Starting phenix.real_space_refine on Mon May 4 10:34:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yai_72728/05_2026/9yai_72728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yai_72728/05_2026/9yai_72728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yai_72728/05_2026/9yai_72728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yai_72728/05_2026/9yai_72728.map" model { file = "/net/cci-nas-00/data/ceres_data/9yai_72728/05_2026/9yai_72728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yai_72728/05_2026/9yai_72728.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 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 16 5.49 5 Mg 3 5.21 5 S 130 5.16 5 C 12340 2.51 5 N 3380 2.21 5 O 3880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19749 Number of models: 1 Model: "" Number of chains: 14 Chain: "K" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2861 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 13, 'TRANS': 350} Chain breaks: 1 Chain: "N" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2940 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 13, 'TRANS': 360} Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3376 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Chain: "E" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3450 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain: "I" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3376 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.96, per 1000 atoms: 0.25 Number of scatterers: 19749 At special positions: 0 Unit cell: (94.424, 109.446, 196.359, 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 130 16.00 P 16 15.00 Mg 3 11.99 O 3880 8.00 N 3380 7.00 C 12340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 901.9 milliseconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4612 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 20 sheets defined 48.4% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'K' and resid 16 through 23 Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 133 removed outlier: 3.679A pdb=" N GLN K 121 " --> pdb=" O GLY K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 163 Processing helix chain 'K' and resid 188 through 203 removed outlier: 3.515A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 259 Processing helix chain 'K' and resid 262 through 291 Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 removed outlier: 3.682A pdb=" N GLY K 320 " --> pdb=" O ARG K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 337 through 354 Processing helix chain 'K' and resid 365 through 375 Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 69 through 77 Processing helix chain 'N' and resid 77 through 87 removed outlier: 3.794A pdb=" N GLU N 87 " --> pdb=" O GLN N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 108 Processing helix chain 'N' and resid 117 through 134 Processing helix chain 'N' and resid 188 through 202 removed outlier: 3.565A pdb=" N ALA N 202 " --> pdb=" O SER N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 291 Processing helix chain 'N' and resid 309 through 315 Processing helix chain 'N' and resid 315 through 320 Processing helix chain 'N' and resid 334 through 336 No H-bonds generated for 'chain 'N' and resid 334 through 336' Processing helix chain 'N' and resid 337 through 351 removed outlier: 4.338A pdb=" N ALA N 351 " --> pdb=" O TYR N 347 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 375 Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 36 through 43 removed outlier: 4.188A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.485A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.516A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.267A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.760A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.571A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 4.065A pdb=" N GLU A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.841A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.001A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.189A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.315A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 125 removed outlier: 3.951A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.610A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.688A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.988A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.718A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.208A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.064A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.846A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.955A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 removed outlier: 3.717A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.588A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 4.482A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.752A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.303A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.729A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 337 Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.638A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG E 390 " --> pdb=" O GLU E 386 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.820A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 435 removed outlier: 4.137A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.689A pdb=" N GLU I 45 " --> pdb=" O ASP I 41 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 41 through 46' Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 69 through 78 removed outlier: 4.353A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 107 through 127 removed outlier: 3.834A pdb=" N GLU I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS I 127 " --> pdb=" O GLU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 Processing helix chain 'I' and resid 180 through 193 removed outlier: 3.577A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.802A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 242 removed outlier: 3.981A pdb=" N ARG I 241 " --> pdb=" O THR I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 275 through 279 removed outlier: 4.075A pdb=" N GLN I 279 " --> pdb=" O ARG I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 295 Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 removed outlier: 3.563A pdb=" N VAL I 326 " --> pdb=" O SER I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 341 Processing helix chain 'I' and resid 373 through 390 removed outlier: 4.154A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG I 390 " --> pdb=" O THR I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 427 removed outlier: 3.847A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.747A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.747A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL K 142 " --> pdb=" O VAL K 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AA6, first strand: chain 'N' and resid 54 through 57 removed outlier: 6.698A pdb=" N CYS N 92 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL N 328 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE N 94 " --> pdb=" O VAL N 328 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA N 330 " --> pdb=" O PHE N 94 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR N 96 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 54 through 57 removed outlier: 6.698A pdb=" N CYS N 92 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL N 328 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE N 94 " --> pdb=" O VAL N 328 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA N 330 " --> pdb=" O PHE N 94 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR N 96 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 28 through 31 Processing sheet with id=AA9, first strand: chain 'N' and resid 168 through 171 Processing sheet with id=AB1, first strand: chain 'N' and resid 205 through 206 removed outlier: 3.615A pdb=" N ALA N 206 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.346A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 139 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.937A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N ILE B 163 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.242A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.538A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.237A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS E 139 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS E 200 " --> pdb=" O LYS E 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 269 through 272 Processing sheet with id=AC1, first strand: chain 'I' and resid 90 through 92 removed outlier: 7.859A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ASN I 165 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE I 133 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N HIS I 137 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 13.768A pdb=" N ASP I 203 " --> pdb=" O PHE I 270 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 51 through 53 1052 hydrogen bonds defined for protein. 3021 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3682 1.33 - 1.45: 5173 1.45 - 1.57: 11070 1.57 - 1.70: 31 1.70 - 1.82: 213 Bond restraints: 20169 Sorted by residual: bond pdb=" CA ILE K 236 " pdb=" C ILE K 236 " ideal model delta sigma weight residual 1.522 1.496 0.026 1.21e-02 6.83e+03 4.78e+00 bond pdb=" CA LEU N 285 " pdb=" C LEU N 285 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.29e-02 6.01e+03 4.61e+00 bond pdb=" CA SER N 283 " pdb=" C SER N 283 " ideal model delta sigma weight residual 1.524 1.498 0.025 1.27e-02 6.20e+03 3.98e+00 bond pdb=" CA GLU K 371 " pdb=" C GLU K 371 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.44e-02 4.82e+03 3.59e+00 bond pdb=" CB ASP K 23 " pdb=" CG ASP K 23 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.44e+00 ... (remaining 20164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 26803 2.33 - 4.67: 487 4.67 - 7.00: 84 7.00 - 9.34: 7 9.34 - 11.67: 3 Bond angle restraints: 27384 Sorted by residual: angle pdb=" C PHE N 303 " pdb=" N ILE N 304 " pdb=" CA ILE N 304 " ideal model delta sigma weight residual 122.59 119.22 3.37 7.20e-01 1.93e+00 2.19e+01 angle pdb=" N ASN K 366 " pdb=" CA ASN K 366 " pdb=" C ASN K 366 " ideal model delta sigma weight residual 111.28 106.24 5.04 1.09e+00 8.42e-01 2.13e+01 angle pdb=" C GLU K 362 " pdb=" CA GLU K 362 " pdb=" CB GLU K 362 " ideal model delta sigma weight residual 115.89 109.81 6.08 1.32e+00 5.74e-01 2.12e+01 angle pdb=" N LEU N 345 " pdb=" CA LEU N 345 " pdb=" C LEU N 345 " ideal model delta sigma weight residual 111.28 106.34 4.94 1.09e+00 8.42e-01 2.06e+01 angle pdb=" N GLU K 239 " pdb=" CA GLU K 239 " pdb=" C GLU K 239 " ideal model delta sigma weight residual 111.24 116.82 -5.58 1.29e+00 6.01e-01 1.87e+01 ... (remaining 27379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 11951 34.78 - 69.56: 299 69.56 - 104.34: 32 104.34 - 139.12: 6 139.12 - 173.90: 2 Dihedral angle restraints: 12290 sinusoidal: 5109 harmonic: 7181 Sorted by residual: dihedral pdb=" C4' GTP A 501 " pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual -99.13 74.78 -173.90 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -164.49 -126.24 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -19.76 124.35 1 2.00e+01 2.50e-03 3.75e+01 ... (remaining 12287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2358 0.049 - 0.099: 502 0.099 - 0.148: 138 0.148 - 0.198: 4 0.198 - 0.247: 4 Chirality restraints: 3006 Sorted by residual: chirality pdb=" C21 TA1 I 502 " pdb=" C20 TA1 I 502 " pdb=" C24 TA1 I 502 " pdb=" O09 TA1 I 502 " both_signs ideal model delta sigma weight residual False -2.30 -2.05 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C10 TA1 B 502 " pdb=" C02 TA1 B 502 " pdb=" C11 TA1 B 502 " pdb=" C18 TA1 B 502 " both_signs ideal model delta sigma weight residual False 2.54 2.33 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3003 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 31 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO I 32 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO I 32 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 32 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 249 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" CG ASP I 249 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP I 249 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP I 249 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 255 " -0.012 2.00e-02 2.50e+03 1.91e-02 6.40e+00 pdb=" CG PHE E 255 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE E 255 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE E 255 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE E 255 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 255 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 255 " 0.000 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 25 2.52 - 3.12: 15154 3.12 - 3.71: 31114 3.71 - 4.31: 43939 4.31 - 4.90: 74710 Nonbonded interactions: 164942 Sorted by model distance: nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 1.926 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.926 2.170 nonbonded pdb=" OG SER K 104 " pdb="MG MG K 501 " model vdw 1.957 2.170 nonbonded pdb=" OD2 ASP K 248 " pdb="MG MG K 501 " model vdw 1.963 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.966 2.170 ... (remaining 164937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 1 through 440 or resid 501 through 502)) } ncs_group { reference = chain 'B' selection = chain 'I' } ncs_group { reference = (chain 'K' and resid 4 through 375) selection = (chain 'N' and (resid 4 through 292 or resid 301 through 375)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 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: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.240 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.004 0.049 20169 Z= 0.205 Angle : 0.767 11.673 27384 Z= 0.405 Chirality : 0.045 0.247 3006 Planarity : 0.005 0.070 3552 Dihedral : 15.579 173.905 7678 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 1.41 % Allowed : 11.67 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2464 helix: 1.10 (0.16), residues: 1022 sheet: -0.68 (0.25), residues: 409 loop : -0.88 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 306 TYR 0.011 0.001 TYR N 96 PHE 0.043 0.001 PHE E 255 TRP 0.011 0.001 TRP E 21 HIS 0.011 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00435 (20169) covalent geometry : angle 0.76688 (27384) hydrogen bonds : bond 0.15648 ( 980) hydrogen bonds : angle 6.38396 ( 3021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 0.751 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: K 81 MET cc_start: 0.8381 (mmm) cc_final: 0.7665 (mmm) REVERT: N 13 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7627 (ttp80) REVERT: N 20 MET cc_start: 0.8908 (mmt) cc_final: 0.8529 (mtt) REVERT: N 138 MET cc_start: 0.8728 (mmm) cc_final: 0.8321 (mmm) REVERT: N 270 ASN cc_start: 0.8898 (m-40) cc_final: 0.8475 (m-40) REVERT: N 296 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6771 (mmtt) REVERT: A 75 ILE cc_start: 0.9198 (mm) cc_final: 0.8825 (mt) REVERT: A 123 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7947 (tpp-160) REVERT: A 155 GLU cc_start: 0.8842 (tt0) cc_final: 0.8161 (tp30) REVERT: A 207 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: A 211 ASP cc_start: 0.8553 (t0) cc_final: 0.8208 (t0) REVERT: A 258 ASN cc_start: 0.9040 (m-40) cc_final: 0.8622 (m110) REVERT: A 326 LYS cc_start: 0.6398 (mttt) cc_final: 0.5426 (mttp) REVERT: A 332 ILE cc_start: 0.9448 (mt) cc_final: 0.9213 (mp) REVERT: A 357 TYR cc_start: 0.8995 (m-80) cc_final: 0.8749 (m-80) REVERT: A 411 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8405 (mt-10) REVERT: B 147 MET cc_start: 0.8664 (tpp) cc_final: 0.8298 (tpp) REVERT: B 195 ASN cc_start: 0.8707 (m-40) cc_final: 0.8331 (m-40) REVERT: B 212 PHE cc_start: 0.8686 (m-80) cc_final: 0.8474 (m-80) REVERT: B 328 GLU cc_start: 0.8605 (tp30) cc_final: 0.8231 (tp30) REVERT: B 347 ASN cc_start: 0.8679 (t0) cc_final: 0.8384 (t0) REVERT: E 155 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8685 (mt-10) REVERT: E 196 GLU cc_start: 0.9049 (tp30) cc_final: 0.8698 (tp30) REVERT: E 311 LYS cc_start: 0.8742 (mttt) cc_final: 0.8434 (mtmm) REVERT: E 327 ASP cc_start: 0.8863 (m-30) cc_final: 0.8564 (m-30) REVERT: E 357 TYR cc_start: 0.8852 (m-80) cc_final: 0.8516 (m-80) REVERT: E 420 GLU cc_start: 0.8625 (tt0) cc_final: 0.8388 (tt0) REVERT: I 181 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8885 (mt-10) REVERT: I 295 ASP cc_start: 0.8832 (t0) cc_final: 0.8495 (t70) REVERT: I 328 GLU cc_start: 0.7308 (pt0) cc_final: 0.6907 (pt0) REVERT: I 332 ASN cc_start: 0.8655 (m-40) cc_final: 0.8391 (m110) REVERT: I 375 GLN cc_start: 0.9080 (pt0) cc_final: 0.8847 (pt0) REVERT: I 414 ASN cc_start: 0.9196 (t0) cc_final: 0.8951 (t0) REVERT: I 426 GLN cc_start: 0.7762 (tt0) cc_final: 0.7019 (pt0) outliers start: 30 outliers final: 10 residues processed: 320 average time/residue: 0.1530 time to fit residues: 73.8682 Evaluate side-chains 279 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 267 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain K residue 368 LEU Chi-restraints excluded: chain N residue 296 LYS Chi-restraints excluded: chain N residue 297 LYS Chi-restraints excluded: chain N residue 301 THR Chi-restraints excluded: chain N residue 302 ASP Chi-restraints excluded: chain N residue 357 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain I residue 169 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN N 337 ASN N 365 ASN N 366 ASN A 300 ASN B 6 HIS B 131 GLN B 134 GLN E 301 GLN I 424 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.117725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093565 restraints weight = 37414.855| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.89 r_work: 0.3224 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20169 Z= 0.122 Angle : 0.539 9.163 27384 Z= 0.270 Chirality : 0.044 0.577 3006 Planarity : 0.004 0.062 3552 Dihedral : 9.907 179.786 3052 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.55 % Allowed : 11.91 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2464 helix: 1.67 (0.16), residues: 1046 sheet: -0.16 (0.26), residues: 397 loop : -0.79 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 306 TYR 0.009 0.001 TYR N 347 PHE 0.014 0.001 PHE I 167 TRP 0.013 0.001 TRP E 21 HIS 0.010 0.001 HIS I 396 Details of bonding type rmsd covalent geometry : bond 0.00267 (20169) covalent geometry : angle 0.53880 (27384) hydrogen bonds : bond 0.04185 ( 980) hydrogen bonds : angle 4.57319 ( 3021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 81 MET cc_start: 0.8382 (mmm) cc_final: 0.7693 (mmm) REVERT: K 147 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8303 (pp-130) REVERT: N 20 MET cc_start: 0.8881 (mmt) cc_final: 0.8519 (mtt) REVERT: N 138 MET cc_start: 0.8756 (mmm) cc_final: 0.8220 (mmm) REVERT: N 267 GLU cc_start: 0.8383 (tt0) cc_final: 0.8156 (tt0) REVERT: N 270 ASN cc_start: 0.8775 (m-40) cc_final: 0.8256 (m-40) REVERT: N 296 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6844 (mmtt) REVERT: N 362 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5636 (pm20) REVERT: A 75 ILE cc_start: 0.9070 (mm) cc_final: 0.8860 (mm) REVERT: A 123 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7863 (tpp-160) REVERT: A 155 GLU cc_start: 0.8804 (tt0) cc_final: 0.8193 (tp30) REVERT: A 183 GLU cc_start: 0.9096 (tt0) cc_final: 0.8745 (tt0) REVERT: A 211 ASP cc_start: 0.8473 (t0) cc_final: 0.8094 (t0) REVERT: A 258 ASN cc_start: 0.9007 (m-40) cc_final: 0.8547 (m110) REVERT: A 326 LYS cc_start: 0.6489 (mttt) cc_final: 0.5216 (mttp) REVERT: A 357 TYR cc_start: 0.8971 (m-80) cc_final: 0.8729 (m-80) REVERT: A 411 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8273 (mt-10) REVERT: A 433 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8549 (mm-30) REVERT: B 53 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8150 (tm-30) REVERT: B 147 MET cc_start: 0.8553 (tpp) cc_final: 0.8184 (tpp) REVERT: B 212 PHE cc_start: 0.8674 (m-80) cc_final: 0.8384 (m-80) REVERT: B 213 ARG cc_start: 0.8406 (ptp-110) cc_final: 0.8186 (ptp-110) REVERT: B 328 GLU cc_start: 0.8553 (tp30) cc_final: 0.8138 (tp30) REVERT: B 347 ASN cc_start: 0.8547 (t0) cc_final: 0.8345 (t0) REVERT: E 255 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8481 (p90) REVERT: E 327 ASP cc_start: 0.8861 (m-30) cc_final: 0.8445 (m-30) REVERT: E 357 TYR cc_start: 0.8791 (m-80) cc_final: 0.8418 (m-80) REVERT: E 420 GLU cc_start: 0.8626 (tt0) cc_final: 0.8320 (tt0) REVERT: I 111 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8334 (mm-30) REVERT: I 181 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8854 (mt-10) REVERT: I 295 ASP cc_start: 0.8759 (t0) cc_final: 0.8311 (t0) REVERT: I 328 GLU cc_start: 0.7150 (pt0) cc_final: 0.6743 (pt0) REVERT: I 332 ASN cc_start: 0.8580 (m-40) cc_final: 0.8298 (m110) outliers start: 33 outliers final: 16 residues processed: 317 average time/residue: 0.1395 time to fit residues: 68.9518 Evaluate side-chains 280 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 296 LYS Chi-restraints excluded: chain N residue 362 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 398 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 267 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 162 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 230 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 357 ASN A 226 ASN B 14 ASN I 195 ASN I 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.116327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.092111 restraints weight = 37638.191| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.90 r_work: 0.3203 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20169 Z= 0.117 Angle : 0.513 9.819 27384 Z= 0.255 Chirality : 0.042 0.252 3006 Planarity : 0.004 0.061 3552 Dihedral : 9.004 178.442 3033 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.59 % Allowed : 13.36 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2464 helix: 1.85 (0.16), residues: 1042 sheet: 0.12 (0.26), residues: 399 loop : -0.81 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 306 TYR 0.008 0.001 TYR N 150 PHE 0.015 0.001 PHE K 303 TRP 0.022 0.001 TRP N 350 HIS 0.009 0.001 HIS I 396 Details of bonding type rmsd covalent geometry : bond 0.00258 (20169) covalent geometry : angle 0.51335 (27384) hydrogen bonds : bond 0.03670 ( 980) hydrogen bonds : angle 4.28249 ( 3021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 81 MET cc_start: 0.8451 (mmm) cc_final: 0.7724 (mmm) REVERT: K 147 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8264 (pp-130) REVERT: N 13 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6824 (ttp80) REVERT: N 20 MET cc_start: 0.8911 (mmt) cc_final: 0.8541 (mtt) REVERT: N 138 MET cc_start: 0.8778 (mmm) cc_final: 0.8280 (mmm) REVERT: N 261 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7710 (mmmt) REVERT: N 296 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6780 (mmtt) REVERT: N 297 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7194 (pttp) REVERT: N 337 ASN cc_start: 0.9163 (m-40) cc_final: 0.8893 (m-40) REVERT: N 362 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5908 (pm20) REVERT: A 123 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7846 (tpp-160) REVERT: A 155 GLU cc_start: 0.8857 (tt0) cc_final: 0.8234 (tp30) REVERT: A 326 LYS cc_start: 0.6300 (mttt) cc_final: 0.5120 (mttm) REVERT: A 357 TYR cc_start: 0.8992 (m-80) cc_final: 0.8766 (m-80) REVERT: A 411 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8280 (mt-10) REVERT: A 433 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8474 (mm-30) REVERT: B 53 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8187 (tm-30) REVERT: B 164 MET cc_start: 0.8919 (tpt) cc_final: 0.8661 (tpt) REVERT: B 212 PHE cc_start: 0.8631 (m-80) cc_final: 0.8398 (m-80) REVERT: B 213 ARG cc_start: 0.8398 (ptp-110) cc_final: 0.8190 (ptp-110) REVERT: B 328 GLU cc_start: 0.8536 (tp30) cc_final: 0.8315 (tp30) REVERT: E 6 SER cc_start: 0.8742 (t) cc_final: 0.8516 (t) REVERT: E 255 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8126 (p90) REVERT: E 327 ASP cc_start: 0.8857 (m-30) cc_final: 0.8461 (m-30) REVERT: E 357 TYR cc_start: 0.8832 (m-80) cc_final: 0.8464 (m-80) REVERT: E 420 GLU cc_start: 0.8685 (tt0) cc_final: 0.8351 (tt0) REVERT: E 424 ASP cc_start: 0.9027 (t0) cc_final: 0.8756 (t0) REVERT: I 111 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8319 (mm-30) REVERT: I 147 MET cc_start: 0.8481 (ttm) cc_final: 0.8154 (ttm) REVERT: I 181 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8723 (mt-10) REVERT: I 213 ARG cc_start: 0.8536 (ptp-110) cc_final: 0.8321 (ptp-110) REVERT: I 262 ARG cc_start: 0.9064 (mtp85) cc_final: 0.8717 (mtm180) REVERT: I 295 ASP cc_start: 0.8714 (t0) cc_final: 0.8289 (t0) REVERT: I 328 GLU cc_start: 0.7118 (pt0) cc_final: 0.6704 (pt0) REVERT: I 332 ASN cc_start: 0.8551 (m-40) cc_final: 0.8277 (m110) outliers start: 34 outliers final: 17 residues processed: 302 average time/residue: 0.1475 time to fit residues: 68.4020 Evaluate side-chains 281 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain K residue 373 LYS Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 296 LYS Chi-restraints excluded: chain N residue 297 LYS Chi-restraints excluded: chain N residue 362 GLU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 377 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 267 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 122 optimal weight: 0.0470 chunk 237 optimal weight: 0.2980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 200 ASN N 270 ASN N 353 GLN A 11 GLN A 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.110796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085405 restraints weight = 37001.954| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.12 r_work: 0.3215 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20169 Z= 0.106 Angle : 0.491 8.834 27384 Z= 0.245 Chirality : 0.041 0.227 3006 Planarity : 0.004 0.063 3552 Dihedral : 8.875 178.142 3033 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.30 % Allowed : 13.50 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2464 helix: 1.99 (0.16), residues: 1044 sheet: 0.29 (0.26), residues: 399 loop : -0.85 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 306 TYR 0.007 0.001 TYR I 59 PHE 0.011 0.001 PHE K 303 TRP 0.012 0.001 TRP E 21 HIS 0.008 0.001 HIS I 396 Details of bonding type rmsd covalent geometry : bond 0.00234 (20169) covalent geometry : angle 0.49114 (27384) hydrogen bonds : bond 0.03354 ( 980) hydrogen bonds : angle 4.12053 ( 3021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 284 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 81 MET cc_start: 0.8465 (mmm) cc_final: 0.7756 (mmm) REVERT: K 147 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8273 (pp-130) REVERT: N 13 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6764 (ttp80) REVERT: N 20 MET cc_start: 0.8918 (mmt) cc_final: 0.8546 (mtt) REVERT: N 41 LYS cc_start: 0.9368 (mppt) cc_final: 0.9167 (mppt) REVERT: N 138 MET cc_start: 0.8785 (mmm) cc_final: 0.8388 (mmm) REVERT: N 261 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7832 (mmmt) REVERT: N 297 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7193 (pttp) REVERT: N 306 TYR cc_start: 0.7845 (m-80) cc_final: 0.7459 (m-10) REVERT: N 362 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5934 (pm20) REVERT: A 123 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7782 (tpp-160) REVERT: A 155 GLU cc_start: 0.8869 (tt0) cc_final: 0.8271 (tp30) REVERT: A 207 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8177 (tp30) REVERT: A 326 LYS cc_start: 0.6379 (mttt) cc_final: 0.5086 (mttm) REVERT: A 357 TYR cc_start: 0.9012 (m-80) cc_final: 0.8788 (m-80) REVERT: A 411 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8368 (mt-10) REVERT: A 420 GLU cc_start: 0.8388 (tt0) cc_final: 0.8039 (mt-10) REVERT: A 433 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8402 (mm-30) REVERT: B 53 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 212 PHE cc_start: 0.8660 (m-80) cc_final: 0.8409 (m-80) REVERT: B 213 ARG cc_start: 0.8435 (ptp-110) cc_final: 0.8227 (ptp-110) REVERT: E 6 SER cc_start: 0.8751 (t) cc_final: 0.8502 (t) REVERT: E 203 MET cc_start: 0.9264 (mmm) cc_final: 0.8820 (mmm) REVERT: E 255 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.7934 (p90) REVERT: E 327 ASP cc_start: 0.8855 (m-30) cc_final: 0.8478 (m-30) REVERT: E 357 TYR cc_start: 0.8893 (m-80) cc_final: 0.8512 (m-80) REVERT: E 411 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8021 (mm-30) REVERT: E 420 GLU cc_start: 0.8723 (tt0) cc_final: 0.8393 (tt0) REVERT: E 424 ASP cc_start: 0.9011 (t0) cc_final: 0.8762 (t0) REVERT: I 111 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8314 (mm-30) REVERT: I 181 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8840 (mt-10) REVERT: I 262 ARG cc_start: 0.9109 (mtp85) cc_final: 0.8794 (mtm180) REVERT: I 295 ASP cc_start: 0.8725 (t0) cc_final: 0.8303 (t0) REVERT: I 328 GLU cc_start: 0.7173 (pt0) cc_final: 0.6740 (pt0) REVERT: I 332 ASN cc_start: 0.8555 (m-40) cc_final: 0.8266 (m110) outliers start: 49 outliers final: 23 residues processed: 316 average time/residue: 0.1394 time to fit residues: 67.9255 Evaluate side-chains 294 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 297 LYS Chi-restraints excluded: chain N residue 362 GLU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 377 MET Chi-restraints excluded: chain E residue 398 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 267 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 138 optimal weight: 0.9990 chunk 234 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 165 ASN ** K 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.113466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089929 restraints weight = 37636.882| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.82 r_work: 0.3163 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20169 Z= 0.167 Angle : 0.535 8.919 27384 Z= 0.268 Chirality : 0.043 0.215 3006 Planarity : 0.004 0.062 3552 Dihedral : 8.879 175.677 3029 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.30 % Allowed : 13.92 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.17), residues: 2464 helix: 1.97 (0.16), residues: 1032 sheet: 0.33 (0.26), residues: 408 loop : -0.77 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 306 TYR 0.011 0.001 TYR N 96 PHE 0.014 0.001 PHE K 221 TRP 0.011 0.001 TRP A 21 HIS 0.007 0.001 HIS I 396 Details of bonding type rmsd covalent geometry : bond 0.00381 (20169) covalent geometry : angle 0.53484 (27384) hydrogen bonds : bond 0.03771 ( 980) hydrogen bonds : angle 4.19522 ( 3021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 275 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 29 GLN cc_start: 0.8106 (mp10) cc_final: 0.7885 (mp10) REVERT: K 81 MET cc_start: 0.8507 (mmm) cc_final: 0.7785 (mmm) REVERT: K 147 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8357 (pp-130) REVERT: N 13 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.6793 (ttp80) REVERT: N 20 MET cc_start: 0.8956 (mmt) cc_final: 0.8622 (mtt) REVERT: N 138 MET cc_start: 0.8796 (mmm) cc_final: 0.8387 (mmm) REVERT: N 306 TYR cc_start: 0.7824 (m-80) cc_final: 0.6848 (m-10) REVERT: A 6 SER cc_start: 0.8953 (t) cc_final: 0.8637 (t) REVERT: A 155 GLU cc_start: 0.8887 (tt0) cc_final: 0.8249 (tm-30) REVERT: A 196 GLU cc_start: 0.9068 (tp30) cc_final: 0.8787 (tp30) REVERT: A 207 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: A 211 ASP cc_start: 0.8453 (t0) cc_final: 0.8112 (t0) REVERT: A 411 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8345 (mt-10) REVERT: A 420 GLU cc_start: 0.8445 (tt0) cc_final: 0.8146 (mt-10) REVERT: A 433 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8384 (mm-30) REVERT: B 212 PHE cc_start: 0.8672 (m-80) cc_final: 0.8454 (m-80) REVERT: E 6 SER cc_start: 0.8852 (t) cc_final: 0.8239 (p) REVERT: E 203 MET cc_start: 0.9198 (mmm) cc_final: 0.8751 (mmm) REVERT: E 255 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8291 (p90) REVERT: E 327 ASP cc_start: 0.8876 (m-30) cc_final: 0.8507 (m-30) REVERT: E 357 TYR cc_start: 0.8852 (m-80) cc_final: 0.8474 (m-80) REVERT: E 411 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8202 (mm-30) REVERT: E 420 GLU cc_start: 0.8728 (tt0) cc_final: 0.8472 (tt0) REVERT: E 424 ASP cc_start: 0.9054 (t0) cc_final: 0.8747 (t0) REVERT: I 45 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8542 (mm-30) REVERT: I 147 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8351 (ttm) REVERT: I 181 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8810 (mt-10) REVERT: I 295 ASP cc_start: 0.8753 (t0) cc_final: 0.8345 (t0) REVERT: I 306 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7916 (mtt180) REVERT: I 328 GLU cc_start: 0.7254 (pt0) cc_final: 0.6820 (pt0) REVERT: I 332 ASN cc_start: 0.8561 (m-40) cc_final: 0.8269 (m110) outliers start: 49 outliers final: 31 residues processed: 309 average time/residue: 0.1384 time to fit residues: 66.2737 Evaluate side-chains 296 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 230 HIS Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 377 MET Chi-restraints excluded: chain E residue 398 MET Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 354 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 239 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN A 15 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN I 6 HIS I 105 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.104957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.080838 restraints weight = 37365.433| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.91 r_work: 0.3108 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20169 Z= 0.253 Angle : 0.601 7.795 27384 Z= 0.304 Chirality : 0.045 0.241 3006 Planarity : 0.004 0.063 3552 Dihedral : 9.025 172.969 3029 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.72 % Allowed : 14.39 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2464 helix: 1.79 (0.16), residues: 1032 sheet: 0.22 (0.26), residues: 416 loop : -0.90 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 339 TYR 0.014 0.001 TYR K 146 PHE 0.018 0.002 PHE I 266 TRP 0.013 0.002 TRP A 21 HIS 0.006 0.001 HIS I 396 Details of bonding type rmsd covalent geometry : bond 0.00579 (20169) covalent geometry : angle 0.60116 (27384) hydrogen bonds : bond 0.04247 ( 980) hydrogen bonds : angle 4.37059 ( 3021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 254 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 29 GLN cc_start: 0.8258 (mp10) cc_final: 0.8022 (mp10) REVERT: K 81 MET cc_start: 0.8494 (mmm) cc_final: 0.7734 (mmm) REVERT: K 327 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.7177 (tpp) REVERT: N 20 MET cc_start: 0.9031 (mmt) cc_final: 0.8673 (mtt) REVERT: N 138 MET cc_start: 0.8854 (mmm) cc_final: 0.8295 (mmm) REVERT: N 288 MET cc_start: 0.8445 (tpp) cc_final: 0.8233 (ttm) REVERT: A 123 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7898 (tpm170) REVERT: A 155 GLU cc_start: 0.8864 (tt0) cc_final: 0.8241 (tm-30) REVERT: A 196 GLU cc_start: 0.9137 (tp30) cc_final: 0.8876 (tp30) REVERT: A 207 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: A 211 ASP cc_start: 0.8474 (t0) cc_final: 0.8130 (t0) REVERT: A 411 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8385 (mt-10) REVERT: A 433 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8366 (mm-30) REVERT: E 6 SER cc_start: 0.8963 (t) cc_final: 0.8461 (p) REVERT: E 113 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: E 203 MET cc_start: 0.9184 (mmm) cc_final: 0.8813 (mmm) REVERT: E 205 ASP cc_start: 0.8224 (t0) cc_final: 0.7844 (t70) REVERT: E 255 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8710 (p90) REVERT: E 327 ASP cc_start: 0.8981 (m-30) cc_final: 0.8622 (m-30) REVERT: E 357 TYR cc_start: 0.8890 (m-80) cc_final: 0.8583 (m-80) REVERT: E 411 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8186 (mm-30) REVERT: E 420 GLU cc_start: 0.8747 (tt0) cc_final: 0.8540 (tt0) REVERT: E 424 ASP cc_start: 0.9072 (t0) cc_final: 0.8772 (t0) REVERT: E 438 ASP cc_start: 0.9099 (p0) cc_final: 0.8835 (p0) REVERT: I 45 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8582 (mm-30) REVERT: I 147 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8307 (ttm) REVERT: I 295 ASP cc_start: 0.8746 (t0) cc_final: 0.8328 (t0) REVERT: I 328 GLU cc_start: 0.7335 (pt0) cc_final: 0.6896 (pt0) REVERT: I 332 ASN cc_start: 0.8597 (m-40) cc_final: 0.8329 (m110) outliers start: 58 outliers final: 37 residues processed: 295 average time/residue: 0.1397 time to fit residues: 64.3131 Evaluate side-chains 282 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 349 ASP Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 356 CYS Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 398 MET Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 131 GLN Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 354 CYS Chi-restraints excluded: chain I residue 417 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 55 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN E 256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.107150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.082689 restraints weight = 37049.573| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.02 r_work: 0.3138 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20169 Z= 0.139 Angle : 0.528 7.857 27384 Z= 0.266 Chirality : 0.042 0.210 3006 Planarity : 0.004 0.062 3552 Dihedral : 8.939 175.798 3029 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.44 % Allowed : 15.05 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2464 helix: 1.95 (0.16), residues: 1033 sheet: 0.34 (0.26), residues: 405 loop : -0.84 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 254 TYR 0.009 0.001 TYR A 312 PHE 0.011 0.001 PHE K 221 TRP 0.014 0.001 TRP E 21 HIS 0.006 0.001 HIS I 396 Details of bonding type rmsd covalent geometry : bond 0.00315 (20169) covalent geometry : angle 0.52787 (27384) hydrogen bonds : bond 0.03621 ( 980) hydrogen bonds : angle 4.21149 ( 3021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 257 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: K 29 GLN cc_start: 0.8232 (mp10) cc_final: 0.7988 (mp10) REVERT: K 81 MET cc_start: 0.8476 (mmm) cc_final: 0.7730 (mmm) REVERT: K 138 MET cc_start: 0.5395 (tpp) cc_final: 0.5124 (tpp) REVERT: K 252 SER cc_start: 0.9466 (p) cc_final: 0.9223 (p) REVERT: K 327 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7071 (tpp) REVERT: N 13 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.6950 (ttp80) REVERT: N 20 MET cc_start: 0.9028 (mmt) cc_final: 0.8663 (mtt) REVERT: N 138 MET cc_start: 0.8858 (mmm) cc_final: 0.8467 (mmm) REVERT: N 288 MET cc_start: 0.8508 (tpp) cc_final: 0.8254 (ttm) REVERT: N 306 TYR cc_start: 0.7740 (m-80) cc_final: 0.7171 (m-10) REVERT: A 123 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7764 (tpm170) REVERT: A 155 GLU cc_start: 0.8857 (tt0) cc_final: 0.8222 (tm-30) REVERT: A 196 GLU cc_start: 0.9157 (tp30) cc_final: 0.8902 (tp30) REVERT: A 207 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8225 (tp30) REVERT: A 211 ASP cc_start: 0.8496 (t0) cc_final: 0.8062 (t0) REVERT: A 411 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8389 (mt-10) REVERT: A 433 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8199 (mm-30) REVERT: E 6 SER cc_start: 0.8925 (t) cc_final: 0.8388 (p) REVERT: E 113 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: E 203 MET cc_start: 0.9098 (mmm) cc_final: 0.8702 (mmm) REVERT: E 205 ASP cc_start: 0.8251 (t0) cc_final: 0.7932 (t70) REVERT: E 255 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8514 (p90) REVERT: E 327 ASP cc_start: 0.8888 (m-30) cc_final: 0.8530 (m-30) REVERT: E 357 TYR cc_start: 0.8927 (m-80) cc_final: 0.8581 (m-80) REVERT: E 377 MET cc_start: 0.8925 (ttt) cc_final: 0.8590 (ttp) REVERT: E 411 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7800 (mm-30) REVERT: E 424 ASP cc_start: 0.9035 (t0) cc_final: 0.8739 (t0) REVERT: E 438 ASP cc_start: 0.9093 (p0) cc_final: 0.8815 (p0) REVERT: I 130 LEU cc_start: 0.8182 (tp) cc_final: 0.7940 (tp) REVERT: I 147 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8133 (ttm) REVERT: I 306 ARG cc_start: 0.8189 (mtt90) cc_final: 0.7744 (mtt90) REVERT: I 328 GLU cc_start: 0.7253 (pt0) cc_final: 0.6813 (pt0) REVERT: I 332 ASN cc_start: 0.8574 (m-40) cc_final: 0.8281 (m110) outliers start: 52 outliers final: 33 residues processed: 292 average time/residue: 0.1361 time to fit residues: 62.1751 Evaluate side-chains 293 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 230 HIS Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 267 GLU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 398 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 354 CYS Chi-restraints excluded: chain I residue 417 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 25 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 189 optimal weight: 0.0770 chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 0.1980 chunk 134 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 6 optimal weight: 7.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.108257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.084014 restraints weight = 36686.792| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.99 r_work: 0.3160 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20169 Z= 0.119 Angle : 0.515 8.014 27384 Z= 0.259 Chirality : 0.042 0.203 3006 Planarity : 0.004 0.062 3552 Dihedral : 8.846 175.939 3029 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.30 % Allowed : 15.85 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2464 helix: 2.02 (0.16), residues: 1039 sheet: 0.50 (0.26), residues: 419 loop : -0.80 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 215 TYR 0.009 0.001 TYR A 312 PHE 0.018 0.001 PHE K 303 TRP 0.015 0.001 TRP E 21 HIS 0.006 0.001 HIS I 396 Details of bonding type rmsd covalent geometry : bond 0.00270 (20169) covalent geometry : angle 0.51463 (27384) hydrogen bonds : bond 0.03409 ( 980) hydrogen bonds : angle 4.12805 ( 3021) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 267 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: K 29 GLN cc_start: 0.8443 (mp10) cc_final: 0.8144 (mp10) REVERT: K 81 MET cc_start: 0.8486 (mmm) cc_final: 0.7784 (mmm) REVERT: K 147 MET cc_start: 0.8819 (ppp) cc_final: 0.8227 (ppp) REVERT: K 252 SER cc_start: 0.9459 (p) cc_final: 0.9214 (p) REVERT: K 327 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.7106 (tpp) REVERT: N 13 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.6962 (ttp80) REVERT: N 20 MET cc_start: 0.8995 (mmt) cc_final: 0.8645 (mtt) REVERT: N 138 MET cc_start: 0.8824 (mmm) cc_final: 0.8447 (mmm) REVERT: N 288 MET cc_start: 0.8550 (tpp) cc_final: 0.8253 (ttm) REVERT: N 306 TYR cc_start: 0.7689 (m-80) cc_final: 0.7134 (m-10) REVERT: A 123 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7703 (tpm170) REVERT: A 155 GLU cc_start: 0.8834 (tt0) cc_final: 0.8199 (tm-30) REVERT: A 196 GLU cc_start: 0.9128 (tp30) cc_final: 0.8875 (tp30) REVERT: A 207 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8235 (tp30) REVERT: A 326 LYS cc_start: 0.6489 (mttt) cc_final: 0.5248 (mttm) REVERT: A 411 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8392 (mt-10) REVERT: A 433 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8211 (mm-30) REVERT: E 6 SER cc_start: 0.8923 (t) cc_final: 0.8345 (p) REVERT: E 113 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: E 203 MET cc_start: 0.9141 (mmm) cc_final: 0.8718 (mmm) REVERT: E 205 ASP cc_start: 0.8218 (t0) cc_final: 0.7903 (t70) REVERT: E 215 ARG cc_start: 0.8750 (ttm110) cc_final: 0.8511 (ttp-110) REVERT: E 255 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8398 (p90) REVERT: E 327 ASP cc_start: 0.8868 (m-30) cc_final: 0.8532 (m-30) REVERT: E 357 TYR cc_start: 0.8938 (m-80) cc_final: 0.8489 (m-80) REVERT: E 377 MET cc_start: 0.8924 (ttt) cc_final: 0.8599 (ttp) REVERT: E 411 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7779 (mm-30) REVERT: E 424 ASP cc_start: 0.9037 (t0) cc_final: 0.8747 (t0) REVERT: E 438 ASP cc_start: 0.9084 (p0) cc_final: 0.8808 (p0) REVERT: I 130 LEU cc_start: 0.8159 (tp) cc_final: 0.7902 (tp) REVERT: I 209 ASP cc_start: 0.8805 (t70) cc_final: 0.8102 (t70) REVERT: I 213 ARG cc_start: 0.8520 (ptp-110) cc_final: 0.7940 (ptp-110) REVERT: I 225 LEU cc_start: 0.9404 (mp) cc_final: 0.9198 (mp) REVERT: I 295 ASP cc_start: 0.8708 (t0) cc_final: 0.8262 (t0) REVERT: I 306 ARG cc_start: 0.8220 (mtt90) cc_final: 0.7777 (mtt90) REVERT: I 328 GLU cc_start: 0.7332 (pt0) cc_final: 0.6916 (pt0) REVERT: I 332 ASN cc_start: 0.8573 (m-40) cc_final: 0.8271 (m110) outliers start: 49 outliers final: 35 residues processed: 303 average time/residue: 0.1332 time to fit residues: 63.3585 Evaluate side-chains 297 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 398 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 354 CYS Chi-restraints excluded: chain I residue 417 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 228 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 205 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.084268 restraints weight = 36489.871| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.95 r_work: 0.3166 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20169 Z= 0.119 Angle : 0.526 8.993 27384 Z= 0.262 Chirality : 0.042 0.263 3006 Planarity : 0.004 0.062 3552 Dihedral : 8.788 175.874 3029 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.34 % Allowed : 15.75 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2464 helix: 2.04 (0.16), residues: 1039 sheet: 0.55 (0.26), residues: 424 loop : -0.78 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 254 TYR 0.011 0.001 TYR A 312 PHE 0.013 0.001 PHE B 212 TRP 0.021 0.001 TRP E 388 HIS 0.006 0.001 HIS I 396 Details of bonding type rmsd covalent geometry : bond 0.00270 (20169) covalent geometry : angle 0.52566 (27384) hydrogen bonds : bond 0.03351 ( 980) hydrogen bonds : angle 4.09625 ( 3021) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: K 29 GLN cc_start: 0.8347 (mp10) cc_final: 0.7993 (mp10) REVERT: K 81 MET cc_start: 0.8486 (mmm) cc_final: 0.7786 (mmm) REVERT: K 147 MET cc_start: 0.8791 (ppp) cc_final: 0.8130 (ppp) REVERT: K 252 SER cc_start: 0.9454 (p) cc_final: 0.9211 (p) REVERT: K 327 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7087 (tpp) REVERT: N 13 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6845 (ttp80) REVERT: N 20 MET cc_start: 0.9001 (mmt) cc_final: 0.8649 (mtt) REVERT: N 138 MET cc_start: 0.8811 (mmm) cc_final: 0.8431 (mmm) REVERT: N 148 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: N 288 MET cc_start: 0.8581 (tpp) cc_final: 0.8249 (ttm) REVERT: N 306 TYR cc_start: 0.7624 (m-80) cc_final: 0.7059 (m-10) REVERT: A 123 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7580 (tpp-160) REVERT: A 155 GLU cc_start: 0.8823 (tt0) cc_final: 0.8203 (tm-30) REVERT: A 196 GLU cc_start: 0.9121 (tp30) cc_final: 0.8868 (tp30) REVERT: A 207 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8249 (tp30) REVERT: A 326 LYS cc_start: 0.6516 (mttt) cc_final: 0.5104 (mttm) REVERT: A 411 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8381 (mt-10) REVERT: A 433 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: E 6 SER cc_start: 0.8913 (t) cc_final: 0.8323 (p) REVERT: E 113 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: E 203 MET cc_start: 0.9131 (mmm) cc_final: 0.8715 (mmm) REVERT: E 205 ASP cc_start: 0.8207 (t0) cc_final: 0.7884 (t70) REVERT: E 215 ARG cc_start: 0.8820 (ttm110) cc_final: 0.8581 (ttp-110) REVERT: E 255 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8323 (p90) REVERT: E 327 ASP cc_start: 0.8816 (m-30) cc_final: 0.8489 (m-30) REVERT: E 357 TYR cc_start: 0.8917 (m-80) cc_final: 0.8472 (m-80) REVERT: E 377 MET cc_start: 0.8923 (ttt) cc_final: 0.8633 (ttp) REVERT: E 411 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7915 (mm-30) REVERT: E 424 ASP cc_start: 0.8992 (t0) cc_final: 0.8718 (t0) REVERT: E 438 ASP cc_start: 0.9077 (p0) cc_final: 0.8795 (p0) REVERT: I 147 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8236 (ttm) REVERT: I 209 ASP cc_start: 0.8765 (t70) cc_final: 0.8014 (t70) REVERT: I 213 ARG cc_start: 0.8479 (ptp-110) cc_final: 0.7886 (ptp-110) REVERT: I 295 ASP cc_start: 0.8727 (t0) cc_final: 0.8273 (t0) REVERT: I 306 ARG cc_start: 0.8205 (mtt90) cc_final: 0.7718 (mtt90) REVERT: I 328 GLU cc_start: 0.7333 (pt0) cc_final: 0.6914 (pt0) REVERT: I 332 ASN cc_start: 0.8572 (m-40) cc_final: 0.8271 (m110) outliers start: 50 outliers final: 36 residues processed: 307 average time/residue: 0.1325 time to fit residues: 63.7938 Evaluate side-chains 303 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 356 CYS Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain E residue 50 ASN Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 398 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 354 CYS Chi-restraints excluded: chain I residue 417 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 158 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 209 optimal weight: 0.3980 chunk 230 optimal weight: 0.5980 chunk 168 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 107 optimal weight: 0.0670 chunk 65 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 225 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 235 ASN N 165 ASN A 11 GLN A 15 GLN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.109207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.084731 restraints weight = 36691.713| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.00 r_work: 0.3181 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20169 Z= 0.108 Angle : 0.523 9.524 27384 Z= 0.260 Chirality : 0.042 0.202 3006 Planarity : 0.004 0.058 3552 Dihedral : 8.753 176.226 3029 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.20 % Allowed : 15.99 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2464 helix: 2.07 (0.16), residues: 1040 sheet: 0.58 (0.26), residues: 424 loop : -0.79 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 254 TYR 0.012 0.001 TYR A 312 PHE 0.016 0.001 PHE E 49 TRP 0.038 0.002 TRP E 388 HIS 0.006 0.001 HIS I 396 Details of bonding type rmsd covalent geometry : bond 0.00242 (20169) covalent geometry : angle 0.52335 (27384) hydrogen bonds : bond 0.03257 ( 980) hydrogen bonds : angle 4.07595 ( 3021) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: K 29 GLN cc_start: 0.8357 (mp10) cc_final: 0.7999 (mp10) REVERT: K 81 MET cc_start: 0.8476 (mmm) cc_final: 0.7776 (mmm) REVERT: K 147 MET cc_start: 0.8816 (ppp) cc_final: 0.8146 (ppp) REVERT: K 327 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7072 (tpp) REVERT: N 13 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.6909 (ttp80) REVERT: N 20 MET cc_start: 0.8992 (mmt) cc_final: 0.8637 (mtt) REVERT: N 138 MET cc_start: 0.8801 (mmm) cc_final: 0.8434 (mmm) REVERT: N 148 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: N 288 MET cc_start: 0.8615 (tpp) cc_final: 0.8283 (ttt) REVERT: N 306 TYR cc_start: 0.7610 (m-80) cc_final: 0.7038 (m-10) REVERT: A 123 ARG cc_start: 0.7992 (tpp80) cc_final: 0.7570 (tpp-160) REVERT: A 155 GLU cc_start: 0.8810 (tt0) cc_final: 0.8184 (tm-30) REVERT: A 196 GLU cc_start: 0.9118 (tp30) cc_final: 0.8864 (tp30) REVERT: A 207 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8240 (tp30) REVERT: A 326 LYS cc_start: 0.6498 (mttt) cc_final: 0.5211 (mttm) REVERT: A 411 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8396 (mt-10) REVERT: A 433 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8199 (mm-30) REVERT: E 6 SER cc_start: 0.8884 (t) cc_final: 0.8272 (p) REVERT: E 113 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: E 203 MET cc_start: 0.9130 (mmm) cc_final: 0.8719 (mmm) REVERT: E 215 ARG cc_start: 0.8806 (ttm110) cc_final: 0.8558 (ttp-110) REVERT: E 255 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8279 (p90) REVERT: E 327 ASP cc_start: 0.8811 (m-30) cc_final: 0.8477 (m-30) REVERT: E 357 TYR cc_start: 0.8897 (m-80) cc_final: 0.8450 (m-80) REVERT: E 377 MET cc_start: 0.8934 (ttt) cc_final: 0.8610 (ttp) REVERT: E 411 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7893 (mm-30) REVERT: E 424 ASP cc_start: 0.8970 (t0) cc_final: 0.8707 (t0) REVERT: E 438 ASP cc_start: 0.9078 (p0) cc_final: 0.8783 (p0) REVERT: I 45 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8534 (mm-30) REVERT: I 147 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8243 (ttm) REVERT: I 209 ASP cc_start: 0.8739 (t70) cc_final: 0.7898 (t70) REVERT: I 213 ARG cc_start: 0.8481 (ptp-110) cc_final: 0.7903 (ptp-110) REVERT: I 295 ASP cc_start: 0.8724 (t0) cc_final: 0.8278 (t0) REVERT: I 306 ARG cc_start: 0.8198 (mtt90) cc_final: 0.7706 (mtt90) REVERT: I 328 GLU cc_start: 0.7309 (pt0) cc_final: 0.6899 (pt0) REVERT: I 332 ASN cc_start: 0.8572 (m-40) cc_final: 0.8272 (m110) outliers start: 47 outliers final: 34 residues processed: 302 average time/residue: 0.1387 time to fit residues: 65.2177 Evaluate side-chains 305 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 262 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 356 CYS Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 398 MET Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 354 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 160 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 4 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.107100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082953 restraints weight = 36943.156| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.95 r_work: 0.3153 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20169 Z= 0.169 Angle : 0.558 9.054 27384 Z= 0.279 Chirality : 0.043 0.226 3006 Planarity : 0.004 0.057 3552 Dihedral : 8.765 174.333 3029 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.30 % Allowed : 16.17 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.17), residues: 2464 helix: 2.02 (0.16), residues: 1031 sheet: 0.43 (0.26), residues: 432 loop : -0.82 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 215 TYR 0.012 0.001 TYR I 200 PHE 0.013 0.001 PHE K 221 TRP 0.031 0.002 TRP E 388 HIS 0.006 0.001 HIS I 396 Details of bonding type rmsd covalent geometry : bond 0.00392 (20169) covalent geometry : angle 0.55794 (27384) hydrogen bonds : bond 0.03667 ( 980) hydrogen bonds : angle 4.18464 ( 3021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3939.13 seconds wall clock time: 68 minutes 52.01 seconds (4132.01 seconds total)