Starting phenix.real_space_refine on Tue Jul 29 09:21:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cft_30347/07_2025/7cft_30347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cft_30347/07_2025/7cft_30347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cft_30347/07_2025/7cft_30347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cft_30347/07_2025/7cft_30347.map" model { file = "/net/cci-nas-00/data/ceres_data/7cft_30347/07_2025/7cft_30347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cft_30347/07_2025/7cft_30347.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 7161 2.51 5 N 1878 2.21 5 O 2133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11283 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3282 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 399} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 451 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: D, F, C, B Time building chain proxies: 6.66, per 1000 atoms: 0.59 Number of scatterers: 11283 At special positions: 0 Unit cell: (107.484, 103.428, 131.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 2133 8.00 N 1878 7.00 C 7161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.02 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.04 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" CA CYS B 61 " - pdb=" SG CYS B 61 " distance=2.84 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.02 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.02 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.04 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.04 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 395 " " NAG A 602 " - " ASN A 368 " " NAG B 601 " - " ASN B 395 " " NAG B 602 " - " ASN B 368 " " NAG C 601 " - " ASN C 395 " " NAG C 602 " - " ASN C 368 " Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.6 seconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 18 sheets defined 31.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 49 through 67 removed outlier: 3.745A pdb=" N ALA A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 4.061A pdb=" N GLN A 102 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 153 through 161 removed outlier: 3.678A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 180 through 184 removed outlier: 4.047A pdb=" N ASP A 183 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.590A pdb=" N TYR A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.888A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.838A pdb=" N ARG A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 322 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.751A pdb=" N LYS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 removed outlier: 3.658A pdb=" N LEU A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.906A pdb=" N LEU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 430 through 440 removed outlier: 4.281A pdb=" N GLY A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 457 removed outlier: 3.519A pdb=" N LEU A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.594A pdb=" N LYS A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 67 removed outlier: 3.745A pdb=" N ALA B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 4.060A pdb=" N GLN B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 103 " --> pdb=" O PHE B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 103' Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.678A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 180 through 184 removed outlier: 4.047A pdb=" N ASP B 183 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 184 " --> pdb=" O ALA B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 184' Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.589A pdb=" N TYR B 229 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.888A pdb=" N GLY B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 removed outlier: 3.838A pdb=" N ARG B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 322 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.752A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 352 removed outlier: 3.659A pdb=" N LEU B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 removed outlier: 3.907A pdb=" N LEU B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 430 through 440 removed outlier: 4.280A pdb=" N GLY B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 457 removed outlier: 3.520A pdb=" N LEU B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.594A pdb=" N LYS B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 67 removed outlier: 3.745A pdb=" N ALA C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.060A pdb=" N GLN C 102 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 103 " --> pdb=" O PHE C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 103' Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.678A pdb=" N ARG C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 180 through 184 removed outlier: 4.047A pdb=" N ASP C 183 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 184 " --> pdb=" O ALA C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 184' Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.590A pdb=" N TYR C 229 " --> pdb=" O GLN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.889A pdb=" N GLY C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 removed outlier: 3.839A pdb=" N ARG C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 322 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.753A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.659A pdb=" N LEU C 350 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 394 removed outlier: 3.907A pdb=" N LEU C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 430 through 440 removed outlier: 4.281A pdb=" N GLY C 437 " --> pdb=" O GLY C 433 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 457 removed outlier: 3.520A pdb=" N LEU C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP C 455 " --> pdb=" O LEU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 462 removed outlier: 3.593A pdb=" N LYS C 462 " --> pdb=" O TYR C 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 77 removed outlier: 3.518A pdb=" N GLU A 421 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N GLU A 418 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU A 277 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE A 420 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG A 279 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLN A 422 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 281 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N LYS A 424 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 274 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A 375 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 373 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 222 removed outlier: 3.516A pdb=" N LEU A 406 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 407 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 409 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 189 removed outlier: 6.734A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 263 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 77 removed outlier: 3.517A pdb=" N GLU B 421 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 274 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 375 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 373 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.516A pdb=" N LEU B 406 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 407 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 409 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.735A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 263 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 77 removed outlier: 3.518A pdb=" N GLU C 421 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N GLU C 418 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU C 277 " --> pdb=" O GLU C 418 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE C 420 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG C 279 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLN C 422 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE C 281 " --> pdb=" O GLN C 422 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N LYS C 424 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 274 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C 375 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 373 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 220 through 222 removed outlier: 3.517A pdb=" N LEU C 406 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL C 407 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 409 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'C' and resid 187 through 189 removed outlier: 6.734A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 263 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB7, first strand: chain 'D' and resid 20 through 22 removed outlier: 3.544A pdb=" N GLY D 36 " --> pdb=" O TYR D 20 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 20 through 22 removed outlier: 3.544A pdb=" N GLY E 36 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 20 through 22 removed outlier: 3.544A pdb=" N GLY F 36 " --> pdb=" O TYR F 20 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 729 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: 3.04 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3536 1.34 - 1.45: 2067 1.45 - 1.57: 5785 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 11532 Sorted by residual: bond pdb=" C VAL C 265 " pdb=" N ALA C 266 " ideal model delta sigma weight residual 1.331 1.235 0.096 2.83e-02 1.25e+03 1.15e+01 bond pdb=" C VAL A 265 " pdb=" N ALA A 266 " ideal model delta sigma weight residual 1.331 1.236 0.095 2.83e-02 1.25e+03 1.13e+01 bond pdb=" C VAL B 265 " pdb=" N ALA B 266 " ideal model delta sigma weight residual 1.331 1.236 0.095 2.83e-02 1.25e+03 1.12e+01 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.23e+00 ... (remaining 11527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 14717 1.92 - 3.84: 750 3.84 - 5.76: 100 5.76 - 7.68: 18 7.68 - 9.60: 9 Bond angle restraints: 15594 Sorted by residual: angle pdb=" C LYS F 17 " pdb=" N PHE F 18 " pdb=" CA PHE F 18 " ideal model delta sigma weight residual 121.31 127.90 -6.59 1.49e+00 4.50e-01 1.96e+01 angle pdb=" C LYS D 17 " pdb=" N PHE D 18 " pdb=" CA PHE D 18 " ideal model delta sigma weight residual 121.31 127.87 -6.56 1.49e+00 4.50e-01 1.94e+01 angle pdb=" C LYS E 17 " pdb=" N PHE E 18 " pdb=" CA PHE E 18 " ideal model delta sigma weight residual 121.31 127.87 -6.56 1.49e+00 4.50e-01 1.94e+01 angle pdb=" C ARG A 201 " pdb=" N ASP A 202 " pdb=" CA ASP A 202 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 angle pdb=" N PHE E 18 " pdb=" CA PHE E 18 " pdb=" C PHE E 18 " ideal model delta sigma weight residual 110.35 115.63 -5.28 1.40e+00 5.10e-01 1.42e+01 ... (remaining 15589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6197 17.97 - 35.93: 697 35.93 - 53.89: 150 53.89 - 71.86: 9 71.86 - 89.82: 12 Dihedral angle restraints: 7065 sinusoidal: 2898 harmonic: 4167 Sorted by residual: dihedral pdb=" CB CYS B 61 " pdb=" CA CYS B 61 " pdb=" SG CYS B 61 " pdb=" CB CYS B 61 " ideal model delta sinusoidal sigma weight residual -86.00 0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS C 290 " pdb=" SG CYS C 290 " pdb=" SG CYS C 367 " pdb=" CB CYS C 367 " ideal model delta sinusoidal sigma weight residual 93.00 142.84 -49.84 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CB CYS A 290 " pdb=" SG CYS A 290 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual 93.00 142.84 -49.84 1 1.00e+01 1.00e-02 3.41e+01 ... (remaining 7062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1240 0.060 - 0.121: 393 0.121 - 0.181: 62 0.181 - 0.242: 6 0.242 - 0.302: 6 Chirality restraints: 1707 Sorted by residual: chirality pdb=" CB VAL B 232 " pdb=" CA VAL B 232 " pdb=" CG1 VAL B 232 " pdb=" CG2 VAL B 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB VAL A 232 " pdb=" CA VAL A 232 " pdb=" CG1 VAL A 232 " pdb=" CG2 VAL A 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB VAL C 232 " pdb=" CA VAL C 232 " pdb=" CG1 VAL C 232 " pdb=" CG2 VAL C 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1704 not shown) Planarity restraints: 2034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 381 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO B 382 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 382 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 382 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 381 " 0.041 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO C 382 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 381 " 0.041 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO A 382 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " 0.035 5.00e-02 4.00e+02 ... (remaining 2031 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 142 2.60 - 3.17: 9071 3.17 - 3.75: 16419 3.75 - 4.32: 22034 4.32 - 4.90: 35729 Nonbonded interactions: 83395 Sorted by model distance: nonbonded pdb=" SG CYS E 50 " pdb=" SG CYS E 55 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS F 50 " pdb=" SG CYS F 55 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS D 50 " pdb=" SG CYS D 55 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS D 12 " pdb=" SG CYS D 37 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS E 41 " pdb=" SG CYS E 49 " model vdw 2.027 3.760 ... (remaining 83390 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: 0.07 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.190 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.011 0.805 11560 Z= 0.538 Angle : 1.291 75.160 15656 Z= 0.681 Chirality : 0.059 0.302 1707 Planarity : 0.006 0.061 2028 Dihedral : 15.043 89.823 4323 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.75 % Allowed : 11.75 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.16), residues: 1413 helix: -4.56 (0.09), residues: 348 sheet: -2.75 (0.32), residues: 213 loop : -3.34 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 233 HIS 0.007 0.002 HIS C 250 PHE 0.021 0.003 PHE A 263 TYR 0.024 0.002 TYR C 417 ARG 0.004 0.001 ARG C 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 6) link_NAG-ASN : angle 2.26263 ( 18) hydrogen bonds : bond 0.30887 ( 273) hydrogen bonds : angle 8.97094 ( 729) SS BOND : bond 0.17169 ( 22) SS BOND : angle 15.64334 ( 44) covalent geometry : bond 0.00862 (11532) covalent geometry : angle 0.98797 (15594) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 THR cc_start: 0.7109 (p) cc_final: 0.6893 (p) REVERT: A 208 LYS cc_start: 0.8899 (mttt) cc_final: 0.8627 (mtpp) REVERT: A 313 ASP cc_start: 0.8385 (t70) cc_final: 0.8056 (t0) REVERT: A 330 MET cc_start: 0.8937 (mtp) cc_final: 0.8693 (mtp) REVERT: B 98 PHE cc_start: 0.8993 (m-80) cc_final: 0.8699 (m-10) REVERT: B 313 ASP cc_start: 0.8346 (t70) cc_final: 0.8095 (t0) REVERT: B 316 THR cc_start: 0.8629 (p) cc_final: 0.8360 (t) REVERT: B 330 MET cc_start: 0.8876 (mtp) cc_final: 0.8481 (mtp) REVERT: C 98 PHE cc_start: 0.9008 (m-80) cc_final: 0.8624 (m-10) REVERT: C 208 LYS cc_start: 0.8807 (mttt) cc_final: 0.8589 (mtpp) REVERT: C 313 ASP cc_start: 0.8267 (t70) cc_final: 0.7961 (t0) REVERT: C 319 LEU cc_start: 0.9393 (tp) cc_final: 0.9150 (tp) REVERT: C 330 MET cc_start: 0.8929 (mtp) cc_final: 0.8583 (mtp) REVERT: D 31 LYS cc_start: 0.7536 (mmtt) cc_final: 0.7325 (mmmt) outliers start: 21 outliers final: 9 residues processed: 267 average time/residue: 0.2974 time to fit residues: 105.7638 Evaluate side-chains 189 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN A 463 HIS B 358 GLN B 463 HIS C 463 HIS D 56 ASN E 56 ASN F 56 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121495 restraints weight = 14979.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121214 restraints weight = 19101.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121334 restraints weight = 18053.731| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11560 Z= 0.172 Angle : 0.930 55.914 15656 Z= 0.465 Chirality : 0.044 0.144 1707 Planarity : 0.004 0.047 2028 Dihedral : 5.687 27.459 1683 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.83 % Allowed : 16.67 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.19), residues: 1413 helix: -2.91 (0.20), residues: 351 sheet: -2.41 (0.28), residues: 321 loop : -2.84 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 233 HIS 0.004 0.001 HIS A 250 PHE 0.009 0.001 PHE B 272 TYR 0.020 0.001 TYR C 417 ARG 0.005 0.001 ARG B 279 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 6) link_NAG-ASN : angle 0.93167 ( 18) hydrogen bonds : bond 0.04629 ( 273) hydrogen bonds : angle 5.64852 ( 729) SS BOND : bond 0.01030 ( 22) SS BOND : angle 10.84749 ( 44) covalent geometry : bond 0.00389 (11532) covalent geometry : angle 0.73183 (15594) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 208 LYS cc_start: 0.8997 (mttt) cc_final: 0.8715 (mtpp) REVERT: A 313 ASP cc_start: 0.8411 (t70) cc_final: 0.8173 (t0) REVERT: B 98 PHE cc_start: 0.8949 (m-80) cc_final: 0.8662 (m-10) REVERT: C 98 PHE cc_start: 0.8918 (m-80) cc_final: 0.8484 (m-10) REVERT: C 208 LYS cc_start: 0.8912 (mttt) cc_final: 0.8539 (mtpp) REVERT: C 313 ASP cc_start: 0.8365 (t70) cc_final: 0.8097 (t0) REVERT: C 330 MET cc_start: 0.8957 (mtp) cc_final: 0.8733 (mtp) REVERT: E 16 MET cc_start: 0.8305 (ttm) cc_final: 0.7967 (mtp) REVERT: E 20 TYR cc_start: 0.8862 (p90) cc_final: 0.8610 (p90) REVERT: F 38 SER cc_start: 0.8485 (t) cc_final: 0.8009 (m) outliers start: 34 outliers final: 22 residues processed: 250 average time/residue: 0.2406 time to fit residues: 84.3133 Evaluate side-chains 210 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS F 21 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123040 restraints weight = 15419.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118295 restraints weight = 18913.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114832 restraints weight = 13487.730| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11560 Z= 0.179 Angle : 0.932 55.943 15656 Z= 0.462 Chirality : 0.044 0.220 1707 Planarity : 0.004 0.046 2028 Dihedral : 5.509 23.940 1678 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.00 % Allowed : 19.17 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.21), residues: 1413 helix: -2.22 (0.23), residues: 360 sheet: -2.21 (0.28), residues: 324 loop : -2.49 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 233 HIS 0.005 0.001 HIS A 250 PHE 0.024 0.001 PHE C 411 TYR 0.025 0.001 TYR C 67 ARG 0.006 0.000 ARG F 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 6) link_NAG-ASN : angle 1.20199 ( 18) hydrogen bonds : bond 0.04008 ( 273) hydrogen bonds : angle 5.15280 ( 729) SS BOND : bond 0.01068 ( 22) SS BOND : angle 10.95915 ( 44) covalent geometry : bond 0.00408 (11532) covalent geometry : angle 0.72948 (15594) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 1.337 Fit side-chains REVERT: A 208 LYS cc_start: 0.8955 (mttt) cc_final: 0.8707 (mtpp) REVERT: A 313 ASP cc_start: 0.8599 (t70) cc_final: 0.8279 (t0) REVERT: A 399 GLN cc_start: 0.7899 (tp40) cc_final: 0.7696 (tp40) REVERT: B 98 PHE cc_start: 0.8979 (m-80) cc_final: 0.8597 (m-10) REVERT: C 98 PHE cc_start: 0.8992 (m-80) cc_final: 0.8403 (m-10) REVERT: C 208 LYS cc_start: 0.8898 (mttt) cc_final: 0.8640 (mtpp) REVERT: C 313 ASP cc_start: 0.8439 (t70) cc_final: 0.8024 (t0) outliers start: 48 outliers final: 31 residues processed: 233 average time/residue: 0.2433 time to fit residues: 79.8516 Evaluate side-chains 213 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.0770 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN F 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105579 restraints weight = 15619.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.106635 restraints weight = 13073.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107142 restraints weight = 11647.927| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11560 Z= 0.257 Angle : 0.960 55.956 15656 Z= 0.478 Chirality : 0.046 0.291 1707 Planarity : 0.003 0.045 2028 Dihedral : 5.906 28.768 1677 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.92 % Allowed : 19.00 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.21), residues: 1413 helix: -1.91 (0.24), residues: 351 sheet: -2.31 (0.28), residues: 324 loop : -2.28 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 233 HIS 0.006 0.001 HIS A 250 PHE 0.015 0.002 PHE C 411 TYR 0.022 0.002 TYR B 417 ARG 0.005 0.000 ARG F 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 6) link_NAG-ASN : angle 1.47203 ( 18) hydrogen bonds : bond 0.04201 ( 273) hydrogen bonds : angle 5.17150 ( 729) SS BOND : bond 0.01152 ( 22) SS BOND : angle 10.94357 ( 44) covalent geometry : bond 0.00594 (11532) covalent geometry : angle 0.76427 (15594) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 180 time to evaluate : 1.262 Fit side-chains REVERT: A 208 LYS cc_start: 0.9077 (mttt) cc_final: 0.8864 (mtpp) REVERT: A 313 ASP cc_start: 0.8736 (t70) cc_final: 0.8376 (t0) REVERT: A 403 GLU cc_start: 0.7887 (tp30) cc_final: 0.7358 (tp30) REVERT: B 98 PHE cc_start: 0.9059 (m-80) cc_final: 0.8662 (m-10) REVERT: B 291 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7968 (mmtm) REVERT: B 322 ASN cc_start: 0.8466 (m110) cc_final: 0.8148 (t0) REVERT: C 98 PHE cc_start: 0.9090 (m-80) cc_final: 0.8464 (m-10) REVERT: C 208 LYS cc_start: 0.9006 (mttt) cc_final: 0.8783 (mtpp) REVERT: C 313 ASP cc_start: 0.8617 (t70) cc_final: 0.8258 (t0) REVERT: C 330 MET cc_start: 0.8105 (mtm) cc_final: 0.7680 (ttp) REVERT: E 31 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7512 (mmmt) outliers start: 59 outliers final: 41 residues processed: 225 average time/residue: 0.2673 time to fit residues: 85.3985 Evaluate side-chains 212 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112583 restraints weight = 15285.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113468 restraints weight = 12801.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113756 restraints weight = 11152.536| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11560 Z= 0.113 Angle : 0.890 55.977 15656 Z= 0.433 Chirality : 0.042 0.185 1707 Planarity : 0.003 0.042 2028 Dihedral : 5.106 26.371 1677 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.25 % Allowed : 21.75 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.22), residues: 1413 helix: -1.65 (0.24), residues: 381 sheet: -2.04 (0.29), residues: 306 loop : -1.99 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS E 21 PHE 0.016 0.001 PHE A 98 TYR 0.018 0.001 TYR C 67 ARG 0.006 0.000 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 6) link_NAG-ASN : angle 1.11173 ( 18) hydrogen bonds : bond 0.03134 ( 273) hydrogen bonds : angle 4.72175 ( 729) SS BOND : bond 0.01031 ( 22) SS BOND : angle 10.83582 ( 44) covalent geometry : bond 0.00253 (11532) covalent geometry : angle 0.68012 (15594) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7320 (tm-30) cc_final: 0.7045 (tm-30) REVERT: A 313 ASP cc_start: 0.8658 (t70) cc_final: 0.8341 (t0) REVERT: B 98 PHE cc_start: 0.8896 (m-80) cc_final: 0.8653 (m-10) REVERT: C 98 PHE cc_start: 0.8770 (m-80) cc_final: 0.8101 (m-10) REVERT: C 208 LYS cc_start: 0.8875 (mttt) cc_final: 0.8670 (mtpp) REVERT: C 313 ASP cc_start: 0.8539 (t70) cc_final: 0.8219 (t0) REVERT: D 31 LYS cc_start: 0.7216 (mmmt) cc_final: 0.7002 (mmmt) REVERT: D 38 SER cc_start: 0.8142 (t) cc_final: 0.7754 (m) REVERT: D 55 CYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7210 (p) REVERT: E 20 TYR cc_start: 0.8997 (p90) cc_final: 0.8701 (p90) outliers start: 39 outliers final: 23 residues processed: 236 average time/residue: 0.2652 time to fit residues: 89.3185 Evaluate side-chains 209 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 8 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 72 optimal weight: 0.0040 chunk 135 optimal weight: 5.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN C 270 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109596 restraints weight = 15693.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110996 restraints weight = 13178.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112198 restraints weight = 10712.155| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11560 Z= 0.145 Angle : 0.907 55.975 15656 Z= 0.445 Chirality : 0.044 0.365 1707 Planarity : 0.003 0.050 2028 Dihedral : 5.090 26.741 1677 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.67 % Allowed : 22.17 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.22), residues: 1413 helix: -1.25 (0.25), residues: 363 sheet: -1.53 (0.30), residues: 297 loop : -1.99 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 233 HIS 0.003 0.001 HIS B 250 PHE 0.024 0.001 PHE C 411 TYR 0.017 0.001 TYR C 67 ARG 0.005 0.000 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 6) link_NAG-ASN : angle 1.34474 ( 18) hydrogen bonds : bond 0.03212 ( 273) hydrogen bonds : angle 4.65777 ( 729) SS BOND : bond 0.01087 ( 22) SS BOND : angle 10.85400 ( 44) covalent geometry : bond 0.00336 (11532) covalent geometry : angle 0.70140 (15594) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 1.306 Fit side-chains REVERT: A 313 ASP cc_start: 0.8755 (t70) cc_final: 0.8340 (t0) REVERT: A 341 GLN cc_start: 0.8362 (pt0) cc_final: 0.7981 (pt0) REVERT: B 98 PHE cc_start: 0.8958 (m-80) cc_final: 0.8637 (m-10) REVERT: B 134 GLN cc_start: 0.7153 (tm-30) cc_final: 0.6815 (tm-30) REVERT: C 98 PHE cc_start: 0.8859 (m-80) cc_final: 0.8183 (m-10) REVERT: C 208 LYS cc_start: 0.8940 (mttt) cc_final: 0.8709 (mtpp) REVERT: C 313 ASP cc_start: 0.8464 (t70) cc_final: 0.7979 (t0) REVERT: C 382 PRO cc_start: 0.8179 (Cg_exo) cc_final: 0.7949 (Cg_endo) REVERT: D 31 LYS cc_start: 0.7165 (mmmt) cc_final: 0.6944 (mmmt) REVERT: E 20 TYR cc_start: 0.9050 (p90) cc_final: 0.8769 (p90) outliers start: 44 outliers final: 35 residues processed: 219 average time/residue: 0.3020 time to fit residues: 93.6166 Evaluate side-chains 218 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 82 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 0.0010 chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107201 restraints weight = 15921.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108637 restraints weight = 12806.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109431 restraints weight = 10954.912| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11560 Z= 0.169 Angle : 0.908 55.978 15656 Z= 0.445 Chirality : 0.044 0.337 1707 Planarity : 0.003 0.048 2028 Dihedral : 5.152 29.285 1677 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.00 % Allowed : 22.00 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.23), residues: 1413 helix: -1.29 (0.25), residues: 381 sheet: -1.97 (0.28), residues: 327 loop : -1.58 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 233 HIS 0.003 0.001 HIS A 250 PHE 0.021 0.001 PHE C 411 TYR 0.022 0.001 TYR B 67 ARG 0.005 0.000 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 6) link_NAG-ASN : angle 1.31923 ( 18) hydrogen bonds : bond 0.03361 ( 273) hydrogen bonds : angle 4.64170 ( 729) SS BOND : bond 0.01073 ( 22) SS BOND : angle 10.83703 ( 44) covalent geometry : bond 0.00392 (11532) covalent geometry : angle 0.70284 (15594) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 1.672 Fit side-chains revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8758 (t70) cc_final: 0.8374 (t0) REVERT: A 341 GLN cc_start: 0.8353 (pt0) cc_final: 0.7985 (pt0) REVERT: B 98 PHE cc_start: 0.8972 (m-80) cc_final: 0.8632 (m-10) REVERT: B 134 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6837 (tm-30) REVERT: C 98 PHE cc_start: 0.8898 (m-80) cc_final: 0.8393 (m-10) REVERT: C 208 LYS cc_start: 0.8940 (mttt) cc_final: 0.8697 (mtpp) REVERT: C 313 ASP cc_start: 0.8544 (t70) cc_final: 0.8134 (t0) REVERT: C 401 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9320 (tp) REVERT: D 31 LYS cc_start: 0.7233 (mmmt) cc_final: 0.7004 (mmmt) REVERT: D 55 CYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7277 (p) REVERT: E 20 TYR cc_start: 0.9000 (p90) cc_final: 0.8639 (p90) outliers start: 48 outliers final: 36 residues processed: 222 average time/residue: 0.3318 time to fit residues: 105.7823 Evaluate side-chains 222 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 66 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107468 restraints weight = 15761.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108849 restraints weight = 12948.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109248 restraints weight = 10235.126| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11560 Z= 0.178 Angle : 0.929 55.979 15656 Z= 0.456 Chirality : 0.045 0.359 1707 Planarity : 0.003 0.053 2028 Dihedral : 5.235 28.529 1677 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.92 % Allowed : 22.75 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.23), residues: 1413 helix: -1.17 (0.25), residues: 381 sheet: -2.01 (0.27), residues: 321 loop : -1.50 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 233 HIS 0.003 0.001 HIS A 250 PHE 0.020 0.001 PHE C 411 TYR 0.019 0.001 TYR B 67 ARG 0.004 0.000 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 6) link_NAG-ASN : angle 1.89597 ( 18) hydrogen bonds : bond 0.03358 ( 273) hydrogen bonds : angle 4.66889 ( 729) SS BOND : bond 0.01090 ( 22) SS BOND : angle 10.92554 ( 44) covalent geometry : bond 0.00416 (11532) covalent geometry : angle 0.72465 (15594) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8779 (t70) cc_final: 0.8368 (t0) REVERT: A 341 GLN cc_start: 0.8432 (pt0) cc_final: 0.7660 (pt0) REVERT: A 344 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: B 98 PHE cc_start: 0.8990 (m-80) cc_final: 0.8686 (m-10) REVERT: B 134 GLN cc_start: 0.7203 (tm-30) cc_final: 0.6852 (tm-30) REVERT: B 368 ASN cc_start: 0.7344 (OUTLIER) cc_final: 0.7144 (m-40) REVERT: C 98 PHE cc_start: 0.8919 (m-80) cc_final: 0.8453 (m-10) REVERT: C 141 LYS cc_start: 0.7539 (mtmt) cc_final: 0.7291 (mtmt) REVERT: C 208 LYS cc_start: 0.8958 (mttt) cc_final: 0.8714 (mtpp) REVERT: C 313 ASP cc_start: 0.8525 (t70) cc_final: 0.8095 (t0) REVERT: C 401 ILE cc_start: 0.9548 (OUTLIER) cc_final: 0.9324 (tp) REVERT: D 55 CYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7362 (p) REVERT: E 20 TYR cc_start: 0.9074 (p90) cc_final: 0.8753 (p90) REVERT: F 20 TYR cc_start: 0.8876 (p90) cc_final: 0.8540 (p90) outliers start: 47 outliers final: 38 residues processed: 221 average time/residue: 0.2989 time to fit residues: 92.9712 Evaluate side-chains 219 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 118 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112839 restraints weight = 15539.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112928 restraints weight = 11827.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112300 restraints weight = 11619.395| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11560 Z= 0.145 Angle : 0.904 55.984 15656 Z= 0.442 Chirality : 0.043 0.341 1707 Planarity : 0.003 0.054 2028 Dihedral : 4.930 25.965 1677 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.25 % Allowed : 22.42 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.23), residues: 1413 helix: -1.17 (0.25), residues: 399 sheet: -1.88 (0.28), residues: 306 loop : -1.38 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 233 HIS 0.003 0.001 HIS B 250 PHE 0.019 0.001 PHE C 411 TYR 0.019 0.001 TYR B 67 ARG 0.004 0.000 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 6) link_NAG-ASN : angle 1.45555 ( 18) hydrogen bonds : bond 0.03090 ( 273) hydrogen bonds : angle 4.58220 ( 729) SS BOND : bond 0.01072 ( 22) SS BOND : angle 10.82153 ( 44) covalent geometry : bond 0.00339 (11532) covalent geometry : angle 0.69797 (15594) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8754 (t70) cc_final: 0.8376 (t0) REVERT: A 341 GLN cc_start: 0.8579 (pt0) cc_final: 0.8165 (pt0) REVERT: B 98 PHE cc_start: 0.8962 (m-80) cc_final: 0.8605 (m-10) REVERT: B 134 GLN cc_start: 0.7197 (tm-30) cc_final: 0.6839 (tm-30) REVERT: C 98 PHE cc_start: 0.8882 (m-80) cc_final: 0.8318 (m-10) REVERT: C 208 LYS cc_start: 0.8942 (mttt) cc_final: 0.8711 (mtpp) REVERT: C 313 ASP cc_start: 0.8530 (t70) cc_final: 0.8119 (t0) REVERT: C 401 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9280 (tp) REVERT: D 31 LYS cc_start: 0.7213 (mmmt) cc_final: 0.6993 (mmmt) REVERT: D 55 CYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7356 (p) REVERT: E 20 TYR cc_start: 0.9079 (p90) cc_final: 0.8795 (p90) REVERT: F 20 TYR cc_start: 0.8851 (p90) cc_final: 0.8526 (p90) outliers start: 51 outliers final: 41 residues processed: 230 average time/residue: 0.2278 time to fit residues: 74.7569 Evaluate side-chains 223 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.0980 chunk 104 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 80 optimal weight: 0.2980 chunk 98 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.157352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112036 restraints weight = 15396.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113412 restraints weight = 12093.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114117 restraints weight = 10468.943| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11560 Z= 0.117 Angle : 0.895 55.985 15656 Z= 0.437 Chirality : 0.043 0.359 1707 Planarity : 0.003 0.056 2028 Dihedral : 4.586 23.541 1677 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.92 % Allowed : 23.67 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.23), residues: 1413 helix: -0.99 (0.26), residues: 399 sheet: -1.46 (0.29), residues: 318 loop : -1.35 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 233 HIS 0.002 0.001 HIS F 21 PHE 0.017 0.001 PHE C 411 TYR 0.018 0.001 TYR B 67 ARG 0.004 0.000 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 6) link_NAG-ASN : angle 1.87631 ( 18) hydrogen bonds : bond 0.02737 ( 273) hydrogen bonds : angle 4.45455 ( 729) SS BOND : bond 0.01066 ( 22) SS BOND : angle 10.78017 ( 44) covalent geometry : bond 0.00268 (11532) covalent geometry : angle 0.68691 (15594) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 GLU cc_start: 0.7270 (pp20) cc_final: 0.6859 (pp20) REVERT: A 313 ASP cc_start: 0.8745 (t70) cc_final: 0.8340 (t0) REVERT: A 341 GLN cc_start: 0.8462 (pt0) cc_final: 0.8042 (pt0) REVERT: B 98 PHE cc_start: 0.8812 (m-80) cc_final: 0.8500 (m-10) REVERT: B 134 GLN cc_start: 0.7231 (tm-30) cc_final: 0.6952 (tm-30) REVERT: B 421 GLU cc_start: 0.7664 (pm20) cc_final: 0.7448 (pm20) REVERT: C 98 PHE cc_start: 0.8718 (m-80) cc_final: 0.8001 (m-10) REVERT: C 208 LYS cc_start: 0.8961 (mttt) cc_final: 0.8677 (mtpp) REVERT: C 313 ASP cc_start: 0.8535 (t70) cc_final: 0.8078 (t0) REVERT: C 401 ILE cc_start: 0.9494 (OUTLIER) cc_final: 0.9233 (tp) REVERT: D 22 ASN cc_start: 0.8999 (t0) cc_final: 0.8481 (t0) REVERT: D 55 CYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7222 (p) REVERT: F 20 TYR cc_start: 0.8733 (p90) cc_final: 0.8414 (p90) outliers start: 35 outliers final: 29 residues processed: 223 average time/residue: 0.2367 time to fit residues: 74.6672 Evaluate side-chains 217 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 5 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 92 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108356 restraints weight = 15568.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109580 restraints weight = 13126.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110084 restraints weight = 11058.621| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11560 Z= 0.191 Angle : 0.931 55.974 15656 Z= 0.457 Chirality : 0.045 0.366 1707 Planarity : 0.003 0.060 2028 Dihedral : 5.019 28.552 1677 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.25 % Allowed : 24.00 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.23), residues: 1413 helix: -0.82 (0.26), residues: 381 sheet: -1.59 (0.29), residues: 321 loop : -1.33 (0.26), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.003 0.001 HIS A 73 PHE 0.018 0.001 PHE C 411 TYR 0.019 0.001 TYR B 67 ARG 0.004 0.000 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 6) link_NAG-ASN : angle 2.06071 ( 18) hydrogen bonds : bond 0.03265 ( 273) hydrogen bonds : angle 4.57425 ( 729) SS BOND : bond 0.01093 ( 22) SS BOND : angle 10.85715 ( 44) covalent geometry : bond 0.00451 (11532) covalent geometry : angle 0.73000 (15594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4291.70 seconds wall clock time: 79 minutes 20.26 seconds (4760.26 seconds total)