Starting phenix.real_space_refine on Thu Sep 18 20:59:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gcu_51237/09_2025/9gcu_51237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gcu_51237/09_2025/9gcu_51237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gcu_51237/09_2025/9gcu_51237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gcu_51237/09_2025/9gcu_51237.map" model { file = "/net/cci-nas-00/data/ceres_data/9gcu_51237/09_2025/9gcu_51237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gcu_51237/09_2025/9gcu_51237.cif" } resolution = 2.8 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= 0.005 sd= 0.040 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 102 5.16 5 C 12509 2.51 5 N 3550 2.21 5 O 3847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s 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: 20023 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3303 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 418, 3292 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 400} Conformer: "B" Number of residues, atoms: 418, 3292 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 400} bond proxies already assigned to first conformer: 3328 Chain: "B" Number of atoms: 3303 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 418, 3292 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 400} Conformer: "B" Number of residues, atoms: 418, 3292 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 400} bond proxies already assigned to first conformer: 3328 Chain: "C" Number of atoms: 3318 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 418, 3292 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 400} Conformer: "B" Number of residues, atoms: 418, 3292 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 400} bond proxies already assigned to first conformer: 3311 Chain: "D" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3292 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 400} Chain: "E" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3292 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 400} Chain: "F" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3292 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG A 366 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 366 " occ=0.50 residue: pdb=" N AARG B 92 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 92 " occ=0.50 residue: pdb=" N ALYS C 224 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 224 " occ=0.50 residue: pdb=" N ASER C 230 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 230 " occ=0.50 residue: pdb=" N AARG C 384 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 384 " occ=0.50 Time building chain proxies: 7.17, per 1000 atoms: 0.36 Number of scatterers: 20023 At special positions: 0 Unit cell: (105.651, 137.592, 149.058, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 10 15.00 Mg 5 11.99 O 3847 8.00 N 3550 7.00 C 12509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4678 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 21 sheets defined 49.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.668A pdb=" N ILE A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 153 through 166 removed outlier: 3.501A pdb=" N LEU A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.587A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.553A pdb=" N LYS A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 4.205A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 removed outlier: 4.376A pdb=" N GLY A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 339' Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.948A pdb=" N ALA A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 391 through 405 removed outlier: 4.585A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 155 through 166 removed outlier: 4.134A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 255 Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.544A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.197A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 372' Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 391 through 405 Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.602A pdb=" N ARG B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 removed outlier: 3.731A pdb=" N LEU C 6 " --> pdb=" O ASN C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.811A pdb=" N SER C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.565A pdb=" N SER C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 157 through 166 removed outlier: 3.769A pdb=" N VAL C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 255 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.719A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'D' and resid 2 through 9 removed outlier: 3.587A pdb=" N LEU D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.636A pdb=" N MET D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.763A pdb=" N SER D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 89 Processing helix chain 'D' and resid 123 through 129 removed outlier: 3.826A pdb=" N ASN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.602A pdb=" N HIS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.515A pdb=" N GLY D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL D 289 " --> pdb=" O THR D 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 285 through 289' Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.738A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 406 removed outlier: 3.589A pdb=" N THR D 406 " --> pdb=" O LYS D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 418 Processing helix chain 'E' and resid 2 through 9 removed outlier: 3.957A pdb=" N LEU E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 30 through 46 Processing helix chain 'E' and resid 82 through 89 Processing helix chain 'E' and resid 123 through 129 removed outlier: 3.713A pdb=" N ASN E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 155 through 166 removed outlier: 4.111A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.637A pdb=" N HIS E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 290 through 303 removed outlier: 4.299A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.620A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.760A pdb=" N LYS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.643A pdb=" N LEU E 370 " --> pdb=" O LYS E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 391 through 404 Processing helix chain 'E' and resid 408 through 418 Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.756A pdb=" N LEU F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 21 Processing helix chain 'F' and resid 30 through 46 Processing helix chain 'F' and resid 82 through 89 Processing helix chain 'F' and resid 123 through 129 removed outlier: 4.230A pdb=" N ASN F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 166 removed outlier: 3.881A pdb=" N SER F 166 " --> pdb=" O LEU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 removed outlier: 4.226A pdb=" N TYR F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 223 Processing helix chain 'F' and resid 235 through 256 Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 285 through 289 removed outlier: 3.957A pdb=" N VAL F 289 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 303 removed outlier: 3.656A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Proline residue: F 297 - end of helix Processing helix chain 'F' and resid 325 through 335 removed outlier: 3.755A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 removed outlier: 3.832A pdb=" N ALA F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 394 through 405 Processing helix chain 'F' and resid 408 through 418 removed outlier: 4.022A pdb=" N PHE F 412 " --> pdb=" O THR F 408 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.602A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.697A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.697A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 10.495A pdb=" N GLU A 342 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N ASN A 361 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N HIS A 344 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.974A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 57 removed outlier: 7.541A pdb=" N TYR B 80 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N LYS B 115 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 112 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 7.146A pdb=" N LEU B 204 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 139 removed outlier: 6.249A pdb=" N GLY B 174 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA B 319 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE B 176 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG B 173 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU B 343 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU B 175 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU B 345 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 177 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N GLU B 342 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ASN B 361 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N HIS B 344 " --> pdb=" O ASP B 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.607A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 57 removed outlier: 6.615A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AB2, first strand: chain 'C' and resid 138 through 139 removed outlier: 6.388A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG C 173 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU C 343 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C 175 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.755A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.864A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.298A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASP D 265 " --> pdb=" O MET D 205 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU D 207 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.231A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG D 173 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU D 343 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU D 175 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU D 345 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL D 177 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N GLU D 342 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN D 361 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N HIS D 344 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.700A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AB9, first strand: chain 'E' and resid 138 through 139 removed outlier: 6.424A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 144 through 145 removed outlier: 4.620A pdb=" N ILE E 168 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 49 through 57 removed outlier: 4.121A pdb=" N LEU F 113 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA F 112 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS F 100 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL F 116 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER F 98 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU F 118 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR F 96 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 175 through 178 removed outlier: 6.810A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE F 262 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR F 318 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU F 264 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N LEU F 320 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU F 263 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N MET F 205 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASP F 265 " --> pdb=" O MET F 205 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU F 207 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2920 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: 3.93 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6655 1.34 - 1.46: 2104 1.46 - 1.57: 11265 1.57 - 1.69: 16 1.69 - 1.81: 198 Bond restraints: 20238 Sorted by residual: bond pdb=" CB PRO A 103 " pdb=" CG PRO A 103 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.20e+00 bond pdb=" C HIS F 388 " pdb=" N PRO F 389 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.28e-02 6.10e+03 2.81e+00 bond pdb=" CA GLU F 342 " pdb=" CB GLU F 342 " ideal model delta sigma weight residual 1.533 1.564 -0.031 2.15e-02 2.16e+03 2.02e+00 bond pdb=" N ASP B 322 " pdb=" CA ASP B 322 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.59e+00 bond pdb=" CG GLU F 333 " pdb=" CD GLU F 333 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.56e+00 ... (remaining 20233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 26330 1.57 - 3.14: 716 3.14 - 4.71: 167 4.71 - 6.28: 53 6.28 - 7.85: 11 Bond angle restraints: 27277 Sorted by residual: angle pdb=" CA PRO A 103 " pdb=" N PRO A 103 " pdb=" CD PRO A 103 " ideal model delta sigma weight residual 112.00 105.27 6.73 1.40e+00 5.10e-01 2.31e+01 angle pdb=" N ASP F 394 " pdb=" CA ASP F 394 " pdb=" C ASP F 394 " ideal model delta sigma weight residual 113.19 105.84 7.35 1.58e+00 4.01e-01 2.16e+01 angle pdb=" C SER D 153 " pdb=" N THR D 154 " pdb=" CA THR D 154 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" N GLU F 333 " pdb=" CA GLU F 333 " pdb=" CB GLU F 333 " ideal model delta sigma weight residual 110.41 116.18 -5.77 1.68e+00 3.54e-01 1.18e+01 angle pdb=" C LEU A 188 " pdb=" N GLN A 189 " pdb=" CA GLN A 189 " ideal model delta sigma weight residual 120.68 114.88 5.80 1.70e+00 3.46e-01 1.16e+01 ... (remaining 27272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 11918 24.53 - 49.07: 561 49.07 - 73.60: 39 73.60 - 98.14: 20 98.14 - 122.67: 1 Dihedral angle restraints: 12539 sinusoidal: 5307 harmonic: 7232 Sorted by residual: dihedral pdb=" O1B ADP B 502 " pdb=" O3A ADP B 502 " pdb=" PB ADP B 502 " pdb=" PA ADP B 502 " ideal model delta sinusoidal sigma weight residual -60.00 62.67 -122.67 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" C5' ADP E 502 " pdb=" O5' ADP E 502 " pdb=" PA ADP E 502 " pdb=" O2A ADP E 502 " ideal model delta sinusoidal sigma weight residual -60.00 15.26 -75.26 1 2.00e+01 2.50e-03 1.79e+01 dihedral pdb=" CA GLN F 193 " pdb=" C GLN F 193 " pdb=" N SER F 194 " pdb=" CA SER F 194 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 12536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2270 0.043 - 0.086: 585 0.086 - 0.129: 231 0.129 - 0.173: 15 0.173 - 0.216: 2 Chirality restraints: 3103 Sorted by residual: chirality pdb=" CB ILE F 247 " pdb=" CA ILE F 247 " pdb=" CG1 ILE F 247 " pdb=" CG2 ILE F 247 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE A 49 " pdb=" CA ILE A 49 " pdb=" CG1 ILE A 49 " pdb=" CG2 ILE A 49 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CA PRO A 124 " pdb=" N PRO A 124 " pdb=" C PRO A 124 " pdb=" CB PRO A 124 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 3100 not shown) Planarity restraints: 3534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 381 " 0.019 2.00e-02 2.50e+03 1.97e-02 9.65e+00 pdb=" CG TRP A 381 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 381 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 381 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 381 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 381 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 381 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 381 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 381 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 381 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 102 " -0.053 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO A 103 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 36 " -0.014 2.00e-02 2.50e+03 1.72e-02 5.15e+00 pdb=" CG PHE A 36 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 36 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 36 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 36 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 36 " -0.000 2.00e-02 2.50e+03 ... (remaining 3531 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 306 2.61 - 3.18: 17867 3.18 - 3.76: 32134 3.76 - 4.33: 45444 4.33 - 4.90: 74060 Nonbonded interactions: 169811 Sorted by model distance: nonbonded pdb="MG MG C 501 " pdb=" O HOH C 617 " model vdw 2.040 2.170 nonbonded pdb="MG MG D 501 " pdb=" O HOH D 602 " model vdw 2.045 2.170 nonbonded pdb="MG MG D 501 " pdb=" O HOH D 601 " model vdw 2.046 2.170 nonbonded pdb="MG MG C 501 " pdb=" O HOH C 612 " model vdw 2.048 2.170 nonbonded pdb="MG MG D 501 " pdb=" O HOH D 623 " model vdw 2.050 2.170 ... (remaining 169806 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 1 through 91 or resid 93 through 223 or resid 225 through \ 229 or resid 231 through 365 or resid 367 through 383 or resid 385 through 418)) \ selection = (chain 'B' and (resid 1 through 91 or resid 93 through 223 or resid 225 through \ 229 or resid 231 through 365 or resid 367 through 383 or resid 385 through 418)) \ selection = (chain 'C' and (resid 1 through 91 or resid 93 through 223 or resid 225 through \ 229 or resid 231 through 365 or resid 367 through 383 or resid 385 through 418)) \ selection = (chain 'D' and (resid 1 through 91 or resid 93 through 223 or resid 225 through \ 229 or resid 231 through 365 or resid 367 through 383 or resid 385 through 418)) \ selection = (chain 'E' and (resid 1 through 91 or resid 93 through 223 or resid 225 through \ 229 or resid 231 through 365 or resid 367 through 383 or resid 385 through 418)) \ selection = (chain 'F' and (resid 1 through 91 or resid 93 through 223 or resid 225 through \ 229 or resid 231 through 365 or resid 367 through 383 or resid 385 through 418)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.140 Find NCS groups from input model: 0.510 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:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.003 0.102 20238 Z= 0.136 Angle : 0.673 7.854 27277 Z= 0.351 Chirality : 0.044 0.216 3103 Planarity : 0.004 0.077 3534 Dihedral : 13.268 122.674 7861 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.09 % Allowed : 0.42 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % 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: 0.35 (0.17), residues: 2511 helix: 0.78 (0.16), residues: 1132 sheet: 0.36 (0.30), residues: 318 loop : -0.28 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 353 TYR 0.017 0.001 TYR E 110 PHE 0.040 0.002 PHE A 36 TRP 0.050 0.004 TRP A 381 HIS 0.007 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00302 (20238) covalent geometry : angle 0.67327 (27277) hydrogen bonds : bond 0.14410 ( 987) hydrogen bonds : angle 6.85037 ( 2920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 292 ASN cc_start: 0.8365 (t0) cc_final: 0.8154 (t0) REVERT: A 336 LYS cc_start: 0.8534 (mmmm) cc_final: 0.8076 (mmmt) REVERT: B 33 ASP cc_start: 0.8384 (m-30) cc_final: 0.7968 (m-30) REVERT: B 326 LYS cc_start: 0.8243 (tmtt) cc_final: 0.8038 (tptp) REVERT: B 348 LYS cc_start: 0.9140 (mppt) cc_final: 0.8480 (mppt) REVERT: C 32 GLN cc_start: 0.9109 (mp10) cc_final: 0.8891 (mp10) REVERT: C 333 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8145 (mm-30) REVERT: C 348 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8586 (mtmm) REVERT: C 374 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8312 (tp-100) REVERT: C 378 GLN cc_start: 0.8550 (mt0) cc_final: 0.8257 (mt0) REVERT: C 407 LYS cc_start: 0.8628 (tptt) cc_final: 0.8147 (tppt) REVERT: C 414 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8542 (mp0) REVERT: D 134 GLU cc_start: 0.8484 (mp0) cc_final: 0.8278 (mp0) REVERT: E 30 ARG cc_start: 0.8240 (mtp-110) cc_final: 0.8026 (mtm-85) REVERT: E 326 LYS cc_start: 0.8975 (tptt) cc_final: 0.8453 (mmmt) REVERT: E 329 GLU cc_start: 0.8316 (pm20) cc_final: 0.7764 (pm20) REVERT: E 415 MET cc_start: 0.9000 (ttp) cc_final: 0.8469 (ttm) REVERT: F 129 ASN cc_start: 0.8444 (p0) cc_final: 0.8179 (p0) REVERT: F 193 GLN cc_start: 0.8570 (pm20) cc_final: 0.8204 (pm20) REVERT: F 244 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8276 (mm-30) REVERT: F 405 MET cc_start: 0.8327 (ptt) cc_final: 0.8027 (pp-130) outliers start: 1 outliers final: 1 residues processed: 378 average time/residue: 0.9585 time to fit residues: 394.0518 Evaluate side-chains 295 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 295 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 241 GLN A 275 ASN A 378 GLN B 374 GLN C 41 GLN C 193 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 193 GLN D 378 GLN E 41 GLN E 117 ASN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.116975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.077087 restraints weight = 132209.185| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 4.59 r_work: 0.2795 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20238 Z= 0.212 Angle : 0.733 9.464 27277 Z= 0.365 Chirality : 0.045 0.202 3103 Planarity : 0.005 0.057 3534 Dihedral : 6.314 117.633 2794 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.63 % Allowed : 10.26 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % 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: 0.58 (0.17), residues: 2511 helix: 0.89 (0.15), residues: 1168 sheet: -0.14 (0.26), residues: 397 loop : 0.19 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 272 TYR 0.016 0.002 TYR A 80 PHE 0.030 0.002 PHE A 36 TRP 0.015 0.002 TRP A 381 HIS 0.007 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00490 (20238) covalent geometry : angle 0.73291 (27277) hydrogen bonds : bond 0.04387 ( 987) hydrogen bonds : angle 5.45731 ( 2920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 309 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8257 (p90) cc_final: 0.7926 (p90) REVERT: A 88 ARG cc_start: 0.8790 (tmm-80) cc_final: 0.8577 (ttp-110) REVERT: A 172 GLN cc_start: 0.8080 (tp40) cc_final: 0.7822 (tp40) REVERT: A 269 ARG cc_start: 0.8475 (mmp80) cc_final: 0.8074 (mmp80) REVERT: A 292 ASN cc_start: 0.8312 (t0) cc_final: 0.7972 (t0) REVERT: A 321 ILE cc_start: 0.7527 (mp) cc_final: 0.7257 (tp) REVERT: A 336 LYS cc_start: 0.8191 (mmmm) cc_final: 0.7306 (mmtt) REVERT: A 378 GLN cc_start: 0.9168 (mm-40) cc_final: 0.8938 (mm110) REVERT: A 415 MET cc_start: 0.7530 (ppp) cc_final: 0.7123 (pp-130) REVERT: B 32 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8003 (mm-40) REVERT: B 333 GLU cc_start: 0.8779 (tt0) cc_final: 0.8472 (tp30) REVERT: B 348 LYS cc_start: 0.9092 (mppt) cc_final: 0.8773 (mppt) REVERT: B 401 ASN cc_start: 0.9327 (m-40) cc_final: 0.8941 (m110) REVERT: C 333 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8619 (mm-30) REVERT: C 348 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8979 (mtmm) REVERT: C 374 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8343 (tp-100) REVERT: C 378 GLN cc_start: 0.8873 (mt0) cc_final: 0.8516 (mt0) REVERT: C 392 GLU cc_start: 0.8263 (pm20) cc_final: 0.7710 (pt0) REVERT: C 407 LYS cc_start: 0.8915 (tptt) cc_final: 0.8464 (tppt) REVERT: C 414 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8496 (mm-30) REVERT: D 347 ARG cc_start: 0.8489 (tpp80) cc_final: 0.8276 (ttm-80) REVERT: E 326 LYS cc_start: 0.9143 (tptt) cc_final: 0.8903 (tppt) REVERT: E 329 GLU cc_start: 0.8722 (pm20) cc_final: 0.8371 (pm20) REVERT: E 415 MET cc_start: 0.9075 (ttp) cc_final: 0.8700 (ttm) REVERT: F 105 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7993 (mmtt) REVERT: F 244 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8171 (mm-30) REVERT: F 274 TYR cc_start: 0.7969 (m-10) cc_final: 0.7692 (m-10) REVERT: F 341 MET cc_start: 0.6934 (pp-130) cc_final: 0.6694 (pmm) REVERT: F 347 ARG cc_start: 0.8199 (tpm-80) cc_final: 0.7900 (tpm-80) REVERT: F 405 MET cc_start: 0.8529 (ptt) cc_final: 0.8238 (pp-130) outliers start: 34 outliers final: 7 residues processed: 322 average time/residue: 0.9484 time to fit residues: 332.3472 Evaluate side-chains 289 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 281 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain F residue 333 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 119 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 275 ASN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 140 HIS C 190 ASN C 340 ASN D 193 GLN D 220 GLN D 292 ASN E 41 GLN E 85 GLN E 388 HIS F 126 ASN F 256 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.117359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.077826 restraints weight = 98008.039| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.06 r_work: 0.2856 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20238 Z= 0.154 Angle : 0.682 9.199 27277 Z= 0.337 Chirality : 0.044 0.267 3103 Planarity : 0.004 0.046 3534 Dihedral : 6.119 116.857 2792 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.95 % Allowed : 12.08 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % 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: 0.65 (0.17), residues: 2511 helix: 1.04 (0.16), residues: 1171 sheet: -0.22 (0.26), residues: 390 loop : 0.14 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 109 TYR 0.019 0.002 TYR E 80 PHE 0.025 0.001 PHE A 36 TRP 0.007 0.001 TRP F 381 HIS 0.007 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00359 (20238) covalent geometry : angle 0.68162 (27277) hydrogen bonds : bond 0.03683 ( 987) hydrogen bonds : angle 5.17628 ( 2920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 294 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8228 (p90) cc_final: 0.7937 (p90) REVERT: A 244 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 249 LYS cc_start: 0.9045 (tptt) cc_final: 0.8844 (tppt) REVERT: A 269 ARG cc_start: 0.8512 (mmp80) cc_final: 0.8120 (mmp80) REVERT: A 292 ASN cc_start: 0.8258 (t0) cc_final: 0.7855 (t0) REVERT: A 334 GLU cc_start: 0.8209 (tp30) cc_final: 0.7950 (tp30) REVERT: A 378 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8922 (mm110) REVERT: A 380 MET cc_start: 0.9607 (mmm) cc_final: 0.9388 (mmm) REVERT: B 109 ARG cc_start: 0.7278 (ttp80) cc_final: 0.6805 (tmt90) REVERT: B 272 ARG cc_start: 0.9057 (mmm-85) cc_final: 0.8828 (mmm-85) REVERT: B 333 GLU cc_start: 0.8743 (tt0) cc_final: 0.8412 (tp30) REVERT: B 348 LYS cc_start: 0.9054 (mppt) cc_final: 0.8721 (mppt) REVERT: B 401 ASN cc_start: 0.9278 (m-40) cc_final: 0.8914 (m110) REVERT: C 32 GLN cc_start: 0.9196 (mp10) cc_final: 0.8981 (mp10) REVERT: C 327 MET cc_start: 0.8610 (ttp) cc_final: 0.8358 (tpp) REVERT: C 333 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8619 (mm-30) REVERT: C 348 LYS cc_start: 0.9179 (mtmm) cc_final: 0.8928 (mtmm) REVERT: C 374 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8309 (tp-100) REVERT: C 378 GLN cc_start: 0.8802 (mt0) cc_final: 0.8433 (mt0) REVERT: C 407 LYS cc_start: 0.8908 (tptt) cc_final: 0.8450 (tppt) REVERT: C 414 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8463 (mm-30) REVERT: D 193 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8004 (mp-120) REVERT: D 347 ARG cc_start: 0.8448 (tpp80) cc_final: 0.8228 (ttm-80) REVERT: E 30 ARG cc_start: 0.8685 (mtm110) cc_final: 0.8470 (mtm-85) REVERT: E 265 ASP cc_start: 0.8908 (t0) cc_final: 0.8445 (t70) REVERT: E 326 LYS cc_start: 0.9118 (tptt) cc_final: 0.8614 (mmmt) REVERT: E 329 GLU cc_start: 0.8650 (pm20) cc_final: 0.8038 (pm20) REVERT: E 405 MET cc_start: 0.9345 (ptt) cc_final: 0.9123 (pmm) REVERT: E 415 MET cc_start: 0.9076 (ttp) cc_final: 0.8772 (ttm) REVERT: F 105 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7832 (mmtt) REVERT: F 189 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: F 193 GLN cc_start: 0.8296 (pm20) cc_final: 0.7737 (pm20) REVERT: F 244 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8133 (mm-30) REVERT: F 341 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6761 (pmm) REVERT: F 405 MET cc_start: 0.8483 (ptt) cc_final: 0.8243 (pp-130) outliers start: 41 outliers final: 11 residues processed: 312 average time/residue: 0.8608 time to fit residues: 293.1317 Evaluate side-chains 274 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 260 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain E residue 392 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain F residue 341 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 118 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 230 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN D 193 GLN D 220 GLN D 378 GLN E 41 GLN E 388 HIS E 401 ASN F 126 ASN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.116529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.076976 restraints weight = 102324.713| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.12 r_work: 0.2817 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20238 Z= 0.168 Angle : 0.672 9.392 27277 Z= 0.332 Chirality : 0.043 0.154 3103 Planarity : 0.004 0.041 3534 Dihedral : 6.037 116.847 2792 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.18 % Allowed : 13.24 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % 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: 0.66 (0.17), residues: 2511 helix: 1.10 (0.16), residues: 1166 sheet: -0.31 (0.26), residues: 392 loop : 0.12 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 30 TYR 0.026 0.001 TYR F 110 PHE 0.023 0.001 PHE A 412 TRP 0.005 0.001 TRP F 381 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00393 (20238) covalent geometry : angle 0.67250 (27277) hydrogen bonds : bond 0.03599 ( 987) hydrogen bonds : angle 5.09524 ( 2920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: A 172 GLN cc_start: 0.8043 (tp40) cc_final: 0.7836 (tp40) REVERT: A 269 ARG cc_start: 0.8559 (mmp80) cc_final: 0.8174 (mmp80) REVERT: A 292 ASN cc_start: 0.8234 (t0) cc_final: 0.7804 (t0) REVERT: A 334 GLU cc_start: 0.8261 (tp30) cc_final: 0.8014 (tp30) REVERT: A 336 LYS cc_start: 0.8317 (mmmm) cc_final: 0.7740 (mmmt) REVERT: A 342 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7191 (tm-30) REVERT: A 378 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8910 (mm110) REVERT: A 380 MET cc_start: 0.9628 (mmm) cc_final: 0.9386 (mmm) REVERT: B 244 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8605 (mm-30) REVERT: B 348 LYS cc_start: 0.9053 (mppt) cc_final: 0.8646 (mppt) REVERT: C 269 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8690 (mmt90) REVERT: C 327 MET cc_start: 0.8604 (ttp) cc_final: 0.8350 (tpp) REVERT: C 333 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8511 (mm-30) REVERT: C 334 GLU cc_start: 0.8648 (mp0) cc_final: 0.8044 (mp0) REVERT: C 374 GLN cc_start: 0.8841 (tp-100) cc_final: 0.8413 (tp-100) REVERT: C 378 GLN cc_start: 0.8844 (mt0) cc_final: 0.8538 (mt0) REVERT: C 392 GLU cc_start: 0.8139 (pm20) cc_final: 0.7489 (pt0) REVERT: C 407 LYS cc_start: 0.8935 (tptt) cc_final: 0.8478 (tppt) REVERT: C 414 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8412 (mm-30) REVERT: D 347 ARG cc_start: 0.8444 (tpp80) cc_final: 0.8225 (ttm-80) REVERT: E 265 ASP cc_start: 0.8922 (t0) cc_final: 0.8497 (t70) REVERT: E 326 LYS cc_start: 0.9131 (tptt) cc_final: 0.8908 (mmmt) REVERT: E 329 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8161 (pm20) REVERT: E 415 MET cc_start: 0.9110 (ttp) cc_final: 0.8829 (ttm) REVERT: F 147 MET cc_start: 0.3105 (OUTLIER) cc_final: 0.2813 (ptp) REVERT: F 193 GLN cc_start: 0.8368 (pt0) cc_final: 0.7666 (pp30) REVERT: F 205 MET cc_start: 0.8254 (mtm) cc_final: 0.7930 (ttp) REVERT: F 244 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8123 (mm-30) REVERT: F 274 TYR cc_start: 0.8017 (m-10) cc_final: 0.7701 (m-10) REVERT: F 334 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8637 (tm-30) REVERT: F 335 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: F 341 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6837 (pmm) REVERT: F 405 MET cc_start: 0.8486 (ptt) cc_final: 0.8252 (pp-130) outliers start: 46 outliers final: 11 residues processed: 297 average time/residue: 0.8451 time to fit residues: 274.3933 Evaluate side-chains 278 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain F residue 341 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 67 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 174 optimal weight: 0.0040 chunk 28 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN D 193 GLN D 220 GLN E 41 GLN E 374 GLN E 388 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.116825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.077488 restraints weight = 104332.447| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.13 r_work: 0.2825 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20238 Z= 0.142 Angle : 0.669 10.076 27277 Z= 0.330 Chirality : 0.043 0.167 3103 Planarity : 0.004 0.043 3534 Dihedral : 5.938 116.887 2792 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.95 % Allowed : 14.35 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % 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: 0.71 (0.17), residues: 2511 helix: 1.16 (0.16), residues: 1167 sheet: -0.29 (0.26), residues: 390 loop : 0.11 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 87 TYR 0.009 0.001 TYR F 72 PHE 0.024 0.001 PHE A 412 TRP 0.004 0.001 TRP F 381 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00330 (20238) covalent geometry : angle 0.66882 (27277) hydrogen bonds : bond 0.03394 ( 987) hydrogen bonds : angle 5.00754 ( 2920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8086 (tp40) cc_final: 0.7842 (tp40) REVERT: A 193 GLN cc_start: 0.9265 (pt0) cc_final: 0.9064 (pp30) REVERT: A 244 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 269 ARG cc_start: 0.8563 (mmp80) cc_final: 0.8171 (mmp80) REVERT: A 292 ASN cc_start: 0.8272 (t0) cc_final: 0.7827 (t0) REVERT: A 334 GLU cc_start: 0.8279 (tp30) cc_final: 0.8026 (tp30) REVERT: A 336 LYS cc_start: 0.8344 (mmmm) cc_final: 0.7723 (mmmt) REVERT: A 342 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 378 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8890 (mm110) REVERT: A 380 MET cc_start: 0.9633 (mmm) cc_final: 0.9400 (mmm) REVERT: B 244 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8557 (mm-30) REVERT: B 348 LYS cc_start: 0.9066 (mppt) cc_final: 0.8757 (mppt) REVERT: C 269 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8708 (mmt90) REVERT: C 327 MET cc_start: 0.8574 (ttp) cc_final: 0.8329 (tpp) REVERT: C 333 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8531 (mm-30) REVERT: C 334 GLU cc_start: 0.8629 (mp0) cc_final: 0.8039 (mp0) REVERT: C 374 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8378 (tp-100) REVERT: C 378 GLN cc_start: 0.8821 (mt0) cc_final: 0.8501 (mt0) REVERT: C 407 LYS cc_start: 0.8943 (tptt) cc_final: 0.8506 (tppt) REVERT: C 414 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8421 (mm-30) REVERT: D 244 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8751 (mm-30) REVERT: D 347 ARG cc_start: 0.8451 (tpp80) cc_final: 0.8229 (ttm-80) REVERT: E 265 ASP cc_start: 0.8898 (t0) cc_final: 0.8510 (t70) REVERT: E 326 LYS cc_start: 0.9134 (tptt) cc_final: 0.8922 (mmmt) REVERT: E 329 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: E 380 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7942 (mtm) REVERT: F 193 GLN cc_start: 0.8290 (pt0) cc_final: 0.7635 (pp30) REVERT: F 244 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8156 (mm-30) REVERT: F 272 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8332 (mtt180) REVERT: F 334 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8648 (tm-30) REVERT: F 335 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: F 396 MET cc_start: 0.3429 (ttt) cc_final: 0.3138 (tpp) REVERT: F 405 MET cc_start: 0.8501 (ptt) cc_final: 0.8268 (pp-130) REVERT: F 416 MET cc_start: 0.2013 (pmt) cc_final: 0.1549 (pp-130) outliers start: 41 outliers final: 18 residues processed: 296 average time/residue: 0.8901 time to fit residues: 288.2905 Evaluate side-chains 283 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 392 GLU Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 272 ARG Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 335 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 87 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 220 GLN D 378 GLN E 41 GLN E 388 HIS E 401 ASN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.115664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075786 restraints weight = 112947.120| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.28 r_work: 0.2792 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20238 Z= 0.197 Angle : 0.687 10.515 27277 Z= 0.339 Chirality : 0.044 0.162 3103 Planarity : 0.004 0.044 3534 Dihedral : 5.965 117.488 2792 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.09 % Allowed : 15.42 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % 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: 0.66 (0.17), residues: 2511 helix: 1.15 (0.16), residues: 1163 sheet: -0.34 (0.26), residues: 390 loop : 0.07 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 347 TYR 0.025 0.001 TYR F 110 PHE 0.016 0.001 PHE E 62 TRP 0.005 0.001 TRP F 381 HIS 0.012 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00461 (20238) covalent geometry : angle 0.68732 (27277) hydrogen bonds : bond 0.03647 ( 987) hydrogen bonds : angle 5.01394 ( 2920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7011 (tmt) cc_final: 0.6414 (tmm) REVERT: A 62 PHE cc_start: 0.8189 (p90) cc_final: 0.7921 (p90) REVERT: A 172 GLN cc_start: 0.7999 (tp40) cc_final: 0.7736 (tp40) REVERT: A 269 ARG cc_start: 0.8498 (mmp80) cc_final: 0.8150 (mmp80) REVERT: A 292 ASN cc_start: 0.8252 (t0) cc_final: 0.7771 (t0) REVERT: A 334 GLU cc_start: 0.8248 (tp30) cc_final: 0.8033 (tp30) REVERT: A 336 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7696 (mmmt) REVERT: A 342 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6998 (tm-30) REVERT: A 378 GLN cc_start: 0.9243 (mm-40) cc_final: 0.9018 (mm-40) REVERT: A 380 MET cc_start: 0.9647 (mmm) cc_final: 0.9420 (mmm) REVERT: B 220 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: B 244 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8606 (mm-30) REVERT: B 348 LYS cc_start: 0.9068 (mppt) cc_final: 0.8777 (mppt) REVERT: B 374 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8692 (tp40) REVERT: B 378 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8191 (mm110) REVERT: B 401 ASN cc_start: 0.9309 (m-40) cc_final: 0.8966 (m110) REVERT: C 269 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8733 (mmt90) REVERT: C 334 GLU cc_start: 0.8677 (mp0) cc_final: 0.8092 (mp0) REVERT: C 374 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8474 (tp-100) REVERT: C 378 GLN cc_start: 0.8876 (mt0) cc_final: 0.8615 (mt0) REVERT: C 392 GLU cc_start: 0.8073 (pm20) cc_final: 0.7489 (pt0) REVERT: C 407 LYS cc_start: 0.9006 (tptt) cc_final: 0.8548 (tppt) REVERT: C 414 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8500 (mm-30) REVERT: D 244 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8787 (mm-30) REVERT: D 347 ARG cc_start: 0.8484 (tpp80) cc_final: 0.8252 (ttm-80) REVERT: E 265 ASP cc_start: 0.8917 (t0) cc_final: 0.8558 (t70) REVERT: E 326 LYS cc_start: 0.9158 (tptt) cc_final: 0.8899 (mmmt) REVERT: E 380 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7888 (mtm) REVERT: E 415 MET cc_start: 0.9118 (ttp) cc_final: 0.8704 (ttm) REVERT: F 193 GLN cc_start: 0.8222 (pt0) cc_final: 0.7586 (pp30) REVERT: F 205 MET cc_start: 0.8142 (mtm) cc_final: 0.7887 (ttp) REVERT: F 244 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8219 (mm-30) REVERT: F 272 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8318 (mtt180) REVERT: F 333 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8691 (pm20) REVERT: F 334 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8687 (tm-30) REVERT: F 335 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: F 405 MET cc_start: 0.8604 (ptt) cc_final: 0.8361 (pp-130) REVERT: F 416 MET cc_start: 0.2402 (OUTLIER) cc_final: 0.2045 (pp-130) outliers start: 44 outliers final: 18 residues processed: 295 average time/residue: 0.9319 time to fit residues: 299.7307 Evaluate side-chains 285 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 392 GLU Chi-restraints excluded: chain F residue 272 ARG Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain F residue 341 MET Chi-restraints excluded: chain F residue 416 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 103 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 220 GLN E 41 GLN E 374 GLN E 388 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.116530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.076711 restraints weight = 118513.756| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.41 r_work: 0.2813 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20238 Z= 0.140 Angle : 0.683 10.984 27277 Z= 0.336 Chirality : 0.043 0.186 3103 Planarity : 0.004 0.041 3534 Dihedral : 5.890 117.395 2792 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.00 % Allowed : 15.51 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % 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: 0.73 (0.17), residues: 2511 helix: 1.22 (0.16), residues: 1163 sheet: -0.35 (0.26), residues: 392 loop : 0.10 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 347 TYR 0.021 0.001 TYR A 80 PHE 0.016 0.001 PHE E 62 TRP 0.005 0.001 TRP D 381 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00327 (20238) covalent geometry : angle 0.68347 (27277) hydrogen bonds : bond 0.03348 ( 987) hydrogen bonds : angle 4.91615 ( 2920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6839 (tmt) cc_final: 0.6244 (ppp) REVERT: A 21 MET cc_start: 0.5897 (ppp) cc_final: 0.5667 (ppp) REVERT: A 33 ASP cc_start: 0.8562 (m-30) cc_final: 0.8099 (p0) REVERT: A 62 PHE cc_start: 0.8264 (p90) cc_final: 0.7932 (p90) REVERT: A 85 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: A 244 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 269 ARG cc_start: 0.8608 (mmp80) cc_final: 0.8243 (mmp80) REVERT: A 292 ASN cc_start: 0.8286 (t0) cc_final: 0.7792 (t0) REVERT: A 334 GLU cc_start: 0.8346 (tp30) cc_final: 0.8092 (tp30) REVERT: A 336 LYS cc_start: 0.8340 (mmmm) cc_final: 0.7721 (mmmt) REVERT: A 378 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8881 (mm110) REVERT: A 380 MET cc_start: 0.9649 (mmm) cc_final: 0.9401 (mmm) REVERT: A 383 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9295 (mm) REVERT: A 415 MET cc_start: 0.7103 (pp-130) cc_final: 0.6889 (pp-130) REVERT: B 220 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: B 244 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8616 (mm-30) REVERT: B 348 LYS cc_start: 0.9076 (mppt) cc_final: 0.8777 (mppt) REVERT: B 359 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8058 (t0) REVERT: B 362 ARG cc_start: 0.9001 (mpp80) cc_final: 0.8785 (ttp-110) REVERT: B 401 ASN cc_start: 0.9260 (m-40) cc_final: 0.8875 (m110) REVERT: C 269 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8721 (mmt90) REVERT: C 333 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8521 (mm-30) REVERT: C 334 GLU cc_start: 0.8654 (mp0) cc_final: 0.7985 (mp0) REVERT: C 374 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8404 (tp-100) REVERT: C 378 GLN cc_start: 0.8859 (mt0) cc_final: 0.8582 (mt0) REVERT: C 392 GLU cc_start: 0.7998 (pm20) cc_final: 0.7380 (pt0) REVERT: C 407 LYS cc_start: 0.8991 (tptt) cc_final: 0.8517 (tppt) REVERT: C 414 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8545 (mm-30) REVERT: D 244 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8724 (mm-30) REVERT: D 347 ARG cc_start: 0.8444 (tpp80) cc_final: 0.8213 (ttm-80) REVERT: E 265 ASP cc_start: 0.8900 (t0) cc_final: 0.8533 (t70) REVERT: E 326 LYS cc_start: 0.9144 (tptt) cc_final: 0.8873 (mmmt) REVERT: E 380 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7890 (mtm) REVERT: F 193 GLN cc_start: 0.8170 (pt0) cc_final: 0.7635 (pp30) REVERT: F 205 MET cc_start: 0.8187 (mtm) cc_final: 0.7949 (ttp) REVERT: F 244 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8211 (mm-30) REVERT: F 333 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8646 (pm20) REVERT: F 334 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8666 (tm-30) REVERT: F 335 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: F 405 MET cc_start: 0.8483 (ptt) cc_final: 0.8264 (pp-130) REVERT: F 416 MET cc_start: 0.2734 (OUTLIER) cc_final: 0.2376 (pp-130) outliers start: 42 outliers final: 15 residues processed: 295 average time/residue: 0.9425 time to fit residues: 303.3512 Evaluate side-chains 288 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 392 GLU Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain F residue 416 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 220 GLN D 374 GLN D 378 GLN E 41 GLN E 388 HIS E 401 ASN F 32 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.115853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.077060 restraints weight = 88008.171| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.77 r_work: 0.2824 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20238 Z= 0.167 Angle : 0.701 11.397 27277 Z= 0.344 Chirality : 0.043 0.173 3103 Planarity : 0.004 0.043 3534 Dihedral : 5.881 117.667 2792 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 16.02 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % 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: 0.70 (0.17), residues: 2511 helix: 1.21 (0.16), residues: 1164 sheet: -0.35 (0.26), residues: 392 loop : 0.07 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 362 TYR 0.026 0.001 TYR A 80 PHE 0.015 0.001 PHE A 412 TRP 0.006 0.001 TRP D 381 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00390 (20238) covalent geometry : angle 0.70128 (27277) hydrogen bonds : bond 0.03443 ( 987) hydrogen bonds : angle 4.93522 ( 2920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 0.882 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 1 MET cc_start: 0.7163 (tmt) cc_final: 0.6742 (tmt) REVERT: A 21 MET cc_start: 0.5869 (ppp) cc_final: 0.5661 (ppp) REVERT: A 33 ASP cc_start: 0.8575 (m-30) cc_final: 0.8139 (p0) REVERT: A 85 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: A 172 GLN cc_start: 0.8225 (tp40) cc_final: 0.7875 (tp40) REVERT: A 244 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7545 (tm-30) REVERT: A 269 ARG cc_start: 0.8567 (mmp80) cc_final: 0.8163 (mmp80) REVERT: A 272 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8332 (tpp80) REVERT: A 292 ASN cc_start: 0.8263 (t0) cc_final: 0.7777 (t0) REVERT: A 327 MET cc_start: 0.7780 (mmt) cc_final: 0.7334 (mmm) REVERT: A 334 GLU cc_start: 0.8326 (tp30) cc_final: 0.8087 (tp30) REVERT: A 336 LYS cc_start: 0.8332 (mmmm) cc_final: 0.7757 (mmmt) REVERT: A 378 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8890 (mm110) REVERT: A 380 MET cc_start: 0.9663 (mmm) cc_final: 0.9428 (mmm) REVERT: B 220 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7650 (mp10) REVERT: B 244 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8559 (mm-30) REVERT: B 348 LYS cc_start: 0.9119 (mppt) cc_final: 0.8765 (mppt) REVERT: B 362 ARG cc_start: 0.9044 (mpp80) cc_final: 0.8811 (ttp-110) REVERT: B 401 ASN cc_start: 0.9311 (m-40) cc_final: 0.9027 (m110) REVERT: C 269 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8687 (mmt90) REVERT: C 333 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8501 (mm-30) REVERT: C 334 GLU cc_start: 0.8623 (mp0) cc_final: 0.7964 (mp0) REVERT: C 374 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8403 (tp-100) REVERT: C 378 GLN cc_start: 0.8843 (mt0) cc_final: 0.8562 (mt0) REVERT: C 407 LYS cc_start: 0.9003 (tptt) cc_final: 0.8530 (tppt) REVERT: C 414 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8521 (mm-30) REVERT: D 244 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8682 (mm-30) REVERT: D 347 ARG cc_start: 0.8451 (tpp80) cc_final: 0.8218 (ttm-80) REVERT: E 265 ASP cc_start: 0.8850 (t0) cc_final: 0.8502 (t70) REVERT: E 326 LYS cc_start: 0.9155 (tptt) cc_final: 0.8900 (mmmt) REVERT: E 380 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7809 (mtm) REVERT: E 415 MET cc_start: 0.9145 (ttp) cc_final: 0.8747 (ttm) REVERT: F 193 GLN cc_start: 0.8134 (pt0) cc_final: 0.7669 (pp30) REVERT: F 244 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8210 (mm-30) REVERT: F 333 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8673 (pm20) REVERT: F 334 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8679 (tm-30) REVERT: F 335 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: F 405 MET cc_start: 0.8572 (ptt) cc_final: 0.8301 (pp-130) REVERT: F 416 MET cc_start: 0.2566 (OUTLIER) cc_final: 0.2219 (pp-130) outliers start: 39 outliers final: 16 residues processed: 288 average time/residue: 0.9398 time to fit residues: 295.7284 Evaluate side-chains 285 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 262 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 392 GLU Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain F residue 416 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 94 optimal weight: 0.4980 chunk 155 optimal weight: 0.0770 chunk 101 optimal weight: 0.3980 chunk 173 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 chunk 100 optimal weight: 0.1980 chunk 110 optimal weight: 5.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 292 ASN B 374 GLN D 193 GLN D 220 GLN E 41 GLN E 374 GLN F 32 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.116947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.077622 restraints weight = 99089.283| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 4.06 r_work: 0.2840 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20238 Z= 0.131 Angle : 0.720 11.725 27277 Z= 0.353 Chirality : 0.043 0.154 3103 Planarity : 0.004 0.041 3534 Dihedral : 5.814 117.445 2792 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.49 % Allowed : 16.26 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % 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: 0.77 (0.17), residues: 2511 helix: 1.22 (0.16), residues: 1169 sheet: -0.22 (0.26), residues: 385 loop : 0.11 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 296 TYR 0.011 0.001 TYR B 197 PHE 0.019 0.001 PHE A 232 TRP 0.008 0.001 TRP D 381 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00302 (20238) covalent geometry : angle 0.72029 (27277) hydrogen bonds : bond 0.03280 ( 987) hydrogen bonds : angle 4.87769 ( 2920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.848 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 1 MET cc_start: 0.7271 (tmt) cc_final: 0.6910 (tmt) REVERT: A 33 ASP cc_start: 0.8519 (m-30) cc_final: 0.8099 (p0) REVERT: A 172 GLN cc_start: 0.8113 (tp40) cc_final: 0.7890 (tp40) REVERT: A 244 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 269 ARG cc_start: 0.8540 (mmp80) cc_final: 0.8165 (mmp80) REVERT: A 272 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.8330 (tpp80) REVERT: A 292 ASN cc_start: 0.8266 (t0) cc_final: 0.7784 (t0) REVERT: A 299 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7249 (ttp-110) REVERT: A 327 MET cc_start: 0.7735 (mmt) cc_final: 0.7286 (mmm) REVERT: A 334 GLU cc_start: 0.8313 (tp30) cc_final: 0.8072 (tp30) REVERT: A 378 GLN cc_start: 0.9248 (mm-40) cc_final: 0.9002 (mm-40) REVERT: A 380 MET cc_start: 0.9669 (mmm) cc_final: 0.9450 (mmm) REVERT: B 220 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: B 348 LYS cc_start: 0.9067 (mppt) cc_final: 0.8750 (mppt) REVERT: B 378 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8177 (mm110) REVERT: B 397 GLU cc_start: 0.9017 (pt0) cc_final: 0.8728 (pm20) REVERT: B 401 ASN cc_start: 0.9338 (m-40) cc_final: 0.9019 (m110) REVERT: C 269 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8665 (mmt90) REVERT: C 333 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8504 (mm-30) REVERT: C 334 GLU cc_start: 0.8651 (mp0) cc_final: 0.7967 (mp0) REVERT: C 374 GLN cc_start: 0.8769 (tp-100) cc_final: 0.8337 (tp-100) REVERT: C 378 GLN cc_start: 0.8827 (mt0) cc_final: 0.8495 (mt0) REVERT: C 392 GLU cc_start: 0.7981 (pm20) cc_final: 0.7397 (pt0) REVERT: C 407 LYS cc_start: 0.9001 (tptt) cc_final: 0.8539 (tppt) REVERT: C 414 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8529 (mm-30) REVERT: D 244 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8656 (mm-30) REVERT: D 347 ARG cc_start: 0.8461 (tpp80) cc_final: 0.8229 (ttm-80) REVERT: E 109 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8027 (ptm160) REVERT: E 265 ASP cc_start: 0.8866 (t0) cc_final: 0.8468 (t70) REVERT: E 326 LYS cc_start: 0.9149 (tptt) cc_final: 0.8895 (mmmt) REVERT: E 380 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7831 (mtm) REVERT: E 415 MET cc_start: 0.9141 (ttp) cc_final: 0.8737 (ttm) REVERT: F 32 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6796 (mt0) REVERT: F 193 GLN cc_start: 0.7992 (pt0) cc_final: 0.7659 (pp30) REVERT: F 205 MET cc_start: 0.8171 (mtm) cc_final: 0.7888 (ttp) REVERT: F 244 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8269 (mm-30) REVERT: F 333 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8663 (pm20) REVERT: F 334 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8692 (tm-30) REVERT: F 335 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8218 (m-80) REVERT: F 341 MET cc_start: 0.7418 (ppp) cc_final: 0.7159 (pmm) REVERT: F 405 MET cc_start: 0.8617 (ptt) cc_final: 0.8344 (pp-130) REVERT: F 416 MET cc_start: 0.2524 (OUTLIER) cc_final: 0.2147 (pp-130) outliers start: 31 outliers final: 15 residues processed: 288 average time/residue: 0.9485 time to fit residues: 298.1443 Evaluate side-chains 276 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain F residue 416 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 183 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 242 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 0.0020 chunk 207 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 220 GLN D 374 GLN D 378 GLN E 41 GLN F 32 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.116844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.077782 restraints weight = 90170.749| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.88 r_work: 0.2853 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 20238 Z= 0.235 Angle : 0.951 59.200 27277 Z= 0.529 Chirality : 0.048 1.124 3103 Planarity : 0.005 0.098 3534 Dihedral : 5.828 117.453 2792 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.30 % Allowed : 16.91 % Favored : 81.79 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % 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: 0.73 (0.17), residues: 2511 helix: 1.19 (0.16), residues: 1169 sheet: -0.22 (0.26), residues: 385 loop : 0.08 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG F 87 TYR 0.078 0.002 TYR B 110 PHE 0.019 0.001 PHE A 232 TRP 0.007 0.001 TRP D 381 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00478 (20238) covalent geometry : angle 0.95103 (27277) hydrogen bonds : bond 0.03314 ( 987) hydrogen bonds : angle 4.88194 ( 2920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 0.624 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 1 MET cc_start: 0.7217 (tmt) cc_final: 0.6820 (tmt) REVERT: A 33 ASP cc_start: 0.8494 (m-30) cc_final: 0.8080 (p0) REVERT: A 172 GLN cc_start: 0.8012 (tp40) cc_final: 0.7776 (tp40) REVERT: A 269 ARG cc_start: 0.8545 (mmp80) cc_final: 0.8168 (mmp80) REVERT: A 272 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8340 (tpp80) REVERT: A 292 ASN cc_start: 0.8281 (t0) cc_final: 0.7782 (t0) REVERT: A 299 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7243 (ttp-110) REVERT: A 327 MET cc_start: 0.7783 (mmt) cc_final: 0.7340 (mmm) REVERT: A 334 GLU cc_start: 0.8319 (tp30) cc_final: 0.8069 (tp30) REVERT: A 378 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8999 (mm-40) REVERT: A 380 MET cc_start: 0.9672 (mmm) cc_final: 0.9452 (mmm) REVERT: B 220 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: B 348 LYS cc_start: 0.9039 (mppt) cc_final: 0.8738 (mppt) REVERT: B 378 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8170 (mm110) REVERT: B 397 GLU cc_start: 0.9001 (pt0) cc_final: 0.8720 (pm20) REVERT: B 401 ASN cc_start: 0.9348 (m-40) cc_final: 0.9018 (m110) REVERT: C 269 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8673 (mmt90) REVERT: C 333 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8576 (mm-30) REVERT: C 374 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8333 (tp-100) REVERT: C 378 GLN cc_start: 0.8818 (mt0) cc_final: 0.8484 (mt0) REVERT: C 392 GLU cc_start: 0.7983 (pm20) cc_final: 0.7397 (pt0) REVERT: C 407 LYS cc_start: 0.8980 (tptt) cc_final: 0.8531 (tppt) REVERT: C 414 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8509 (mm-30) REVERT: D 244 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8638 (mm-30) REVERT: D 347 ARG cc_start: 0.8464 (tpp80) cc_final: 0.8234 (ttm-80) REVERT: E 109 ARG cc_start: 0.8361 (mtm-85) cc_final: 0.7998 (ptm160) REVERT: E 265 ASP cc_start: 0.8831 (t0) cc_final: 0.8433 (t70) REVERT: E 326 LYS cc_start: 0.9141 (tptt) cc_final: 0.8883 (mmmt) REVERT: E 380 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7842 (mtm) REVERT: E 415 MET cc_start: 0.9136 (ttp) cc_final: 0.8737 (ttm) REVERT: F 193 GLN cc_start: 0.7973 (pt0) cc_final: 0.7649 (pp30) REVERT: F 205 MET cc_start: 0.8155 (mtm) cc_final: 0.7860 (ttp) REVERT: F 244 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8248 (mm-30) REVERT: F 272 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8448 (mtt180) REVERT: F 333 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8646 (pm20) REVERT: F 334 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8690 (tm-30) REVERT: F 335 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: F 341 MET cc_start: 0.7425 (ppp) cc_final: 0.7164 (pmm) REVERT: F 405 MET cc_start: 0.8575 (ptt) cc_final: 0.8309 (pp-130) REVERT: F 416 MET cc_start: 0.2475 (OUTLIER) cc_final: 0.2119 (pp-130) outliers start: 27 outliers final: 14 residues processed: 271 average time/residue: 0.8870 time to fit residues: 262.5645 Evaluate side-chains 272 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain F residue 272 ARG Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain F residue 416 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 137 optimal weight: 3.9990 chunk 191 optimal weight: 0.0870 chunk 81 optimal weight: 3.9990 chunk 230 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 168 optimal weight: 0.0670 chunk 229 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 2 optimal weight: 40.0000 chunk 84 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 220 GLN D 374 GLN D 378 GLN E 41 GLN ** E 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** 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 = 0.3825 r_free = 0.3825 target = 0.116868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.078049 restraints weight = 83686.796| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.72 r_work: 0.2862 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 20238 Z= 0.235 Angle : 0.951 59.200 27277 Z= 0.529 Chirality : 0.048 1.124 3103 Planarity : 0.005 0.098 3534 Dihedral : 5.828 117.453 2792 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.07 % Allowed : 17.09 % Favored : 81.84 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % 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: 0.73 (0.17), residues: 2511 helix: 1.19 (0.16), residues: 1169 sheet: -0.22 (0.26), residues: 385 loop : 0.08 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG F 87 TYR 0.078 0.002 TYR B 110 PHE 0.019 0.001 PHE A 232 TRP 0.007 0.001 TRP D 381 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00478 (20238) covalent geometry : angle 0.95103 (27277) hydrogen bonds : bond 0.03314 ( 987) hydrogen bonds : angle 4.88194 ( 2920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9844.48 seconds wall clock time: 167 minutes 48.61 seconds (10068.61 seconds total)