Starting phenix.real_space_refine on Thu Sep 18 21:28:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z2f_39744/09_2025/8z2f_39744.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z2f_39744/09_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_39744/09_2025/8z2f_39744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z2f_39744/09_2025/8z2f_39744.map" model { file = "/net/cci-nas-00/data/ceres_data/8z2f_39744/09_2025/8z2f_39744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z2f_39744/09_2025/8z2f_39744.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLN:plan1': 1} 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: {'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1} 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: {'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLN:plan1': 1} 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: {'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLN:plan1': 1} 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: {'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 4.49, per 1000 atoms: 0.22 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: 1.98 Conformation dependent library (CDL) restraints added in 772.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.81 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: 3.39 Time building geometry restraints manager: 2.52 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.730 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- 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 : 40.18 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.017 0.001 ARG E 67 TYR 0.024 0.002 TYR E 199 PHE 0.046 0.003 PHE B 27 TRP 0.051 0.003 TRP E 371 HIS 0.006 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.01270 (20809) covalent geometry : angle 1.18879 (28176) hydrogen bonds : bond 0.16905 ( 1007) hydrogen bonds : angle 8.04763 ( 2997) 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 : 0.696 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 outliers start: 6 outliers final: 5 residues processed: 277 average time/residue: 0.1583 time to fit residues: 66.9394 Evaluate side-chains 277 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 272 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** B 71 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 109 ASN C 168 GLN C 323 ASN C 346 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 ASN ** F 364 ASN ** 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 D 331 GLN D 392 GLN ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.195023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.174235 restraints weight = 39902.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.175045 restraints weight = 32067.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.175552 restraints weight = 26351.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.175512 restraints weight = 22050.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.175652 restraints weight = 22377.485| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 20810 Z= 0.351 Angle : 0.967 13.776 28176 Z= 0.514 Chirality : 0.053 0.237 3057 Planarity : 0.008 0.092 3737 Dihedral : 7.193 81.106 2949 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 35.86 Ramachandran Plot: Outliers : 0.66 % Allowed : 14.73 % Favored : 84.61 % Rotamer: Outliers : 8.63 % Allowed : 29.83 % Favored : 61.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.78 (0.14), residues: 2736 helix: -1.66 (0.13), residues: 1304 sheet: -3.42 (0.30), residues: 229 loop : -3.27 (0.15), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 67 TYR 0.035 0.004 TYR B 77 PHE 0.046 0.005 PHE D 70 TRP 0.048 0.003 TRP E 371 HIS 0.012 0.002 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00800 (20809) covalent geometry : angle 0.96710 (28176) hydrogen bonds : bond 0.06862 ( 1007) hydrogen bonds : angle 7.59998 ( 2997) Misc. bond : bond 0.00212 ( 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 450 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 279 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.6816 (mp) REVERT: A 27 PHE cc_start: 0.6117 (OUTLIER) cc_final: 0.5578 (m-10) REVERT: A 136 PHE cc_start: 0.6696 (t80) cc_final: 0.6353 (t80) REVERT: B 21 LEU cc_start: 0.7857 (tp) cc_final: 0.7641 (tp) REVERT: B 50 ARG cc_start: 0.5269 (OUTLIER) cc_final: 0.3510 (ptp-170) REVERT: B 77 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.5968 (m-80) REVERT: B 136 PHE cc_start: 0.6841 (t80) cc_final: 0.6529 (t80) REVERT: B 139 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: B 219 PHE cc_start: 0.2543 (OUTLIER) cc_final: 0.2216 (t80) REVERT: B 426 TYR cc_start: 0.5525 (m-80) cc_final: 0.5187 (m-80) REVERT: C 137 MET cc_start: 0.7260 (tpp) cc_final: 0.6725 (tpp) REVERT: C 361 ARG cc_start: 0.4167 (ttm170) cc_final: 0.3934 (ttm170) REVERT: F 250 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.6134 (tp) REVERT: D 66 PHE cc_start: 0.5571 (OUTLIER) cc_final: 0.4980 (m-80) REVERT: D 93 LYS cc_start: 0.6727 (mttt) cc_final: 0.6422 (mtmt) REVERT: D 181 THR cc_start: 0.7115 (p) cc_final: 0.6821 (p) REVERT: D 195 GLU cc_start: 0.5110 (OUTLIER) cc_final: 0.4100 (mm-30) REVERT: E 63 ASN cc_start: 0.6519 (OUTLIER) cc_final: 0.5872 (p0) REVERT: E 181 THR cc_start: 0.6457 (t) cc_final: 0.6149 (m) REVERT: E 390 MET cc_start: 0.6228 (mmm) cc_final: 0.5894 (mmm) outliers start: 171 outliers final: 89 residues processed: 413 average time/residue: 0.1413 time to fit residues: 89.2675 Evaluate side-chains 352 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 253 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 21 LEU 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 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 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 301 LEU Chi-restraints excluded: chain A residue 309 HIS 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 40 VAL Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 139 GLU 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 343 GLU Chi-restraints excluded: chain B residue 354 ILE 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 428 THR 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 144 ILE 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 256 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 284 GLN 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 385 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 125 SER 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 250 LEU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 338 CYS 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 424 LYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 81 LEU 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 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 325 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 280 VAL 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 231 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 267 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 255 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 168 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 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 = 0.4686 r_free = 0.4686 target = 0.203190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.183445 restraints weight = 39811.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.184846 restraints weight = 28414.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.185609 restraints weight = 22408.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.186250 restraints weight = 19408.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.186494 restraints weight = 17731.331| |-----------------------------------------------------------------------------| r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20810 Z= 0.165 Angle : 0.716 13.577 28176 Z= 0.375 Chirality : 0.044 0.187 3057 Planarity : 0.005 0.062 3737 Dihedral : 6.190 78.649 2943 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 24.57 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.38 % Favored : 89.00 % Rotamer: Outliers : 6.81 % Allowed : 30.04 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.14), residues: 2736 helix: -1.08 (0.13), residues: 1305 sheet: -2.95 (0.31), residues: 236 loop : -2.93 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.020 0.002 TYR B 77 PHE 0.034 0.002 PHE D 70 TRP 0.031 0.002 TRP E 371 HIS 0.004 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00353 (20809) covalent geometry : angle 0.71581 (28176) hydrogen bonds : bond 0.04859 ( 1007) hydrogen bonds : angle 6.58608 ( 2997) Misc. bond : bond 0.00325 ( 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 455 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 320 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 PHE cc_start: 0.6418 (t80) cc_final: 0.6048 (t80) REVERT: A 266 SER cc_start: 0.1193 (OUTLIER) cc_final: -0.0441 (p) REVERT: A 458 ASP cc_start: 0.6230 (OUTLIER) cc_final: 0.5948 (p0) REVERT: B 17 LEU cc_start: 0.6452 (tp) cc_final: 0.6228 (mm) REVERT: B 150 VAL cc_start: 0.7769 (OUTLIER) cc_final: 0.7532 (m) REVERT: B 229 SER cc_start: 0.6888 (p) cc_final: 0.6623 (p) REVERT: C 137 MET cc_start: 0.7118 (tpp) cc_final: 0.6536 (tpp) REVERT: C 256 SER cc_start: 0.4569 (OUTLIER) cc_final: 0.4362 (t) REVERT: C 361 ARG cc_start: 0.4069 (ttm170) cc_final: 0.3856 (ttm170) REVERT: C 372 TYR cc_start: 0.5734 (OUTLIER) cc_final: 0.4696 (t80) REVERT: F 250 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5443 (tp) REVERT: F 305 ARG cc_start: -0.1048 (OUTLIER) cc_final: -0.1734 (mtp180) REVERT: D 4 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6306 (tt) REVERT: D 45 ARG cc_start: 0.4104 (OUTLIER) cc_final: 0.2970 (ttm110) REVERT: D 181 THR cc_start: 0.7212 (p) cc_final: 0.6983 (p) REVERT: D 195 GLU cc_start: 0.5484 (OUTLIER) cc_final: 0.4432 (mm-30) REVERT: D 413 LYS cc_start: 0.7306 (ttmm) cc_final: 0.6867 (tptt) REVERT: E 243 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6003 (tt) REVERT: E 314 ASP cc_start: 0.5215 (m-30) cc_final: 0.4709 (m-30) REVERT: E 365 LYS cc_start: 0.5219 (mmmm) cc_final: 0.4911 (mmmm) REVERT: E 390 MET cc_start: 0.6113 (mmm) cc_final: 0.5798 (mmm) outliers start: 135 outliers final: 71 residues processed: 417 average time/residue: 0.1413 time to fit residues: 92.1311 Evaluate side-chains 351 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 269 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 127 SER 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 266 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 325 VAL 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 229 SER Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 308 VAL 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 C residue 390 MET Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain F residue 42 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 191 LEU Chi-restraints excluded: chain F residue 207 HIS Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 325 VAL 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 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 66 PHE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 157 VAL 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 325 VAL 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 172 LEU Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 243 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 39 optimal weight: 0.0470 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 220 optimal weight: 0.9980 overall best weight: 2.1682 ------------------------------------------------------------------------------- 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 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** 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 = 0.4667 r_free = 0.4667 target = 0.202405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.182378 restraints weight = 40114.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.183774 restraints weight = 29857.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.184139 restraints weight = 24127.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.184422 restraints weight = 21716.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.184618 restraints weight = 20764.412| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.2786 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= 0.179 Angle : 0.718 13.339 28176 Z= 0.377 Chirality : 0.045 0.273 3057 Planarity : 0.005 0.060 3737 Dihedral : 6.125 77.745 2943 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.62 % Allowed : 11.84 % Favored : 87.54 % Rotamer: Outliers : 7.27 % Allowed : 30.54 % Favored : 62.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.83 (0.15), residues: 2736 helix: -0.90 (0.14), residues: 1308 sheet: -2.76 (0.32), residues: 240 loop : -2.80 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 67 TYR 0.033 0.002 TYR B 77 PHE 0.032 0.003 PHE D 70 TRP 0.032 0.002 TRP E 371 HIS 0.004 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00398 (20809) covalent geometry : angle 0.71838 (28176) hydrogen bonds : bond 0.04808 ( 1007) hydrogen bonds : angle 6.43873 ( 2997) Misc. bond : bond 0.00152 ( 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 440 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 296 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.5751 (OUTLIER) cc_final: 0.5351 (m-10) REVERT: A 180 LEU cc_start: 0.5212 (OUTLIER) cc_final: 0.4884 (mp) REVERT: A 266 SER cc_start: 0.1222 (OUTLIER) cc_final: -0.0474 (p) REVERT: B 219 PHE cc_start: 0.2691 (OUTLIER) cc_final: 0.2458 (t80) REVERT: C 26 LEU cc_start: 0.6883 (tp) cc_final: 0.6260 (pp) REVERT: C 102 LYS cc_start: 0.4281 (OUTLIER) cc_final: 0.3848 (tttt) REVERT: C 137 MET cc_start: 0.7346 (tpp) cc_final: 0.6682 (tpp) REVERT: C 256 SER cc_start: 0.4414 (OUTLIER) cc_final: 0.4117 (t) REVERT: C 361 ARG cc_start: 0.4014 (ttm170) cc_final: 0.3803 (ttm170) REVERT: C 372 TYR cc_start: 0.5648 (OUTLIER) cc_final: 0.4313 (t80) REVERT: F 305 ARG cc_start: -0.0789 (OUTLIER) cc_final: -0.1584 (mtp180) REVERT: F 372 TYR cc_start: 0.5039 (OUTLIER) cc_final: 0.4634 (m-80) REVERT: D 4 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6267 (tt) REVERT: D 45 ARG cc_start: 0.4331 (OUTLIER) cc_final: 0.2714 (ttm110) REVERT: D 181 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.7187 (p) REVERT: D 195 GLU cc_start: 0.5291 (OUTLIER) cc_final: 0.3614 (mm-30) REVERT: D 298 PHE cc_start: 0.3403 (m-80) cc_final: 0.3179 (m-80) REVERT: D 413 LYS cc_start: 0.7416 (ttmm) cc_final: 0.6899 (tptt) REVERT: E 243 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6283 (tt) outliers start: 144 outliers final: 88 residues processed: 399 average time/residue: 0.1451 time to fit residues: 90.0690 Evaluate side-chains 369 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 267 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 37 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 127 SER 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 180 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 385 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 172 LEU 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 308 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 349 CYS 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 95 LEU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 308 VAL 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 C residue 390 MET Chi-restraints excluded: chain C residue 420 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 191 LEU Chi-restraints excluded: chain F residue 207 HIS Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 325 VAL 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 424 LYS 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 147 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 272 ILE 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 30 ASN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU 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 229 SER Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 459 TRP 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 14 optimal weight: 3.9990 chunk 126 optimal weight: 0.0870 chunk 186 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 80 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** 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 = 0.4671 r_free = 0.4671 target = 0.198924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.179944 restraints weight = 39728.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.181074 restraints weight = 30205.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.181125 restraints weight = 22129.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.181174 restraints weight = 21637.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.181223 restraints weight = 20946.363| |-----------------------------------------------------------------------------| r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20810 Z= 0.151 Angle : 0.685 12.390 28176 Z= 0.357 Chirality : 0.043 0.190 3057 Planarity : 0.005 0.056 3737 Dihedral : 5.743 78.924 2942 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.47 % Favored : 89.91 % Rotamer: Outliers : 7.22 % Allowed : 31.20 % Favored : 61.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.15), residues: 2736 helix: -0.64 (0.14), residues: 1310 sheet: -2.54 (0.32), residues: 240 loop : -2.69 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 67 TYR 0.024 0.002 TYR B 77 PHE 0.032 0.002 PHE D 70 TRP 0.032 0.002 TRP E 371 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00330 (20809) covalent geometry : angle 0.68498 (28176) hydrogen bonds : bond 0.04413 ( 1007) hydrogen bonds : angle 6.09612 ( 2997) Misc. bond : bond 0.00124 ( 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 439 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 296 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.5055 (OUTLIER) cc_final: 0.4711 (mp) REVERT: A 266 SER cc_start: 0.0902 (OUTLIER) cc_final: -0.0709 (p) REVERT: B 219 PHE cc_start: 0.3062 (OUTLIER) cc_final: 0.2699 (t80) REVERT: B 365 LYS cc_start: 0.4045 (OUTLIER) cc_final: 0.3344 (mmmt) REVERT: C 26 LEU cc_start: 0.6751 (tp) cc_final: 0.6253 (pp) REVERT: C 102 LYS cc_start: 0.4090 (OUTLIER) cc_final: 0.3830 (tttt) REVERT: C 372 TYR cc_start: 0.5470 (OUTLIER) cc_final: 0.4321 (t80) REVERT: F 305 ARG cc_start: -0.0994 (OUTLIER) cc_final: -0.1426 (mmm160) REVERT: F 372 TYR cc_start: 0.4685 (m-80) cc_final: 0.4380 (m-80) REVERT: D 4 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6210 (tt) REVERT: D 45 ARG cc_start: 0.3834 (OUTLIER) cc_final: 0.3160 (ttm110) REVERT: D 181 THR cc_start: 0.7261 (OUTLIER) cc_final: 0.7037 (p) REVERT: D 413 LYS cc_start: 0.7412 (ttmm) cc_final: 0.6953 (tptt) REVERT: E 243 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6257 (tt) REVERT: E 390 MET cc_start: 0.6276 (mmm) cc_final: 0.5989 (mmm) outliers start: 143 outliers final: 85 residues processed: 402 average time/residue: 0.1528 time to fit residues: 95.0703 Evaluate side-chains 364 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 268 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 100 ILE 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 180 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 385 VAL Chi-restraints excluded: chain B residue 39 VAL 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 139 GLU 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 308 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 397 LEU 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 25 THR Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 279 LYS 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 47 ILE Chi-restraints excluded: chain F residue 176 TRP 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 229 SER Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 285 ILE 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 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 180 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 256 SER 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 321 THR Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 349 CYS 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 30 ASN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU 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 261 ASP Chi-restraints excluded: chain E residue 280 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 459 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 183 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** 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** C 71 ASN C 168 GLN ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.194787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.175983 restraints weight = 39695.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.176817 restraints weight = 30591.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.176876 restraints weight = 25546.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.176907 restraints weight = 22339.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.176948 restraints weight = 22230.153| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20810 Z= 0.208 Angle : 0.757 12.140 28176 Z= 0.397 Chirality : 0.046 0.213 3057 Planarity : 0.005 0.061 3737 Dihedral : 6.076 75.430 2942 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 26.22 Ramachandran Plot: Outliers : 0.62 % Allowed : 11.84 % Favored : 87.54 % Rotamer: Outliers : 8.33 % Allowed : 29.93 % Favored : 61.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.15), residues: 2736 helix: -0.76 (0.14), residues: 1312 sheet: -2.77 (0.35), residues: 207 loop : -2.78 (0.16), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 67 TYR 0.033 0.002 TYR B 77 PHE 0.039 0.003 PHE B 70 TRP 0.038 0.003 TRP E 371 HIS 0.007 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00466 (20809) covalent geometry : angle 0.75711 (28176) hydrogen bonds : bond 0.04965 ( 1007) hydrogen bonds : angle 6.40691 ( 2997) Misc. bond : bond 0.00133 ( 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 440 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 275 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.4550 (mttt) cc_final: 0.4196 (mttm) REVERT: A 180 LEU cc_start: 0.5151 (OUTLIER) cc_final: 0.4857 (mp) REVERT: A 266 SER cc_start: 0.0823 (OUTLIER) cc_final: -0.0554 (p) REVERT: A 390 MET cc_start: 0.5785 (mmm) cc_final: 0.5515 (tpt) REVERT: A 458 ASP cc_start: 0.6291 (OUTLIER) cc_final: 0.5983 (p0) REVERT: B 139 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: B 219 PHE cc_start: 0.3511 (OUTLIER) cc_final: 0.3036 (t80) REVERT: C 26 LEU cc_start: 0.6918 (tp) cc_final: 0.6299 (pp) REVERT: C 102 LYS cc_start: 0.4119 (OUTLIER) cc_final: 0.3759 (tttt) REVERT: C 110 MET cc_start: 0.4864 (OUTLIER) cc_final: 0.4397 (mtp) REVERT: C 137 MET cc_start: 0.7486 (tpp) cc_final: 0.6780 (tpp) REVERT: C 268 THR cc_start: 0.5975 (OUTLIER) cc_final: 0.5619 (m) REVERT: C 372 TYR cc_start: 0.5465 (OUTLIER) cc_final: 0.4264 (t80) REVERT: F 305 ARG cc_start: -0.0799 (OUTLIER) cc_final: -0.1103 (mmm160) REVERT: F 372 TYR cc_start: 0.4957 (m-80) cc_final: 0.4384 (m-80) REVERT: D 4 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6382 (tt) REVERT: D 45 ARG cc_start: 0.3947 (OUTLIER) cc_final: 0.2745 (ttm110) REVERT: D 82 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7801 (mtp85) REVERT: D 137 MET cc_start: 0.7745 (tpp) cc_final: 0.6789 (tpp) REVERT: D 181 THR cc_start: 0.7229 (OUTLIER) cc_final: 0.6912 (p) REVERT: D 413 LYS cc_start: 0.7323 (ttmm) cc_final: 0.6932 (tptt) REVERT: D 420 LEU cc_start: -0.1100 (OUTLIER) cc_final: -0.1529 (mp) REVERT: E 181 THR cc_start: 0.5975 (t) cc_final: 0.5775 (m) REVERT: E 243 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6370 (tt) outliers start: 165 outliers final: 107 residues processed: 396 average time/residue: 0.1426 time to fit residues: 88.1131 Evaluate side-chains 387 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 264 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 180 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 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 317 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 458 ASP Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 172 LEU 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 308 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 LYS 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 428 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 25 THR Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 268 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 47 ILE Chi-restraints excluded: chain F residue 172 LEU 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 229 SER Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 386 SER 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 49 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 256 SER 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 321 THR Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU 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 261 ASP Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 354 ILE 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 459 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 125 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 201 optimal weight: 0.0040 chunk 56 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 230 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** 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 71 ASN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** 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 = 0.4671 r_free = 0.4671 target = 0.198756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.180043 restraints weight = 39578.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.180935 restraints weight = 30045.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.181027 restraints weight = 23766.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.181112 restraints weight = 22259.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.181135 restraints weight = 21207.559| |-----------------------------------------------------------------------------| r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20810 Z= 0.150 Angle : 0.701 13.015 28176 Z= 0.365 Chirality : 0.044 0.189 3057 Planarity : 0.005 0.059 3737 Dihedral : 5.752 75.850 2942 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.25 % Favored : 90.13 % Rotamer: Outliers : 7.07 % Allowed : 31.15 % Favored : 61.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.15), residues: 2736 helix: -0.59 (0.14), residues: 1308 sheet: -2.30 (0.35), residues: 225 loop : -2.57 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 67 TYR 0.028 0.002 TYR B 77 PHE 0.033 0.002 PHE F 101 TRP 0.049 0.002 TRP B 371 HIS 0.008 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00327 (20809) covalent geometry : angle 0.70132 (28176) hydrogen bonds : bond 0.04331 ( 1007) hydrogen bonds : angle 6.03348 ( 2997) Misc. bond : bond 0.00113 ( 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 406 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 266 time to evaluate : 0.798 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 124 LYS cc_start: 0.4485 (mttt) cc_final: 0.4202 (mttm) REVERT: A 130 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.4920 (ttm-80) REVERT: A 266 SER cc_start: 0.0335 (OUTLIER) cc_final: -0.1012 (p) REVERT: B 365 LYS cc_start: 0.4145 (OUTLIER) cc_final: 0.3595 (mmmt) REVERT: B 371 TRP cc_start: 0.4667 (t60) cc_final: 0.4261 (t60) REVERT: B 412 MET cc_start: 0.2547 (tmm) cc_final: 0.1998 (ttp) REVERT: C 26 LEU cc_start: 0.6784 (tp) cc_final: 0.6263 (pp) REVERT: C 102 LYS cc_start: 0.4342 (OUTLIER) cc_final: 0.4001 (tttt) REVERT: C 137 MET cc_start: 0.7452 (tpp) cc_final: 0.6663 (tpp) REVERT: C 372 TYR cc_start: 0.5077 (OUTLIER) cc_final: 0.3856 (t80) REVERT: D 45 ARG cc_start: 0.3283 (OUTLIER) cc_final: 0.2638 (ttm110) REVERT: D 181 THR cc_start: 0.7102 (OUTLIER) cc_final: 0.6880 (p) REVERT: D 413 LYS cc_start: 0.7406 (ttmm) cc_final: 0.7082 (tptt) REVERT: E 243 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6336 (tt) REVERT: E 390 MET cc_start: 0.5973 (mmm) cc_final: 0.5649 (mmm) outliers start: 140 outliers final: 95 residues processed: 369 average time/residue: 0.1462 time to fit residues: 83.8378 Evaluate side-chains 357 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 254 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 130 ARG Chi-restraints excluded: chain A residue 144 ILE 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 301 LEU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 87 VAL 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 139 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 338 CYS 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 434 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 71 ASN Chi-restraints excluded: chain C residue 102 LYS 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 296 ASP Chi-restraints excluded: chain C residue 308 VAL 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 47 ILE Chi-restraints excluded: chain F residue 69 GLN 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 229 SER Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 385 VAL 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 147 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR 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 334 ILE Chi-restraints excluded: chain D residue 349 CYS 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 30 ASN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU 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 280 VAL 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 Chi-restraints excluded: chain E residue 459 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 207 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 226 optimal weight: 8.9990 chunk 26 optimal weight: 0.2980 chunk 71 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 247 optimal weight: 20.0000 chunk 213 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 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 309 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 456 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 F 364 ASN D 71 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.201258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.183075 restraints weight = 39575.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.184080 restraints weight = 28021.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.183998 restraints weight = 22024.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.184121 restraints weight = 22112.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.184148 restraints weight = 20688.870| |-----------------------------------------------------------------------------| r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5717 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20810 Z= 0.136 Angle : 0.693 14.753 28176 Z= 0.358 Chirality : 0.043 0.188 3057 Planarity : 0.005 0.174 3737 Dihedral : 5.630 80.787 2942 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.39 % Favored : 90.06 % Rotamer: Outliers : 6.11 % Allowed : 31.50 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.15), residues: 2736 helix: -0.41 (0.14), residues: 1309 sheet: -2.05 (0.35), residues: 225 loop : -2.41 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG F 305 TYR 0.022 0.002 TYR D 199 PHE 0.036 0.002 PHE F 101 TRP 0.035 0.002 TRP E 371 HIS 0.010 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00293 (20809) covalent geometry : angle 0.69319 (28176) hydrogen bonds : bond 0.04109 ( 1007) hydrogen bonds : angle 5.80741 ( 2997) Misc. bond : bond 0.00625 ( 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 407 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 286 time to evaluate : 0.805 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 124 LYS cc_start: 0.4123 (mttt) cc_final: 0.3912 (mttm) REVERT: A 130 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.4855 (ttm-80) REVERT: A 266 SER cc_start: 0.0619 (OUTLIER) cc_final: -0.0775 (p) REVERT: B 35 LYS cc_start: 0.5944 (mmmt) cc_final: 0.5269 (ptpp) REVERT: B 365 LYS cc_start: 0.4228 (OUTLIER) cc_final: 0.3688 (mmmt) REVERT: C 26 LEU cc_start: 0.6623 (tp) cc_final: 0.6227 (pp) REVERT: C 372 TYR cc_start: 0.4916 (OUTLIER) cc_final: 0.3821 (t80) REVERT: C 383 VAL cc_start: 0.3113 (OUTLIER) cc_final: 0.2742 (m) REVERT: F 124 LYS cc_start: 0.4310 (mttt) cc_final: 0.3837 (mttt) REVERT: F 347 MET cc_start: 0.5688 (tpp) cc_final: 0.5487 (tpt) REVERT: F 372 TYR cc_start: 0.3849 (OUTLIER) cc_final: 0.2903 (m-80) REVERT: D 45 ARG cc_start: 0.3031 (OUTLIER) cc_final: 0.2726 (ttm110) REVERT: D 82 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7616 (mtp85) REVERT: D 181 THR cc_start: 0.6871 (OUTLIER) cc_final: 0.6439 (p) REVERT: D 413 LYS cc_start: 0.7399 (ttmm) cc_final: 0.7158 (tptt) REVERT: D 420 LEU cc_start: -0.1315 (OUTLIER) cc_final: -0.1875 (mp) REVERT: E 130 ARG cc_start: 0.6517 (ttm-80) cc_final: 0.6089 (ttm110) REVERT: E 202 VAL cc_start: 0.5462 (t) cc_final: 0.4782 (m) REVERT: E 243 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6405 (tt) outliers start: 121 outliers final: 86 residues processed: 377 average time/residue: 0.1467 time to fit residues: 86.2754 Evaluate side-chains 365 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 268 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 95 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 144 ILE 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 301 LEU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 338 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 434 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 186 SER 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 296 ASP 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 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 69 GLN 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 229 SER Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 265 ASP 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 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 45 ARG Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 186 SER 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 349 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 95 LEU 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 Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 459 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 54 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 169 optimal weight: 0.0670 chunk 127 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN ** C 309 HIS ** 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 F 364 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.195965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.176625 restraints weight = 39756.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.177423 restraints weight = 30506.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.177532 restraints weight = 23389.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.177568 restraints weight = 22698.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.177609 restraints weight = 22040.503| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20810 Z= 0.206 Angle : 0.790 14.387 28176 Z= 0.411 Chirality : 0.048 0.735 3057 Planarity : 0.006 0.172 3737 Dihedral : 6.072 77.357 2942 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.62 % Favored : 87.79 % Rotamer: Outliers : 6.46 % Allowed : 31.30 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.15), residues: 2736 helix: -0.63 (0.14), residues: 1304 sheet: -2.23 (0.39), residues: 183 loop : -2.61 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG F 305 TYR 0.025 0.002 TYR D 199 PHE 0.049 0.003 PHE D 70 TRP 0.056 0.003 TRP C 187 HIS 0.011 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00465 (20809) covalent geometry : angle 0.79039 (28176) hydrogen bonds : bond 0.04833 ( 1007) hydrogen bonds : angle 6.17928 ( 2997) Misc. bond : bond 0.00472 ( 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 394 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 266 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 SER cc_start: 0.0524 (OUTLIER) cc_final: -0.0832 (p) REVERT: B 254 GLN cc_start: 0.5607 (OUTLIER) cc_final: 0.5215 (pp30) REVERT: B 437 LEU cc_start: 0.5480 (OUTLIER) cc_final: 0.5230 (mt) REVERT: C 26 LEU cc_start: 0.6949 (tp) cc_final: 0.6381 (pp) REVERT: C 137 MET cc_start: 0.7388 (tpp) cc_final: 0.6991 (tpp) REVERT: C 268 THR cc_start: 0.5885 (OUTLIER) cc_final: 0.5507 (m) REVERT: C 334 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5764 (mt) REVERT: C 372 TYR cc_start: 0.5195 (OUTLIER) cc_final: 0.3811 (t80) REVERT: F 110 MET cc_start: 0.5475 (mpp) cc_final: 0.4675 (mtm) REVERT: D 45 ARG cc_start: 0.3827 (OUTLIER) cc_final: 0.2786 (ttm110) REVERT: D 82 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7774 (mtp85) REVERT: D 181 THR cc_start: 0.7150 (OUTLIER) cc_final: 0.6941 (p) REVERT: D 413 LYS cc_start: 0.7434 (ttmm) cc_final: 0.7074 (tptt) REVERT: D 420 LEU cc_start: -0.1011 (OUTLIER) cc_final: -0.1586 (mp) outliers start: 128 outliers final: 101 residues processed: 362 average time/residue: 0.1370 time to fit residues: 78.1505 Evaluate side-chains 366 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 255 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 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 301 LEU Chi-restraints excluded: chain A residue 309 HIS 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 B residue 91 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 338 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 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 25 THR Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 308 VAL 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 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 69 GLN 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 229 SER Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 386 SER 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 49 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 186 SER 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 321 THR Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU 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 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 Chi-restraints excluded: chain E residue 459 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 254 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 233 optimal weight: 0.0870 chunk 18 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 overall best weight: 3.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 360 HIS C 71 ASN ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.194205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.173884 restraints weight = 39935.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.174692 restraints weight = 30391.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.175193 restraints weight = 24421.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.175341 restraints weight = 22201.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.175399 restraints weight = 21246.736| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 20810 Z= 0.238 Angle : 0.837 13.957 28176 Z= 0.436 Chirality : 0.051 0.878 3057 Planarity : 0.006 0.152 3737 Dihedral : 6.367 79.348 2942 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.21 % Favored : 87.24 % Rotamer: Outliers : 6.36 % Allowed : 31.70 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.15), residues: 2736 helix: -0.91 (0.14), residues: 1307 sheet: -2.54 (0.37), residues: 183 loop : -2.76 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG F 305 TYR 0.030 0.003 TYR D 199 PHE 0.049 0.004 PHE D 70 TRP 0.059 0.003 TRP D 371 HIS 0.010 0.002 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00545 (20809) covalent geometry : angle 0.83726 (28176) hydrogen bonds : bond 0.05136 ( 1007) hydrogen bonds : angle 6.43441 ( 2997) Misc. bond : bond 0.00403 ( 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 390 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 264 time to evaluate : 0.781 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: 0.4662 (mttt) cc_final: 0.4373 (mttm) REVERT: A 266 SER cc_start: 0.0760 (OUTLIER) cc_final: -0.0614 (p) REVERT: B 254 GLN cc_start: 0.6251 (OUTLIER) cc_final: 0.5986 (pp30) REVERT: B 371 TRP cc_start: 0.4730 (OUTLIER) cc_final: 0.4277 (t60) REVERT: B 437 LEU cc_start: 0.5466 (OUTLIER) cc_final: 0.4856 (mt) REVERT: C 26 LEU cc_start: 0.6943 (tp) cc_final: 0.6476 (pp) REVERT: C 137 MET cc_start: 0.7406 (tpp) cc_final: 0.6807 (tpp) REVERT: C 181 THR cc_start: 0.6212 (t) cc_final: 0.5631 (m) REVERT: C 268 THR cc_start: 0.6152 (OUTLIER) cc_final: 0.5729 (m) REVERT: C 334 ILE cc_start: 0.5986 (OUTLIER) cc_final: 0.5707 (mt) REVERT: C 372 TYR cc_start: 0.4654 (OUTLIER) cc_final: 0.3393 (t80) REVERT: F 421 ASP cc_start: 0.6179 (t0) cc_final: 0.5830 (t0) REVERT: D 45 ARG cc_start: 0.3935 (OUTLIER) cc_final: 0.2737 (ttm110) REVERT: D 82 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7817 (mtp85) REVERT: D 124 LYS cc_start: 0.4157 (mttt) cc_final: 0.3734 (mttt) REVERT: D 137 MET cc_start: 0.7936 (tpp) cc_final: 0.6676 (tpp) REVERT: D 181 THR cc_start: 0.7318 (OUTLIER) cc_final: 0.7049 (p) REVERT: D 413 LYS cc_start: 0.7456 (ttmm) cc_final: 0.7050 (tptt) REVERT: D 420 LEU cc_start: -0.1005 (OUTLIER) cc_final: -0.1584 (mp) REVERT: E 202 VAL cc_start: 0.5352 (t) cc_final: 0.5099 (t) outliers start: 126 outliers final: 107 residues processed: 358 average time/residue: 0.1369 time to fit residues: 76.7868 Evaluate side-chains 376 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 258 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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 180 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 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 371 TRP 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 437 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 308 VAL 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 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 69 GLN 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 229 SER Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 386 SER 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 49 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 186 SER 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 321 THR Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 LEU 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 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 260 LYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 354 ILE 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 29 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 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 309 HIS ** 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS F 364 ASN D 71 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.198882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.181686 restraints weight = 39307.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.181734 restraints weight = 27611.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.181821 restraints weight = 24991.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.181814 restraints weight = 21476.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.182003 restraints weight = 20329.064| |-----------------------------------------------------------------------------| r_work (final): 0.4484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 moved from start: 0.4340 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= 0.152 Angle : 0.743 13.417 28176 Z= 0.385 Chirality : 0.047 0.708 3057 Planarity : 0.005 0.134 3737 Dihedral : 5.903 71.503 2942 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.83 % Favored : 89.66 % Rotamer: Outliers : 5.45 % Allowed : 32.51 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.15), residues: 2736 helix: -0.63 (0.14), residues: 1309 sheet: -2.16 (0.36), residues: 207 loop : -2.61 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG F 305 TYR 0.026 0.002 TYR D 199 PHE 0.041 0.003 PHE F 101 TRP 0.057 0.003 TRP C 187 HIS 0.007 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00336 (20809) covalent geometry : angle 0.74344 (28176) hydrogen bonds : bond 0.04321 ( 1007) hydrogen bonds : angle 5.97737 ( 2997) Misc. bond : bond 0.00386 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3097.94 seconds wall clock time: 54 minutes 47.40 seconds (3287.40 seconds total)