonded pdb=" CE2 PHE D 166 " pdb=" CZ3 TRP D 187 " model vdw 1.998 3.640 nonbonded pdb=" NH1 ARG F 305 " pdb=" N GLU F 324 " model vdw 2.056 2.560 nonbonded pdb=" OG SER E 227 " pdb=" O LEU E 317 " model vdw 2.076 3.040 ... (remaining 183641 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' and (resid 3 through 378 or (resid 379 through 380 and (name N or nam \ e CA or name C or name O or name CB )) or resid 381 through 457 or (resid 458 an \ d (name N or name CA or name C or name O or name CB )) or resid 459 through 460) \ ) selection = (chain 'B' and (resid 3 through 378 or (resid 379 through 380 and (name N or nam \ e CA or name C or name O or name CB )) or resid 381 through 427 or (resid 428 th \ rough 431 and (name N or name CA or name C or name O or name CB )) or resid 432 \ or (resid 433 through 439 and (name N or name CA or name C or name O or name CB \ )) or resid 440 or (resid 441 through 444 and (name N or name CA or name C or na \ me O or name CB )) or resid 445 or (resid 446 through 456 and (name N or name CA \ or name C or name O or name CB )) or resid 457 or (resid 458 and (name N or nam \ e CA or name C or name O or name CB )) or resid 459 through 460)) selection = chain 'C' selection = (chain 'D' and (resid 3 through 378 or (resid 379 through 380 and (name N or nam \ e CA or name C or name O or name CB )) or resid 381 through 457 or (resid 458 an \ d (name N or name CA or name C or name O or name CB )) or resid 459 through 460) \ ) selection = (chain 'E' and (resid 3 through 378 or (resid 379 through 380 and (name N or nam \ e CA or name C or name O or name CB )) or resid 381 through 457 or (resid 458 an \ d (name N or name CA or name C or name O or name CB )) or resid 459 through 460) \ ) selection = (chain 'F' and (resid 3 through 378 or (resid 379 through 380 and (name N or nam \ e CA or name C or name O or name CB )) or resid 381 through 457 or (resid 458 an \ d (name N or name CA or name C or name O or name CB )) or resid 459 through 460) \ ) } 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 48.570 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 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 : 0.013 1.138 20810 Z= 0.646 Angle : 1.189 106.079 28176 Z= 0.617 Chirality : 0.046 0.370 3057 Planarity : 0.007 0.122 3737 Dihedral : 18.505 98.947 7341 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 40.20 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.72 % Favored : 86.70 % Rotamer: Outliers : 0.30 % Allowed : 34.23 % Favored : 65.47 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.04 % 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: -3.25 (0.14), residues: 2736 helix: -1.28 (0.13), residues: 1275 sheet: -3.13 (0.31), residues: 231 loop : -2.90 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP E 371 HIS 0.006 0.001 HIS F 207 PHE 0.046 0.003 PHE B 27 TYR 0.024 0.002 TYR E 199 ARG 0.017 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.16905 ( 1007) hydrogen bonds : angle 8.04763 ( 2997) covalent geometry : bond 0.01270 (20809) covalent geometry : angle 1.18879 (28176) Misc. bond : bond 0.11939 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 275 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 277 average time/residue: 0.3304 time to fit residues: 138.8720 Evaluate side-chains 278 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 273 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 199 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 0.8980 chunk 204 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 245 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN E 30 ASN E 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.202230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.181703 restraints weight = 38355.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.182340 restraints weight = 31394.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.182473 restraints weight = 26067.410| |-----------------------------------------------------------------------------| r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20810 Z= 0.199 Angle : 0.754 13.357 28176 Z= 0.397 Chirality : 0.045 0.165 3057 Planarity : 0.006 0.099 3737 Dihedral : 6.239 81.939 2949 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 26.92 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.02 % Favored : 87.39 % Rotamer: Outliers : 6.11 % Allowed : 29.73 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: -3.02 (0.14), residues: 2736 helix: -1.00 (0.13), residues: 1295 sheet: -3.01 (0.32), residues: 223 loop : -2.92 (0.15), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 371 HIS 0.006 0.001 HIS F 207 PHE 0.032 0.003 PHE D 70 TYR 0.024 0.002 TYR B 77 ARG 0.008 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 1007) hydrogen bonds : angle 6.71406 ( 2997) covalent geometry : bond 0.00445 (20809) covalent geometry : angle 0.75373 (28176) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 313 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.5761 (OUTLIER) cc_final: 0.5312 (m-10) REVERT: A 84 HIS cc_start: 0.5700 (OUTLIER) cc_final: 0.5326 (t-170) REVERT: B 17 LEU cc_start: 0.6647 (tp) cc_final: 0.6388 (mm) REVERT: B 21 LEU cc_start: 0.7480 (tp) cc_final: 0.7155 (tp) REVERT: B 53 TRP cc_start: 0.6587 (p-90) cc_final: 0.6291 (p-90) REVERT: B 70 PHE cc_start: 0.6245 (t80) cc_final: 0.6041 (t80) REVERT: B 257 LEU cc_start: 0.6826 (mp) cc_final: 0.6089 (tt) REVERT: B 426 TYR cc_start: 0.5489 (m-80) cc_final: 0.5009 (m-80) REVERT: C 137 MET cc_start: 0.6962 (tpp) cc_final: 0.6588 (tpp) REVERT: C 268 THR cc_start: 0.6191 (OUTLIER) cc_final: 0.5920 (m) REVERT: C 372 TYR cc_start: 0.5176 (OUTLIER) cc_final: 0.4795 (t80) REVERT: D 45 ARG cc_start: 0.4270 (OUTLIER) cc_final: 0.3315 (ttm110) REVERT: D 181 THR cc_start: 0.6993 (p) cc_final: 0.6449 (p) REVERT: D 195 GLU cc_start: 0.5163 (OUTLIER) cc_final: 0.4221 (mm-30) REVERT: D 390 MET cc_start: 0.6147 (mmm) cc_final: 0.5678 (mmm) REVERT: E 243 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5814 (mm) REVERT: E 390 MET cc_start: 0.6188 (mmm) cc_final: 0.5927 (tpt) outliers start: 121 outliers final: 58 residues processed: 397 average time/residue: 0.3150 time to fit residues: 190.8651 Evaluate side-chains 335 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 270 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 207 HIS Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 385 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 57 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 240 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** E 69 GLN ** 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 = 0.4676 r_free = 0.4676 target = 0.199181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.179977 restraints weight = 39254.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.180518 restraints weight = 31686.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.180919 restraints weight = 25024.686| |-----------------------------------------------------------------------------| r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20810 Z= 0.168 Angle : 0.698 13.630 28176 Z= 0.366 Chirality : 0.044 0.191 3057 Planarity : 0.005 0.061 3737 Dihedral : 5.935 82.572 2943 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.27 % Favored : 89.11 % Rotamer: Outliers : 7.02 % Allowed : 28.77 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: -2.75 (0.15), residues: 2736 helix: -0.82 (0.14), residues: 1306 sheet: -2.88 (0.32), residues: 234 loop : -2.74 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 371 HIS 0.004 0.001 HIS F 207 PHE 0.032 0.002 PHE D 70 TYR 0.022 0.002 TYR F 199 ARG 0.006 0.001 ARG F 305 Details of bonding type rmsd hydrogen bonds : bond 0.04759 ( 1007) hydrogen bonds : angle 6.43564 ( 2997) covalent geometry : bond 0.00371 (20809) covalent geometry : angle 0.69817 (28176) Misc. bond : bond 0.00101 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 298 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.5747 (OUTLIER) cc_final: 0.5393 (t-170) REVERT: B 17 LEU cc_start: 0.6276 (tp) cc_final: 0.6062 (mm) REVERT: B 21 LEU cc_start: 0.7326 (tp) cc_final: 0.7006 (tp) REVERT: B 50 ARG cc_start: 0.4731 (OUTLIER) cc_final: 0.3420 (ptp-170) REVERT: B 70 PHE cc_start: 0.6361 (t80) cc_final: 0.5924 (t80) REVERT: B 219 PHE cc_start: 0.2422 (OUTLIER) cc_final: 0.1971 (t80) REVERT: C 26 LEU cc_start: 0.6603 (tp) cc_final: 0.5952 (pp) REVERT: C 137 MET cc_start: 0.7082 (tpp) cc_final: 0.6510 (tpp) REVERT: C 372 TYR cc_start: 0.5605 (OUTLIER) cc_final: 0.4742 (t80) REVERT: F 314 ASP cc_start: 0.3690 (OUTLIER) cc_final: 0.3436 (m-30) REVERT: D 45 ARG cc_start: 0.3697 (OUTLIER) cc_final: 0.2850 (ttm110) REVERT: D 181 THR cc_start: 0.7012 (p) cc_final: 0.6695 (p) REVERT: D 195 GLU cc_start: 0.5338 (OUTLIER) cc_final: 0.3505 (mm-30) REVERT: D 252 ASP cc_start: 0.5670 (OUTLIER) cc_final: 0.5451 (m-30) REVERT: D 298 PHE cc_start: 0.3183 (m-80) cc_final: 0.2964 (m-80) REVERT: D 413 LYS cc_start: 0.7271 (ttmm) cc_final: 0.6810 (tptt) outliers start: 139 outliers final: 74 residues processed: 400 average time/residue: 0.3223 time to fit residues: 197.8213 Evaluate side-chains 349 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 267 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 385 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 162 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 243 optimal weight: 8.9990 chunk 73 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.201754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.183414 restraints weight = 39767.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.184109 restraints weight = 28643.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.184286 restraints weight = 24093.656| |-----------------------------------------------------------------------------| r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20810 Z= 0.136 Angle : 0.663 13.000 28176 Z= 0.345 Chirality : 0.043 0.190 3057 Planarity : 0.004 0.054 3737 Dihedral : 5.609 79.722 2943 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.92 % Favored : 90.46 % Rotamer: Outliers : 6.51 % Allowed : 28.77 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: -2.37 (0.15), residues: 2736 helix: -0.52 (0.14), residues: 1305 sheet: -2.51 (0.33), residues: 238 loop : -2.56 (0.16), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 53 HIS 0.004 0.001 HIS E 211 PHE 0.028 0.002 PHE F 101 TYR 0.016 0.002 TYR D 235 ARG 0.005 0.000 ARG D 396 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 1007) hydrogen bonds : angle 6.06487 ( 2997) covalent geometry : bond 0.00287 (20809) covalent geometry : angle 0.66281 (28176) Misc. bond : bond 0.00084 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 309 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 SER cc_start: 0.0758 (OUTLIER) cc_final: -0.0797 (p) REVERT: B 47 ILE cc_start: 0.5289 (OUTLIER) cc_final: 0.4993 (tp) REVERT: B 70 PHE cc_start: 0.5891 (OUTLIER) cc_final: 0.5644 (t80) REVERT: B 213 THR cc_start: 0.6063 (t) cc_final: 0.5780 (t) REVERT: B 219 PHE cc_start: 0.2820 (OUTLIER) cc_final: 0.2555 (t80) REVERT: C 26 LEU cc_start: 0.6534 (tp) cc_final: 0.6132 (pp) REVERT: C 137 MET cc_start: 0.7029 (tpp) cc_final: 0.6461 (tpp) REVERT: C 372 TYR cc_start: 0.5685 (OUTLIER) cc_final: 0.4503 (t80) REVERT: F 100 ILE cc_start: 0.4136 (mp) cc_final: 0.3869 (mp) REVERT: F 305 ARG cc_start: -0.1158 (OUTLIER) cc_final: -0.2121 (mtp180) REVERT: F 372 TYR cc_start: 0.4827 (m-80) cc_final: 0.4466 (m-80) REVERT: D 45 ARG cc_start: 0.3608 (OUTLIER) cc_final: 0.2962 (ttm110) REVERT: D 181 THR cc_start: 0.6764 (OUTLIER) cc_final: 0.6388 (p) REVERT: D 413 LYS cc_start: 0.7217 (ttmm) cc_final: 0.6877 (tptt) REVERT: E 314 ASP cc_start: 0.5026 (m-30) cc_final: 0.4616 (m-30) outliers start: 129 outliers final: 65 residues processed: 396 average time/residue: 0.3258 time to fit residues: 197.1248 Evaluate side-chains 342 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 269 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 187 TRP Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 385 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 181 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 266 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.202163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.182706 restraints weight = 39678.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.184130 restraints weight = 29426.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.184409 restraints weight = 23334.228| |-----------------------------------------------------------------------------| r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5728 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20810 Z= 0.137 Angle : 0.657 11.650 28176 Z= 0.343 Chirality : 0.043 0.195 3057 Planarity : 0.004 0.053 3737 Dihedral : 5.326 77.218 2940 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.06 % Favored : 90.31 % Rotamer: Outliers : 6.31 % Allowed : 28.77 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: -2.11 (0.15), residues: 2736 helix: -0.32 (0.14), residues: 1295 sheet: -2.27 (0.34), residues: 237 loop : -2.43 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 371 HIS 0.005 0.001 HIS E 211 PHE 0.029 0.002 PHE F 101 TYR 0.020 0.001 TYR F 199 ARG 0.005 0.000 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 1007) hydrogen bonds : angle 5.87635 ( 2997) covalent geometry : bond 0.00297 (20809) covalent geometry : angle 0.65675 (28176) Misc. bond : bond 0.00091 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 296 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.4714 (ttm-80) REVERT: A 266 SER cc_start: 0.1367 (OUTLIER) cc_final: -0.0255 (p) REVERT: B 40 VAL cc_start: 0.6507 (m) cc_final: 0.6185 (p) REVERT: B 47 ILE cc_start: 0.5187 (OUTLIER) cc_final: 0.4430 (pt) REVERT: B 70 PHE cc_start: 0.5978 (OUTLIER) cc_final: 0.5692 (t80) REVERT: B 213 THR cc_start: 0.6249 (t) cc_final: 0.6045 (t) REVERT: B 219 PHE cc_start: 0.3190 (OUTLIER) cc_final: 0.2639 (t80) REVERT: B 371 TRP cc_start: 0.4781 (t60) cc_final: 0.4576 (t60) REVERT: C 26 LEU cc_start: 0.6735 (tp) cc_final: 0.6393 (pp) REVERT: C 137 MET cc_start: 0.7227 (tpp) cc_final: 0.6595 (tpp) REVERT: C 246 ARG cc_start: 0.6472 (mmp-170) cc_final: 0.6012 (mmp-170) REVERT: C 372 TYR cc_start: 0.5537 (OUTLIER) cc_final: 0.4297 (t80) REVERT: F 305 ARG cc_start: -0.1088 (OUTLIER) cc_final: -0.2198 (mtp180) REVERT: F 372 TYR cc_start: 0.4777 (OUTLIER) cc_final: 0.4254 (m-80) REVERT: D 45 ARG cc_start: 0.3556 (OUTLIER) cc_final: 0.3326 (ttm110) REVERT: D 181 THR cc_start: 0.7000 (p) cc_final: 0.6642 (p) REVERT: D 195 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.3660 (mm-30) REVERT: D 413 LYS cc_start: 0.7222 (ttmm) cc_final: 0.6837 (tptt) outliers start: 125 outliers final: 76 residues processed: 378 average time/residue: 0.3129 time to fit residues: 182.1527 Evaluate side-chains 353 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 267 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 393 ASN Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 385 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 20.0000 chunk 256 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS D 71 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.199411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.181208 restraints weight = 39620.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.181930 restraints weight = 30478.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.181886 restraints weight = 26537.991| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20810 Z= 0.164 Angle : 0.694 11.317 28176 Z= 0.362 Chirality : 0.044 0.186 3057 Planarity : 0.005 0.062 3737 Dihedral : 5.486 78.669 2940 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.94 % Favored : 89.44 % Rotamer: Outliers : 6.92 % Allowed : 28.67 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: -2.21 (0.15), residues: 2736 helix: -0.42 (0.14), residues: 1298 sheet: -2.19 (0.36), residues: 216 loop : -2.49 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 371 HIS 0.005 0.001 HIS E 211 PHE 0.035 0.003 PHE A 83 TYR 0.029 0.002 TYR D 235 ARG 0.005 0.001 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 1007) hydrogen bonds : angle 5.97609 ( 2997) covalent geometry : bond 0.00367 (20809) covalent geometry : angle 0.69379 (28176) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 275 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.4057 (mttt) cc_final: 0.3746 (mttm) REVERT: A 266 SER cc_start: 0.0490 (OUTLIER) cc_final: -0.0959 (p) REVERT: B 40 VAL cc_start: 0.6583 (m) cc_final: 0.6201 (p) REVERT: B 47 ILE cc_start: 0.5296 (OUTLIER) cc_final: 0.4554 (tp) REVERT: B 50 ARG cc_start: 0.4978 (OUTLIER) cc_final: 0.3523 (ptp-170) REVERT: B 70 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5842 (t80) REVERT: B 213 THR cc_start: 0.5991 (t) cc_final: 0.5748 (t) REVERT: B 219 PHE cc_start: 0.3622 (OUTLIER) cc_final: 0.3001 (t80) REVERT: C 137 MET cc_start: 0.7356 (tpp) cc_final: 0.6759 (tpp) REVERT: C 246 ARG cc_start: 0.6469 (mmp-170) cc_final: 0.5961 (mmp-170) REVERT: C 252 ASP cc_start: 0.5883 (OUTLIER) cc_final: 0.5594 (m-30) REVERT: C 268 THR cc_start: 0.5730 (OUTLIER) cc_final: 0.5443 (m) REVERT: C 372 TYR cc_start: 0.5523 (OUTLIER) cc_final: 0.4230 (t80) REVERT: F 42 VAL cc_start: 0.7788 (t) cc_final: 0.7268 (t) REVERT: F 305 ARG cc_start: -0.0980 (OUTLIER) cc_final: -0.2259 (mtp180) REVERT: F 372 TYR cc_start: 0.4371 (OUTLIER) cc_final: 0.3944 (m-80) REVERT: D 45 ARG cc_start: 0.3508 (OUTLIER) cc_final: 0.2831 (ttm110) REVERT: D 120 ASP cc_start: 0.5889 (OUTLIER) cc_final: 0.5479 (t70) REVERT: D 181 THR cc_start: 0.7152 (OUTLIER) cc_final: 0.6722 (p) REVERT: D 413 LYS cc_start: 0.7343 (ttmm) cc_final: 0.7104 (tptt) REVERT: E 421 ASP cc_start: 0.6478 (t0) cc_final: 0.5953 (m-30) outliers start: 137 outliers final: 97 residues processed: 375 average time/residue: 0.3089 time to fit residues: 179.7866 Evaluate side-chains 372 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 262 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 207 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 393 ASN Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 415 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 243 optimal weight: 9.9990 chunk 233 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 204 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 168 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.200831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.182714 restraints weight = 39612.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.183503 restraints weight = 29468.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.183643 restraints weight = 25318.477| |-----------------------------------------------------------------------------| r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5747 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20810 Z= 0.145 Angle : 0.679 10.894 28176 Z= 0.354 Chirality : 0.043 0.187 3057 Planarity : 0.004 0.061 3737 Dihedral : 5.380 78.404 2940 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.17 % Favored : 90.24 % Rotamer: Outliers : 6.41 % Allowed : 29.43 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: -2.13 (0.15), residues: 2736 helix: -0.38 (0.14), residues: 1304 sheet: -2.20 (0.34), residues: 227 loop : -2.41 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 371 HIS 0.005 0.001 HIS E 211 PHE 0.037 0.002 PHE F 101 TYR 0.022 0.001 TYR F 199 ARG 0.004 0.000 ARG F 305 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 1007) hydrogen bonds : angle 5.84222 ( 2997) covalent geometry : bond 0.00320 (20809) covalent geometry : angle 0.67936 (28176) Misc. bond : bond 0.00074 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 282 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.4190 (mttt) cc_final: 0.3931 (mttm) REVERT: A 266 SER cc_start: 0.0889 (OUTLIER) cc_final: -0.0564 (p) REVERT: B 40 VAL cc_start: 0.6467 (m) cc_final: 0.6191 (p) REVERT: B 47 ILE cc_start: 0.4913 (OUTLIER) cc_final: 0.4328 (pt) REVERT: B 50 ARG cc_start: 0.4752 (OUTLIER) cc_final: 0.3409 (ptp-170) REVERT: B 70 PHE cc_start: 0.5703 (OUTLIER) cc_final: 0.5450 (t80) REVERT: B 219 PHE cc_start: 0.3559 (OUTLIER) cc_final: 0.3139 (t80) REVERT: B 371 TRP cc_start: 0.4424 (t60) cc_final: 0.3977 (t60) REVERT: C 27 PHE cc_start: 0.6006 (OUTLIER) cc_final: 0.5704 (m-80) REVERT: C 137 MET cc_start: 0.7337 (tpp) cc_final: 0.6686 (tpp) REVERT: C 246 ARG cc_start: 0.6415 (mmp-170) cc_final: 0.5893 (mmp-170) REVERT: C 252 ASP cc_start: 0.5883 (OUTLIER) cc_final: 0.5592 (m-30) REVERT: C 372 TYR cc_start: 0.5213 (OUTLIER) cc_final: 0.3898 (t80) REVERT: F 42 VAL cc_start: 0.7706 (t) cc_final: 0.7143 (t) REVERT: F 305 ARG cc_start: -0.0988 (OUTLIER) cc_final: -0.2121 (mtp180) REVERT: F 372 TYR cc_start: 0.4086 (OUTLIER) cc_final: 0.3667 (m-80) REVERT: F 420 LEU cc_start: -0.0989 (OUTLIER) cc_final: -0.1281 (mp) REVERT: D 45 ARG cc_start: 0.3449 (OUTLIER) cc_final: 0.3164 (ttm110) REVERT: D 181 THR cc_start: 0.6924 (OUTLIER) cc_final: 0.6510 (p) REVERT: D 195 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.3712 (mm-30) REVERT: E 314 ASP cc_start: 0.5053 (m-30) cc_final: 0.4591 (m-30) REVERT: E 421 ASP cc_start: 0.6333 (t0) cc_final: 0.6017 (m-30) outliers start: 127 outliers final: 92 residues processed: 370 average time/residue: 0.3099 time to fit residues: 178.0650 Evaluate side-chains 369 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 263 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 393 ASN Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 385 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 191 optimal weight: 7.9990 chunk 184 optimal weight: 0.7980 chunk 66 optimal weight: 0.0570 chunk 146 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 207 HIS ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS E 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.203435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.185749 restraints weight = 39450.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.186458 restraints weight = 29321.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.186661 restraints weight = 23366.684| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 20810 Z= 0.131 Angle : 0.662 12.039 28176 Z= 0.344 Chirality : 0.043 0.195 3057 Planarity : 0.004 0.053 3737 Dihedral : 5.234 72.537 2940 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.95 % Favored : 90.50 % Rotamer: Outliers : 5.91 % Allowed : 30.39 % Favored : 63.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: -1.92 (0.16), residues: 2736 helix: -0.20 (0.14), residues: 1294 sheet: -2.10 (0.35), residues: 224 loop : -2.29 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 371 HIS 0.009 0.001 HIS F 207 PHE 0.041 0.002 PHE F 101 TYR 0.034 0.001 TYR D 235 ARG 0.005 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 1007) hydrogen bonds : angle 5.64642 ( 2997) covalent geometry : bond 0.00283 (20809) covalent geometry : angle 0.66242 (28176) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 285 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.3863 (mttt) cc_final: 0.3659 (mttm) REVERT: A 266 SER cc_start: 0.0892 (OUTLIER) cc_final: -0.0503 (p) REVERT: A 421 ASP cc_start: 0.6657 (t0) cc_final: 0.6356 (t0) REVERT: B 26 LEU cc_start: 0.5349 (pt) cc_final: 0.5095 (pt) REVERT: B 47 ILE cc_start: 0.4792 (OUTLIER) cc_final: 0.4326 (tp) REVERT: B 219 PHE cc_start: 0.4055 (OUTLIER) cc_final: 0.3632 (t80) REVERT: C 137 MET cc_start: 0.7284 (tpp) cc_final: 0.6664 (tpp) REVERT: C 246 ARG cc_start: 0.6315 (mmp-170) cc_final: 0.5811 (mmp-170) REVERT: C 333 LEU cc_start: 0.4294 (mt) cc_final: 0.3988 (mp) REVERT: C 372 TYR cc_start: 0.4734 (OUTLIER) cc_final: 0.3500 (t80) REVERT: F 305 ARG cc_start: -0.1073 (OUTLIER) cc_final: -0.1900 (mtp180) REVERT: F 372 TYR cc_start: 0.4066 (OUTLIER) cc_final: 0.3384 (m-80) REVERT: F 425 GLU cc_start: 0.5581 (tt0) cc_final: 0.4649 (tp30) REVERT: D 23 ASN cc_start: 0.5368 (m-40) cc_final: 0.5128 (p0) REVERT: D 181 THR cc_start: 0.6869 (OUTLIER) cc_final: 0.6451 (p) REVERT: E 124 LYS cc_start: 0.3837 (mttm) cc_final: 0.3594 (mttm) REVERT: E 314 ASP cc_start: 0.5001 (m-30) cc_final: 0.4542 (m-30) REVERT: E 421 ASP cc_start: 0.6321 (t0) cc_final: 0.6054 (m-30) outliers start: 117 outliers final: 78 residues processed: 368 average time/residue: 0.3101 time to fit residues: 177.8880 Evaluate side-chains 348 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 263 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 415 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 53 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 207 HIS ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.202130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.182695 restraints weight = 39691.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.184006 restraints weight = 28739.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.184869 restraints weight = 22671.508| |-----------------------------------------------------------------------------| r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 20810 Z= 0.144 Angle : 0.687 11.501 28176 Z= 0.357 Chirality : 0.045 0.562 3057 Planarity : 0.004 0.070 3737 Dihedral : 5.316 70.030 2940 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.99 % Favored : 90.46 % Rotamer: Outliers : 5.55 % Allowed : 30.84 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: -1.90 (0.16), residues: 2736 helix: -0.23 (0.14), residues: 1300 sheet: -2.14 (0.34), residues: 224 loop : -2.23 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 187 HIS 0.009 0.001 HIS F 207 PHE 0.043 0.002 PHE F 101 TYR 0.021 0.001 TYR C 235 ARG 0.009 0.001 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1007) hydrogen bonds : angle 5.68306 ( 2997) covalent geometry : bond 0.00318 (20809) covalent geometry : angle 0.68718 (28176) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 269 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.4952 (ttm-80) REVERT: A 266 SER cc_start: 0.1124 (OUTLIER) cc_final: -0.0246 (p) REVERT: A 421 ASP cc_start: 0.6745 (t0) cc_final: 0.6484 (t0) REVERT: B 26 LEU cc_start: 0.5326 (pt) cc_final: 0.4949 (pt) REVERT: B 35 LYS cc_start: 0.5976 (mmmt) cc_final: 0.5472 (ptpp) REVERT: B 47 ILE cc_start: 0.5280 (OUTLIER) cc_final: 0.4464 (pt) REVERT: B 219 PHE cc_start: 0.4010 (OUTLIER) cc_final: 0.3663 (t80) REVERT: C 137 MET cc_start: 0.7321 (tpp) cc_final: 0.6734 (tpp) REVERT: C 372 TYR cc_start: 0.4786 (OUTLIER) cc_final: 0.3489 (t80) REVERT: F 305 ARG cc_start: -0.1138 (OUTLIER) cc_final: -0.2346 (mtp180) REVERT: F 372 TYR cc_start: 0.4045 (OUTLIER) cc_final: 0.3422 (m-80) REVERT: F 425 GLU cc_start: 0.5458 (tt0) cc_final: 0.4563 (tp30) REVERT: D 181 THR cc_start: 0.6905 (OUTLIER) cc_final: 0.6544 (p) REVERT: E 124 LYS cc_start: 0.3928 (mttm) cc_final: 0.3691 (mttm) REVERT: E 412 MET cc_start: 0.3074 (tmm) cc_final: 0.2154 (tmm) REVERT: E 421 ASP cc_start: 0.6192 (t0) cc_final: 0.5986 (m-30) outliers start: 110 outliers final: 82 residues processed: 349 average time/residue: 0.3098 time to fit residues: 169.3335 Evaluate side-chains 340 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 250 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 415 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 65 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 230 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 246 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 chunk 193 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS F 393 ASN E 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.204407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.186954 restraints weight = 39238.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.187909 restraints weight = 28694.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.188098 restraints weight = 22274.903| |-----------------------------------------------------------------------------| r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5637 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 20810 Z= 0.137 Angle : 0.693 11.074 28176 Z= 0.360 Chirality : 0.044 0.453 3057 Planarity : 0.004 0.053 3737 Dihedral : 5.240 65.629 2940 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.66 % Favored : 90.86 % Rotamer: Outliers : 4.85 % Allowed : 31.95 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: -1.78 (0.16), residues: 2736 helix: -0.15 (0.14), residues: 1306 sheet: -1.90 (0.36), residues: 219 loop : -2.18 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 371 HIS 0.008 0.001 HIS F 207 PHE 0.042 0.002 PHE F 101 TYR 0.026 0.002 TYR A 235 ARG 0.008 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1007) hydrogen bonds : angle 5.56524 ( 2997) covalent geometry : bond 0.00304 (20809) covalent geometry : angle 0.69324 (28176) Misc. bond : bond 0.00056 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 267 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.6088 (tt) cc_final: 0.5881 (mm) REVERT: A 130 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.4843 (ttm-80) REVERT: A 144 ILE cc_start: 0.7189 (pt) cc_final: 0.6977 (pt) REVERT: A 266 SER cc_start: 0.0748 (OUTLIER) cc_final: -0.0506 (p) REVERT: A 421 ASP cc_start: 0.6537 (t0) cc_final: 0.6306 (t0) REVERT: B 26 LEU cc_start: 0.5239 (pt) cc_final: 0.4971 (pt) REVERT: B 35 LYS cc_start: 0.6003 (mmmt) cc_final: 0.5371 (ptpp) REVERT: B 47 ILE cc_start: 0.4848 (OUTLIER) cc_final: 0.4311 (pt) REVERT: B 155 ILE cc_start: 0.6538 (mp) cc_final: 0.6111 (pt) REVERT: B 219 PHE cc_start: 0.4008 (OUTLIER) cc_final: 0.3675 (t80) REVERT: C 110 MET cc_start: 0.5600 (pmm) cc_final: 0.5355 (pmm) REVERT: C 137 MET cc_start: 0.7315 (tpp) cc_final: 0.6709 (tpp) REVERT: C 239 LYS cc_start: 0.6377 (tppt) cc_final: 0.6054 (tppp) REVERT: C 341 ILE cc_start: 0.3948 (mt) cc_final: 0.3701 (mt) REVERT: C 372 TYR cc_start: 0.4630 (OUTLIER) cc_final: 0.3352 (t80) REVERT: F 208 MET cc_start: 0.5754 (tpp) cc_final: 0.5112 (tpp) REVERT: F 239 LYS cc_start: 0.6100 (tppt) cc_final: 0.5529 (tppt) REVERT: F 257 LEU cc_start: 0.6928 (pt) cc_final: 0.6622 (mt) REVERT: F 305 ARG cc_start: -0.1006 (OUTLIER) cc_final: -0.1939 (mmm160) REVERT: F 390 MET cc_start: 0.5875 (mmm) cc_final: 0.5398 (mmp) REVERT: F 425 GLU cc_start: 0.5474 (tt0) cc_final: 0.4617 (tp30) REVERT: D 181 THR cc_start: 0.6916 (OUTLIER) cc_final: 0.6523 (p) REVERT: D 195 GLU cc_start: 0.5082 (OUTLIER) cc_final: 0.4229 (mm-30) REVERT: E 124 LYS cc_start: 0.3893 (mttm) cc_final: 0.3645 (mttm) REVERT: E 412 MET cc_start: 0.2910 (tmm) cc_final: 0.1822 (tmm) REVERT: E 421 ASP cc_start: 0.6345 (t0) cc_final: 0.6086 (m-30) outliers start: 96 outliers final: 77 residues processed: 336 average time/residue: 0.3171 time to fit residues: 166.6867 Evaluate side-chains 333 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 248 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 309 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 393 ASN Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 415 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 220 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 265 optimal weight: 0.4980 chunk 266 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.203191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.185360 restraints weight = 39336.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.186475 restraints weight = 29531.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.186569 restraints weight = 24229.457| |-----------------------------------------------------------------------------| r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 20810 Z= 0.147 Angle : 0.708 10.840 28176 Z= 0.367 Chirality : 0.045 0.572 3057 Planarity : 0.004 0.061 3737 Dihedral : 5.276 63.970 2940 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.92 % Favored : 90.64 % Rotamer: Outliers : 4.80 % Allowed : 32.41 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: -1.83 (0.16), residues: 2736 helix: -0.19 (0.14), residues: 1314 sheet: -1.95 (0.36), residues: 216 loop : -2.23 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 187 HIS 0.008 0.001 HIS F 207 PHE 0.041 0.002 PHE F 101 TYR 0.019 0.001 TYR C 199 ARG 0.008 0.001 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 1007) hydrogen bonds : angle 5.61269 ( 2997) covalent geometry : bond 0.00328 (20809) covalent geometry : angle 0.70775 (28176) Misc. bond : bond 0.00053 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6036.68 seconds wall clock time: 106 minutes 56.40 seconds (6416.40 seconds total)