Starting phenix.real_space_refine on Tue Jun 17 15:46:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gcu_51237/06_2025/9gcu_51237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gcu_51237/06_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_51237/06_2025/9gcu_51237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gcu_51237/06_2025/9gcu_51237.map" model { file = "/net/cci-nas-00/data/ceres_data/9gcu_51237/06_2025/9gcu_51237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gcu_51237/06_2025/9gcu_51237.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.77, per 1000 atoms: 0.89 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: 5.57 Conformation dependent library (CDL) restraints added in 5.6 seconds 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: 2.24 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: 7.75 Time building geometry restraints manager: 6.32 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: 4.700 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: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 55.370 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:61.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (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 TRP 0.050 0.004 TRP A 381 HIS 0.007 0.001 HIS A 344 PHE 0.040 0.002 PHE A 36 TYR 0.017 0.001 TYR E 110 ARG 0.013 0.001 ARG B 353 Details of bonding type rmsd hydrogen bonds : bond 0.14410 ( 987) hydrogen bonds : angle 6.85037 ( 2920) covalent geometry : bond 0.00302 (20238) covalent geometry : angle 0.67327 (27277) *********************** 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 : 2.266 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: 2.0406 time to fit residues: 841.9916 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 : 2.451 ------------------------------------------------------------------------------- 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 207 optimal weight: 10.0000 chunk 186 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- 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** A 275 ASN A 378 GLN B 374 GLN C 41 GLN C 193 GLN C 340 ASN D 193 GLN D 378 GLN E 41 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.117929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.078350 restraints weight = 123658.869| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.48 r_work: 0.2827 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20238 Z= 0.171 Angle : 0.715 9.015 27277 Z= 0.356 Chirality : 0.045 0.188 3103 Planarity : 0.005 0.050 3534 Dihedral : 6.227 116.888 2794 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.58 % Allowed : 10.17 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2511 helix: 0.95 (0.16), residues: 1168 sheet: -0.11 (0.25), residues: 429 loop : 0.11 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 381 HIS 0.007 0.001 HIS A 239 PHE 0.029 0.002 PHE A 36 TYR 0.017 0.002 TYR A 80 ARG 0.009 0.001 ARG C 347 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 987) hydrogen bonds : angle 5.41769 ( 2920) covalent geometry : bond 0.00395 (20238) covalent geometry : angle 0.71496 (27277) *********************** 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 345 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 312 time to evaluate : 2.030 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 62 PHE cc_start: 0.8225 (p90) cc_final: 0.7899 (p90) REVERT: A 172 GLN cc_start: 0.8060 (tp40) cc_final: 0.7803 (tp40) REVERT: A 244 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 292 ASN cc_start: 0.8299 (t0) cc_final: 0.7956 (t0) REVERT: A 321 ILE cc_start: 0.7452 (mp) cc_final: 0.7196 (tp) REVERT: A 336 LYS cc_start: 0.8135 (mmmm) cc_final: 0.7256 (mmtt) REVERT: A 378 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8958 (mm110) REVERT: A 415 MET cc_start: 0.7499 (ppp) cc_final: 0.7091 (pp-130) REVERT: B 32 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8036 (mm-40) REVERT: B 33 ASP cc_start: 0.8433 (m-30) cc_final: 0.8123 (m-30) REVERT: B 109 ARG cc_start: 0.7387 (tmt170) cc_final: 0.7038 (tmt90) REVERT: B 333 GLU cc_start: 0.8761 (tt0) cc_final: 0.8457 (tp30) REVERT: B 348 LYS cc_start: 0.9070 (mppt) cc_final: 0.8747 (mppt) REVERT: B 401 ASN cc_start: 0.9324 (m-40) cc_final: 0.8929 (m110) REVERT: C 2 ASN cc_start: 0.8264 (t0) cc_final: 0.7989 (t0) REVERT: C 333 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8608 (mm-30) REVERT: C 348 LYS cc_start: 0.9163 (mtmm) cc_final: 0.8957 (mtmm) REVERT: C 374 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8317 (tp-100) REVERT: C 378 GLN cc_start: 0.8849 (mt0) cc_final: 0.8489 (mt0) REVERT: C 392 GLU cc_start: 0.8199 (pm20) cc_final: 0.7647 (pt0) REVERT: C 407 LYS cc_start: 0.8895 (tptt) cc_final: 0.8419 (tppt) REVERT: C 414 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8492 (mm-30) REVERT: D 224 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8602 (ttpt) REVERT: D 347 ARG cc_start: 0.8433 (tpp80) cc_final: 0.8213 (ttm-80) REVERT: E 326 LYS cc_start: 0.9123 (tptt) cc_final: 0.8764 (tppt) REVERT: E 329 GLU cc_start: 0.8695 (pm20) cc_final: 0.8371 (pm20) REVERT: E 415 MET cc_start: 0.9064 (ttp) cc_final: 0.8697 (ttm) REVERT: F 105 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7986 (mmtt) REVERT: F 244 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8178 (mm-30) REVERT: F 274 TYR cc_start: 0.7894 (m-10) cc_final: 0.7633 (m-10) REVERT: F 334 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8717 (tm-30) REVERT: F 341 MET cc_start: 0.6915 (pp-130) cc_final: 0.6672 (pmm) REVERT: F 347 ARG cc_start: 0.8134 (tpm-80) cc_final: 0.7810 (tpm-80) REVERT: F 405 MET cc_start: 0.8535 (ptt) cc_final: 0.8246 (pp-130) outliers start: 33 outliers final: 8 residues processed: 324 average time/residue: 2.1925 time to fit residues: 777.0986 Evaluate side-chains 289 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 280 time to evaluate : 3.213 ------------------------------------------------------------------------------- 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 E residue 341 MET 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 42 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 216 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 241 GLN A 275 ASN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 190 ASN D 193 GLN E 117 ASN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS F 126 ASN F 256 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.115790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075808 restraints weight = 105809.946| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.16 r_work: 0.2798 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 20238 Z= 0.239 Angle : 0.719 9.450 27277 Z= 0.358 Chirality : 0.046 0.255 3103 Planarity : 0.004 0.053 3534 Dihedral : 6.236 117.254 2792 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.90 % Allowed : 11.89 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2511 helix: 0.98 (0.16), residues: 1164 sheet: -0.28 (0.26), residues: 386 loop : 0.07 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 381 HIS 0.007 0.001 HIS A 239 PHE 0.024 0.002 PHE A 36 TYR 0.015 0.002 TYR F 332 ARG 0.009 0.001 ARG C 347 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 987) hydrogen bonds : angle 5.28288 ( 2920) covalent geometry : bond 0.00558 (20238) covalent geometry : angle 0.71904 (27277) *********************** 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 328 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 3.515 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: 0.8248 (p90) cc_final: 0.7872 (p90) REVERT: A 85 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.6728 (pm20) REVERT: A 249 LYS cc_start: 0.9031 (tptt) cc_final: 0.8813 (tppt) REVERT: A 269 ARG cc_start: 0.8517 (mmp80) cc_final: 0.8133 (mmp80) REVERT: A 292 ASN cc_start: 0.8258 (t0) cc_final: 0.7862 (t0) REVERT: A 336 LYS cc_start: 0.8322 (mmmm) cc_final: 0.7675 (mmmt) REVERT: A 378 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8926 (mm110) REVERT: A 380 MET cc_start: 0.9599 (mmm) cc_final: 0.9371 (mmm) REVERT: B 32 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7910 (mm-40) REVERT: B 33 ASP cc_start: 0.8511 (m-30) cc_final: 0.8252 (m-30) REVERT: B 272 ARG cc_start: 0.9077 (mmm-85) cc_final: 0.8839 (mmm-85) REVERT: B 348 LYS cc_start: 0.9060 (mppt) cc_final: 0.8741 (mppt) REVERT: B 401 ASN cc_start: 0.9302 (m-40) cc_final: 0.8953 (m110) REVERT: C 327 MET cc_start: 0.8650 (ttp) cc_final: 0.8387 (ttm) REVERT: C 374 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8452 (tp-100) REVERT: C 378 GLN cc_start: 0.8862 (mt0) cc_final: 0.8565 (mt0) REVERT: C 407 LYS cc_start: 0.8944 (tptt) cc_final: 0.8478 (tppt) REVERT: C 414 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8480 (mm-30) REVERT: D 347 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8279 (ttm-80) REVERT: E 265 ASP cc_start: 0.8970 (t0) cc_final: 0.8531 (t70) REVERT: E 326 LYS cc_start: 0.9162 (tptt) cc_final: 0.8627 (mmmt) REVERT: E 329 GLU cc_start: 0.8696 (pm20) cc_final: 0.8092 (pm20) REVERT: E 405 MET cc_start: 0.9360 (ptt) cc_final: 0.9148 (pmm) REVERT: E 415 MET cc_start: 0.9091 (ttp) cc_final: 0.8698 (ttm) REVERT: F 105 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7849 (mmtt) REVERT: F 193 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7631 (pp30) REVERT: F 244 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8175 (mm-30) REVERT: F 334 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8484 (tm-30) REVERT: F 335 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: F 405 MET cc_start: 0.8492 (ptt) cc_final: 0.8249 (pp-130) outliers start: 40 outliers final: 13 residues processed: 305 average time/residue: 2.5625 time to fit residues: 854.3577 Evaluate side-chains 277 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 260 time to evaluate : 3.004 ------------------------------------------------------------------------------- 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 B residue 32 GLN 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 E residue 241 GLN Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 392 GLU Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 335 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 180 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 202 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS D 193 GLN D 220 GLN D 378 GLN E 41 GLN E 85 GLN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN ** 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 = 0.3817 r_free = 0.3817 target = 0.116323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.076733 restraints weight = 102838.708| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.10 r_work: 0.2815 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2081 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= 0.158 Angle : 0.679 9.412 27277 Z= 0.336 Chirality : 0.043 0.157 3103 Planarity : 0.004 0.045 3534 Dihedral : 6.089 116.995 2792 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.04 % Allowed : 13.28 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2511 helix: 1.09 (0.16), residues: 1163 sheet: -0.35 (0.26), residues: 390 loop : 0.09 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 381 HIS 0.006 0.001 HIS A 239 PHE 0.023 0.001 PHE A 412 TYR 0.025 0.001 TYR F 110 ARG 0.010 0.001 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 987) hydrogen bonds : angle 5.10954 ( 2920) covalent geometry : bond 0.00371 (20238) covalent geometry : angle 0.67931 (27277) *********************** 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 321 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 3.510 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 85 GLN cc_start: 0.7318 (pm20) cc_final: 0.7049 (pm20) REVERT: A 172 GLN cc_start: 0.7980 (tp40) cc_final: 0.7767 (tp40) REVERT: A 244 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 269 ARG cc_start: 0.8514 (mmp80) cc_final: 0.8140 (mmp80) REVERT: A 292 ASN cc_start: 0.8231 (t0) cc_final: 0.7814 (t0) REVERT: A 336 LYS cc_start: 0.8234 (mmmm) cc_final: 0.7674 (mmmt) REVERT: A 342 GLU cc_start: 0.7339 (tm-30) cc_final: 0.7130 (tm-30) REVERT: A 378 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8910 (mm110) REVERT: A 380 MET cc_start: 0.9620 (mmm) cc_final: 0.9384 (mmm) REVERT: B 33 ASP cc_start: 0.8382 (m-30) cc_final: 0.8055 (m-30) REVERT: B 244 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8620 (mm-30) REVERT: B 348 LYS cc_start: 0.9057 (mppt) cc_final: 0.8758 (mppt) REVERT: B 401 ASN cc_start: 0.9303 (m-40) cc_final: 0.8947 (m110) REVERT: C 269 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8724 (mmt90) REVERT: C 327 MET cc_start: 0.8610 (ttp) cc_final: 0.8377 (tpp) REVERT: C 333 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8483 (mm-30) REVERT: C 334 GLU cc_start: 0.8627 (mp0) cc_final: 0.8007 (mp0) REVERT: C 374 GLN cc_start: 0.8829 (tp-100) cc_final: 0.8437 (tp-100) REVERT: C 378 GLN cc_start: 0.8825 (mt0) cc_final: 0.8569 (mt0) REVERT: C 392 GLU cc_start: 0.8026 (pm20) cc_final: 0.7489 (pt0) REVERT: C 407 LYS cc_start: 0.8951 (tptt) cc_final: 0.8498 (tppt) REVERT: C 414 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8490 (mm-30) REVERT: D 347 ARG cc_start: 0.8461 (tpp80) cc_final: 0.8238 (ttm-80) REVERT: E 265 ASP cc_start: 0.8922 (t0) cc_final: 0.8512 (t70) REVERT: E 326 LYS cc_start: 0.9137 (tptt) cc_final: 0.8865 (mmmt) REVERT: E 415 MET cc_start: 0.9110 (ttp) cc_final: 0.8811 (ttm) REVERT: F 147 MET cc_start: 0.3140 (OUTLIER) cc_final: 0.2606 (ptp) REVERT: F 193 GLN cc_start: 0.8335 (pt0) cc_final: 0.7635 (pp30) REVERT: F 205 MET cc_start: 0.8272 (mtm) cc_final: 0.7959 (ttp) REVERT: F 244 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8178 (mm-30) REVERT: F 334 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8470 (tm-30) REVERT: F 335 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: F 341 MET cc_start: 0.7336 (ppp) cc_final: 0.7105 (pmm) REVERT: F 405 MET cc_start: 0.8541 (ptt) cc_final: 0.8297 (pp-130) outliers start: 43 outliers final: 17 residues processed: 298 average time/residue: 3.0718 time to fit residues: 1004.4979 Evaluate side-chains 283 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 2.226 ------------------------------------------------------------------------------- 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 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 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 D residue 392 GLU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 392 GLU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 335 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 78 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 217 optimal weight: 0.3980 chunk 148 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 chunk 223 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 210 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN D 193 GLN D 220 GLN E 374 GLN E 388 HIS E 401 ASN ** 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 = 0.3827 r_free = 0.3827 target = 0.116958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.077913 restraints weight = 84642.672| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.77 r_work: 0.2849 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20238 Z= 0.133 Angle : 0.667 9.910 27277 Z= 0.329 Chirality : 0.043 0.148 3103 Planarity : 0.004 0.046 3534 Dihedral : 5.940 116.833 2792 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.86 % Allowed : 14.77 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2511 helix: 1.18 (0.16), residues: 1164 sheet: -0.32 (0.26), residues: 390 loop : 0.11 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 381 HIS 0.006 0.001 HIS A 239 PHE 0.022 0.001 PHE A 412 TYR 0.011 0.001 TYR F 72 ARG 0.009 0.001 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 987) hydrogen bonds : angle 4.97985 ( 2920) covalent geometry : bond 0.00308 (20238) covalent geometry : angle 0.66721 (27277) *********************** 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 319 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 280 time to evaluate : 3.297 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 85 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: A 269 ARG cc_start: 0.8527 (mmp80) cc_final: 0.8149 (mmp80) REVERT: A 292 ASN cc_start: 0.8251 (t0) cc_final: 0.7817 (t0) REVERT: A 336 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7702 (mmmt) REVERT: A 342 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 378 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8919 (mm110) REVERT: A 380 MET cc_start: 0.9634 (mmm) cc_final: 0.9415 (mmm) REVERT: B 33 ASP cc_start: 0.8362 (m-30) cc_final: 0.8094 (m-30) REVERT: B 109 ARG cc_start: 0.7128 (ttp80) cc_final: 0.6429 (tmt90) REVERT: B 244 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8535 (mm-30) REVERT: B 348 LYS cc_start: 0.9091 (mppt) cc_final: 0.8619 (mppt) REVERT: B 401 ASN cc_start: 0.9287 (m-40) cc_final: 0.8931 (m110) REVERT: C 269 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8704 (mmt90) REVERT: C 327 MET cc_start: 0.8570 (ttp) cc_final: 0.8329 (tpp) REVERT: C 333 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8420 (mm-30) REVERT: C 334 GLU cc_start: 0.8592 (mp0) cc_final: 0.7957 (mp0) REVERT: C 374 GLN cc_start: 0.8769 (tp-100) cc_final: 0.8341 (tp-100) REVERT: C 378 GLN cc_start: 0.8823 (mt0) cc_final: 0.8492 (mt0) REVERT: C 407 LYS cc_start: 0.8972 (tptt) cc_final: 0.8519 (tppt) REVERT: C 414 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8488 (mm-30) REVERT: D 347 ARG cc_start: 0.8434 (tpp80) cc_final: 0.8211 (ttm-80) REVERT: E 265 ASP cc_start: 0.8852 (t0) cc_final: 0.8456 (t70) REVERT: E 326 LYS cc_start: 0.9137 (tptt) cc_final: 0.8879 (mmmt) REVERT: F 193 GLN cc_start: 0.8289 (pt0) cc_final: 0.7642 (pp30) REVERT: F 244 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8255 (mm-30) REVERT: F 272 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8390 (mtt180) REVERT: F 334 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8523 (tm-30) REVERT: F 335 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: F 396 MET cc_start: 0.3213 (ttt) cc_final: 0.2927 (tpp) REVERT: F 405 MET cc_start: 0.8560 (ptt) cc_final: 0.8239 (pp-130) REVERT: F 415 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6304 (mtp) REVERT: F 416 MET cc_start: 0.2043 (pmt) cc_final: 0.1563 (pp-130) outliers start: 39 outliers final: 19 residues processed: 301 average time/residue: 2.2141 time to fit residues: 732.0701 Evaluate side-chains 286 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 2.303 ------------------------------------------------------------------------------- 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 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 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 392 GLU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 245 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 415 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN D 193 GLN D 220 GLN D 378 GLN E 41 GLN E 140 HIS ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN F 256 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.114197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.074429 restraints weight = 97885.356| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.97 r_work: 0.2773 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 20238 Z= 0.295 Angle : 0.739 10.261 27277 Z= 0.366 Chirality : 0.046 0.196 3103 Planarity : 0.005 0.077 3534 Dihedral : 6.134 117.939 2792 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.14 % Allowed : 15.10 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2511 helix: 0.99 (0.16), residues: 1164 sheet: -0.40 (0.26), residues: 377 loop : 0.03 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 381 HIS 0.006 0.001 HIS C 239 PHE 0.021 0.002 PHE A 232 TYR 0.025 0.002 TYR A 80 ARG 0.010 0.001 ARG C 362 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 987) hydrogen bonds : angle 5.18309 ( 2920) covalent geometry : bond 0.00686 (20238) covalent geometry : angle 0.73935 (27277) *********************** 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 323 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 278 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8595 (m-30) cc_final: 0.8081 (p0) REVERT: A 172 GLN cc_start: 0.8057 (tp40) cc_final: 0.7793 (tp40) REVERT: A 244 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7571 (tm-30) REVERT: A 269 ARG cc_start: 0.8541 (mmp80) cc_final: 0.8184 (mmp80) REVERT: A 292 ASN cc_start: 0.8261 (t0) cc_final: 0.7793 (t0) REVERT: A 336 LYS cc_start: 0.8286 (mmmm) cc_final: 0.7722 (mmmt) REVERT: A 342 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6944 (tm-30) REVERT: A 378 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8910 (mm110) REVERT: A 380 MET cc_start: 0.9650 (mmm) cc_final: 0.9415 (mmm) REVERT: A 390 MET cc_start: 0.7671 (ptm) cc_final: 0.7434 (ptm) REVERT: B 33 ASP cc_start: 0.8458 (m-30) cc_final: 0.8056 (m-30) REVERT: B 109 ARG cc_start: 0.7106 (ttp80) cc_final: 0.6872 (ttp80) REVERT: B 244 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8581 (mm-30) REVERT: B 348 LYS cc_start: 0.9048 (mppt) cc_final: 0.8773 (mppt) REVERT: B 359 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8288 (t0) REVERT: B 401 ASN cc_start: 0.9312 (m-40) cc_final: 0.8969 (m110) REVERT: C 269 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8676 (mmt90) REVERT: C 333 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8473 (mm-30) REVERT: C 334 GLU cc_start: 0.8673 (mp0) cc_final: 0.8030 (mp0) REVERT: C 374 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8484 (tp-100) REVERT: C 378 GLN cc_start: 0.8868 (mt0) cc_final: 0.8550 (mt0) REVERT: C 392 GLU cc_start: 0.8155 (pm20) cc_final: 0.7598 (pt0) REVERT: C 407 LYS cc_start: 0.9057 (tptt) cc_final: 0.8571 (tppt) REVERT: C 414 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8536 (mm-30) REVERT: D 347 ARG cc_start: 0.8502 (tpp80) cc_final: 0.8265 (ttm-80) REVERT: E 265 ASP cc_start: 0.8925 (t0) cc_final: 0.8553 (t70) REVERT: E 326 LYS cc_start: 0.9179 (tptt) cc_final: 0.8921 (mmmt) REVERT: F 193 GLN cc_start: 0.8265 (pt0) cc_final: 0.7611 (pp30) REVERT: F 205 MET cc_start: 0.8191 (mtm) cc_final: 0.7970 (ttp) REVERT: F 244 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8322 (mm-30) REVERT: F 252 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6819 (mmp-170) REVERT: F 334 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8477 (tm-30) REVERT: F 335 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8183 (m-80) REVERT: F 405 MET cc_start: 0.8578 (ptt) cc_final: 0.8316 (pp-130) REVERT: F 416 MET cc_start: 0.2389 (OUTLIER) cc_final: 0.2033 (pp-130) outliers start: 45 outliers final: 17 residues processed: 302 average time/residue: 1.8407 time to fit residues: 608.2206 Evaluate side-chains 287 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 2.252 ------------------------------------------------------------------------------- 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 393 ILE 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 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 336 LYS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain E residue 233 ASP 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 F residue 252 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 15 optimal weight: 9.9990 chunk 229 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 105 optimal weight: 0.1980 chunk 214 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 175 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** D 140 HIS D 193 GLN D 220 GLN D 378 GLN E 41 GLN E 85 GLN E 374 GLN E 388 HIS ** 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 = 0.3807 r_free = 0.3807 target = 0.115681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.075934 restraints weight = 112160.151| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.24 r_work: 0.2796 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20238 Z= 0.152 Angle : 0.700 10.860 27277 Z= 0.345 Chirality : 0.043 0.189 3103 Planarity : 0.004 0.043 3534 Dihedral : 5.992 117.668 2792 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.95 % Allowed : 15.61 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2511 helix: 1.14 (0.16), residues: 1163 sheet: -0.40 (0.26), residues: 385 loop : 0.08 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 381 HIS 0.006 0.001 HIS A 239 PHE 0.020 0.001 PHE A 412 TYR 0.012 0.001 TYR F 72 ARG 0.010 0.001 ARG F 347 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 987) hydrogen bonds : angle 4.98486 ( 2920) covalent geometry : bond 0.00355 (20238) covalent geometry : angle 0.69980 (27277) *********************** 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 317 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 2.449 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: 0.7012 (tmt) cc_final: 0.6419 (ppp) REVERT: A 33 ASP cc_start: 0.8533 (m-30) cc_final: 0.8069 (p0) REVERT: A 244 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 269 ARG cc_start: 0.8532 (mmp80) cc_final: 0.8186 (mmp80) REVERT: A 292 ASN cc_start: 0.8246 (t0) cc_final: 0.7747 (t0) REVERT: A 334 GLU cc_start: 0.8196 (tp30) cc_final: 0.7933 (tm-30) REVERT: A 336 LYS cc_start: 0.8252 (mmmm) cc_final: 0.7690 (mmmt) REVERT: A 378 GLN cc_start: 0.9236 (mm-40) cc_final: 0.9011 (mm-40) REVERT: A 380 MET cc_start: 0.9657 (mmm) cc_final: 0.9411 (mmm) REVERT: B 33 ASP cc_start: 0.8362 (m-30) cc_final: 0.8096 (m-30) REVERT: B 109 ARG cc_start: 0.7103 (ttp80) cc_final: 0.6833 (ttp80) REVERT: B 244 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8623 (mm-30) REVERT: B 348 LYS cc_start: 0.9080 (mppt) cc_final: 0.8715 (mppt) REVERT: B 401 ASN cc_start: 0.9296 (m-40) cc_final: 0.8903 (m110) REVERT: C 269 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8709 (mmt90) REVERT: C 333 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8597 (mm-30) REVERT: C 334 GLU cc_start: 0.8675 (mp0) cc_final: 0.8002 (mp0) REVERT: C 347 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8181 (ttm-80) REVERT: C 374 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8431 (tp-100) REVERT: C 378 GLN cc_start: 0.8849 (mt0) cc_final: 0.8566 (mt0) REVERT: C 392 GLU cc_start: 0.8132 (pm20) cc_final: 0.7469 (pt0) REVERT: C 397 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8840 (mt-10) REVERT: C 407 LYS cc_start: 0.9048 (tptt) cc_final: 0.8577 (tppt) REVERT: C 414 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8521 (mm-30) REVERT: D 30 ARG cc_start: 0.8678 (mtp-110) cc_final: 0.8467 (mtm-85) REVERT: D 347 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8256 (ttm-80) REVERT: E 265 ASP cc_start: 0.8894 (t0) cc_final: 0.8541 (t70) REVERT: E 326 LYS cc_start: 0.9176 (tptt) cc_final: 0.8922 (mmmt) REVERT: F 193 GLN cc_start: 0.8144 (pt0) cc_final: 0.7595 (pp30) REVERT: F 205 MET cc_start: 0.8210 (mtm) cc_final: 0.7939 (ttp) REVERT: F 244 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8217 (mm-30) REVERT: F 334 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8542 (tm-30) REVERT: F 335 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: F 405 MET cc_start: 0.8584 (ptt) cc_final: 0.8312 (pp-130) REVERT: F 415 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6684 (mmp) REVERT: F 416 MET cc_start: 0.2705 (OUTLIER) cc_final: 0.2366 (pp-130) outliers start: 41 outliers final: 16 residues processed: 298 average time/residue: 1.8928 time to fit residues: 622.3763 Evaluate side-chains 286 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 2.447 ------------------------------------------------------------------------------- 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 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 193 GLN Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain E residue 329 GLU 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 415 MET 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 243 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 234 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 241 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 41 GLN B 374 GLN D 193 GLN D 220 GLN E 85 GLN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3800 r_free = 0.3800 target = 0.115130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.075631 restraints weight = 101737.732| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.08 r_work: 0.2797 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 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 = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20238 Z= 0.182 Angle : 0.723 11.275 27277 Z= 0.355 Chirality : 0.044 0.173 3103 Planarity : 0.004 0.044 3534 Dihedral : 5.978 117.643 2792 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.00 % Allowed : 15.98 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2511 helix: 1.12 (0.16), residues: 1163 sheet: -0.45 (0.26), residues: 387 loop : 0.08 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 381 HIS 0.005 0.001 HIS A 239 PHE 0.021 0.001 PHE E 62 TYR 0.024 0.001 TYR A 80 ARG 0.009 0.001 ARG C 347 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 987) hydrogen bonds : angle 5.01034 ( 2920) covalent geometry : bond 0.00427 (20238) covalent geometry : angle 0.72316 (27277) *********************** 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 310 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 2.447 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: 0.6939 (tmt) cc_final: 0.6681 (tmt) REVERT: A 33 ASP cc_start: 0.8465 (m-30) cc_final: 0.8042 (p0) REVERT: A 244 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 269 ARG cc_start: 0.8610 (mmp80) cc_final: 0.8210 (mmp80) REVERT: A 272 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8393 (tpp80) REVERT: A 292 ASN cc_start: 0.8312 (t0) cc_final: 0.7801 (t0) REVERT: A 327 MET cc_start: 0.7885 (mmt) cc_final: 0.7414 (mmm) REVERT: A 334 GLU cc_start: 0.8252 (tp30) cc_final: 0.7994 (tm-30) REVERT: A 336 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7729 (mmmt) REVERT: A 378 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8968 (mm-40) REVERT: A 380 MET cc_start: 0.9664 (mmm) cc_final: 0.9429 (mmm) REVERT: B 33 ASP cc_start: 0.8450 (m-30) cc_final: 0.8111 (m-30) REVERT: B 109 ARG cc_start: 0.7104 (ttp80) cc_final: 0.6849 (ttp80) REVERT: B 244 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8574 (mm-30) REVERT: B 348 LYS cc_start: 0.9045 (mppt) cc_final: 0.8726 (mppt) REVERT: B 401 ASN cc_start: 0.9317 (m-40) cc_final: 0.8967 (m110) REVERT: C 269 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8685 (mmt90) REVERT: C 333 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8575 (mm-30) REVERT: C 334 GLU cc_start: 0.8656 (mp0) cc_final: 0.7999 (mp0) REVERT: C 374 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8455 (tp-100) REVERT: C 378 GLN cc_start: 0.8865 (mt0) cc_final: 0.8592 (mt0) REVERT: C 397 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8762 (mt-10) REVERT: C 407 LYS cc_start: 0.9029 (tptt) cc_final: 0.8559 (tppt) REVERT: C 414 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8503 (mm-30) REVERT: D 193 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7944 (mp-120) REVERT: D 333 GLU cc_start: 0.8834 (tp30) cc_final: 0.8248 (tp30) REVERT: D 336 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8787 (tttt) REVERT: D 347 ARG cc_start: 0.8477 (tpp80) cc_final: 0.8240 (ttm-80) REVERT: E 30 ARG cc_start: 0.8737 (mtm110) cc_final: 0.8478 (mtm-85) REVERT: E 265 ASP cc_start: 0.8902 (t0) cc_final: 0.8551 (t70) REVERT: E 326 LYS cc_start: 0.9181 (tptt) cc_final: 0.8914 (mmmt) REVERT: F 193 GLN cc_start: 0.8138 (pt0) cc_final: 0.7644 (pp30) REVERT: F 244 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8202 (mm-30) REVERT: F 333 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: F 334 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8553 (tm-30) REVERT: F 335 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: F 405 MET cc_start: 0.8494 (ptt) cc_final: 0.8224 (pp-130) REVERT: F 415 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6778 (mmp) REVERT: F 416 MET cc_start: 0.2651 (OUTLIER) cc_final: 0.2260 (pp-130) outliers start: 42 outliers final: 15 residues processed: 288 average time/residue: 1.8138 time to fit residues: 572.4694 Evaluate side-chains 281 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 259 time to evaluate : 2.271 ------------------------------------------------------------------------------- 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 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 193 GLN 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 233 ASP Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 392 GLU Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain F residue 415 MET 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 204 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 220 optimal weight: 0.0470 chunk 215 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN D 193 GLN D 220 GLN D 378 GLN E 41 GLN E 85 GLN E 374 GLN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3816 r_free = 0.3816 target = 0.116106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.076350 restraints weight = 129838.214| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.55 r_work: 0.2800 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 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 = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20238 Z= 0.141 Angle : 0.728 11.874 27277 Z= 0.356 Chirality : 0.043 0.163 3103 Planarity : 0.004 0.042 3534 Dihedral : 5.894 117.372 2792 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.44 % Allowed : 16.40 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2511 helix: 1.18 (0.16), residues: 1164 sheet: -0.40 (0.26), residues: 389 loop : 0.12 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 381 HIS 0.005 0.001 HIS A 239 PHE 0.018 0.001 PHE A 412 TYR 0.022 0.001 TYR F 110 ARG 0.008 0.001 ARG F 347 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 987) hydrogen bonds : angle 4.91876 ( 2920) covalent geometry : bond 0.00329 (20238) covalent geometry : angle 0.72773 (27277) *********************** 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 298 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 268 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7233 (tmt) cc_final: 0.6772 (tmm) REVERT: A 33 ASP cc_start: 0.8503 (m-30) cc_final: 0.8080 (p0) REVERT: A 244 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 269 ARG cc_start: 0.8545 (mmp80) cc_final: 0.8153 (mmp80) REVERT: A 272 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8286 (tpp80) REVERT: A 292 ASN cc_start: 0.8286 (t0) cc_final: 0.7804 (t0) REVERT: A 327 MET cc_start: 0.7794 (mmt) cc_final: 0.7366 (mmm) REVERT: A 334 GLU cc_start: 0.8231 (tp30) cc_final: 0.7935 (tm-30) REVERT: A 336 LYS cc_start: 0.8210 (mmmm) cc_final: 0.7652 (mmmt) REVERT: A 378 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8971 (mm-40) REVERT: A 380 MET cc_start: 0.9678 (mmm) cc_final: 0.9447 (mmm) REVERT: B 33 ASP cc_start: 0.8406 (m-30) cc_final: 0.8095 (m-30) REVERT: B 109 ARG cc_start: 0.7030 (ttp80) cc_final: 0.6741 (ttp80) REVERT: B 220 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: B 348 LYS cc_start: 0.9033 (mppt) cc_final: 0.8698 (mppt) REVERT: B 362 ARG cc_start: 0.9077 (mpp80) cc_final: 0.8680 (mtm-85) REVERT: B 397 GLU cc_start: 0.9033 (pt0) cc_final: 0.8730 (pm20) REVERT: B 401 ASN cc_start: 0.9313 (m-40) cc_final: 0.9006 (m110) REVERT: C 269 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8676 (mmt90) REVERT: C 333 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8602 (mm-30) REVERT: C 334 GLU cc_start: 0.8677 (mp0) cc_final: 0.7998 (mp0) REVERT: C 374 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8389 (tp-100) REVERT: C 378 GLN cc_start: 0.8878 (mt0) cc_final: 0.8595 (mt0) REVERT: C 397 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8819 (mt-10) REVERT: C 407 LYS cc_start: 0.9044 (tptt) cc_final: 0.8562 (tppt) REVERT: C 414 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8541 (mm-30) REVERT: D 30 ARG cc_start: 0.8685 (mtp-110) cc_final: 0.8461 (mtm-85) REVERT: D 347 ARG cc_start: 0.8513 (tpp80) cc_final: 0.8263 (ttm-80) REVERT: E 265 ASP cc_start: 0.8890 (t0) cc_final: 0.8537 (t70) REVERT: E 329 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: F 32 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6824 (mt0) REVERT: F 193 GLN cc_start: 0.7956 (pt0) cc_final: 0.7594 (pp30) REVERT: F 205 MET cc_start: 0.8252 (mtm) cc_final: 0.7991 (ttp) REVERT: F 244 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8168 (mm-30) REVERT: F 333 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8702 (pm20) REVERT: F 334 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8603 (tm-30) REVERT: F 335 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: F 405 MET cc_start: 0.8587 (ptt) cc_final: 0.8299 (pp-130) REVERT: F 416 MET cc_start: 0.2543 (OUTLIER) cc_final: 0.2220 (pp-130) outliers start: 30 outliers final: 14 residues processed: 283 average time/residue: 1.8035 time to fit residues: 557.7154 Evaluate side-chains 276 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 197 TYR 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 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 336 LYS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 392 GLU 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 2 optimal weight: 8.9990 chunk 172 optimal weight: 0.0980 chunk 189 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 206 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN D 193 GLN D 220 GLN D 275 ASN E 85 GLN ** 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 = 0.3813 r_free = 0.3813 target = 0.116036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.075999 restraints weight = 144052.461| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.78 r_work: 0.2791 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 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 = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.414 20238 Z= 0.324 Angle : 1.019 59.191 27277 Z= 0.583 Chirality : 0.046 0.555 3103 Planarity : 0.006 0.165 3534 Dihedral : 5.928 117.378 2792 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.35 % Allowed : 16.81 % Favored : 81.84 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2511 helix: 1.16 (0.16), residues: 1164 sheet: -0.39 (0.26), residues: 389 loop : 0.08 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 381 HIS 0.005 0.001 HIS A 239 PHE 0.295 0.002 PHE A 232 TYR 0.040 0.001 TYR A 197 ARG 0.060 0.001 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 987) hydrogen bonds : angle 4.92444 ( 2920) covalent geometry : bond 0.00659 (20238) covalent geometry : angle 1.01944 (27277) ********************** 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 284 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7303 (tmt) cc_final: 0.6810 (tmm) REVERT: A 33 ASP cc_start: 0.8511 (m-30) cc_final: 0.8086 (p0) REVERT: A 244 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 269 ARG cc_start: 0.8538 (mmp80) cc_final: 0.8147 (mmp80) REVERT: A 272 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8273 (tpp80) REVERT: A 292 ASN cc_start: 0.8270 (t0) cc_final: 0.7792 (t0) REVERT: A 327 MET cc_start: 0.7785 (mmt) cc_final: 0.7347 (mmm) REVERT: A 334 GLU cc_start: 0.8223 (tp30) cc_final: 0.7928 (tm-30) REVERT: A 336 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7646 (mmmt) REVERT: A 378 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8985 (mm-40) REVERT: A 380 MET cc_start: 0.9672 (mmm) cc_final: 0.9447 (mmm) REVERT: B 33 ASP cc_start: 0.8410 (m-30) cc_final: 0.8098 (m-30) REVERT: B 109 ARG cc_start: 0.7055 (ttp80) cc_final: 0.6762 (ttp80) REVERT: B 220 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: B 348 LYS cc_start: 0.8998 (mppt) cc_final: 0.8705 (mppt) REVERT: B 362 ARG cc_start: 0.9087 (mpp80) cc_final: 0.8689 (mtm-85) REVERT: B 378 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8276 (mm110) REVERT: B 397 GLU cc_start: 0.9053 (pt0) cc_final: 0.8739 (pm20) REVERT: B 401 ASN cc_start: 0.9339 (m-40) cc_final: 0.9008 (m110) REVERT: C 269 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8686 (mmt90) REVERT: C 333 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8605 (mm-30) REVERT: C 334 GLU cc_start: 0.8688 (mp0) cc_final: 0.8012 (mp0) REVERT: C 374 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8396 (tp-100) REVERT: C 378 GLN cc_start: 0.8895 (mt0) cc_final: 0.8614 (mt0) REVERT: C 397 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8840 (mt-10) REVERT: C 407 LYS cc_start: 0.9066 (tptt) cc_final: 0.8577 (tppt) REVERT: C 414 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8549 (mm-30) REVERT: D 30 ARG cc_start: 0.8697 (mtp-110) cc_final: 0.8469 (mtm-85) REVERT: D 347 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8276 (ttm-80) REVERT: E 265 ASP cc_start: 0.8917 (t0) cc_final: 0.8567 (t70) REVERT: E 329 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: E 380 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7980 (mtm) REVERT: F 193 GLN cc_start: 0.7962 (pt0) cc_final: 0.7595 (pp30) REVERT: F 205 MET cc_start: 0.8260 (mtm) cc_final: 0.8002 (ttp) REVERT: F 244 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8197 (mm-30) REVERT: F 272 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8457 (mtt180) REVERT: F 333 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8718 (pm20) REVERT: F 334 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8613 (tm-30) REVERT: F 335 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: F 405 MET cc_start: 0.8614 (ptt) cc_final: 0.8323 (pp-130) REVERT: F 416 MET cc_start: 0.2560 (OUTLIER) cc_final: 0.2244 (pp-130) outliers start: 28 outliers final: 12 residues processed: 272 average time/residue: 1.8875 time to fit residues: 562.5831 Evaluate side-chains 273 residues out of total 2143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 253 time to evaluate : 2.449 ------------------------------------------------------------------------------- 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 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 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 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 416 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.7864 > 50: distance: 16 - 21: 14.893 distance: 21 - 22: 10.065 distance: 22 - 23: 12.461 distance: 22 - 25: 8.335 distance: 23 - 24: 24.217 distance: 23 - 30: 18.618 distance: 25 - 26: 7.003 distance: 26 - 27: 9.453 distance: 27 - 28: 8.070 distance: 28 - 29: 11.226 distance: 30 - 31: 17.478 distance: 31 - 32: 13.965 distance: 31 - 34: 20.395 distance: 32 - 33: 25.478 distance: 32 - 38: 10.939 distance: 34 - 35: 10.982 distance: 34 - 36: 17.119 distance: 35 - 37: 13.369 distance: 38 - 39: 9.132 distance: 39 - 42: 4.165 distance: 40 - 41: 4.294 distance: 43 - 44: 4.700 distance: 43 - 45: 10.911 distance: 46 - 47: 11.822 distance: 47 - 48: 5.370 distance: 47 - 50: 7.155 distance: 48 - 49: 28.693 distance: 48 - 57: 12.351 distance: 51 - 52: 4.795 distance: 54 - 56: 4.432 distance: 57 - 58: 5.458 distance: 58 - 59: 7.124 distance: 58 - 61: 4.329 distance: 59 - 60: 14.112 distance: 59 - 66: 5.521 distance: 61 - 62: 8.788 distance: 62 - 63: 3.639 distance: 63 - 64: 10.935 distance: 63 - 65: 16.958 distance: 66 - 67: 5.528 distance: 67 - 68: 13.578 distance: 67 - 70: 7.626 distance: 68 - 69: 16.596 distance: 68 - 74: 18.340 distance: 71 - 72: 4.546 distance: 71 - 73: 8.888 distance: 74 - 75: 4.256 distance: 75 - 76: 19.948 distance: 75 - 78: 12.811 distance: 76 - 77: 17.790 distance: 78 - 79: 17.295 distance: 79 - 80: 18.608 distance: 79 - 81: 15.727 distance: 83 - 84: 6.919 distance: 83 - 86: 12.565 distance: 84 - 85: 12.302 distance: 84 - 89: 8.617 distance: 86 - 87: 22.315 distance: 86 - 88: 35.706 distance: 89 - 90: 17.736 distance: 89 - 95: 3.873 distance: 90 - 91: 13.581 distance: 90 - 93: 11.665 distance: 91 - 92: 11.170 distance: 91 - 96: 12.731 distance: 93 - 94: 16.635 distance: 94 - 95: 8.756 distance: 96 - 97: 7.071 distance: 97 - 98: 3.118 distance: 97 - 100: 10.614 distance: 98 - 99: 14.580 distance: 98 - 104: 28.575 distance: 100 - 101: 22.449 distance: 101 - 102: 5.911 distance: 101 - 103: 37.470