Starting phenix.real_space_refine on Mon Aug 25 14:25:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghz_40054/08_2025/8ghz_40054_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghz_40054/08_2025/8ghz_40054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ghz_40054/08_2025/8ghz_40054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghz_40054/08_2025/8ghz_40054.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghz_40054/08_2025/8ghz_40054_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghz_40054/08_2025/8ghz_40054_trim.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 9058 2.51 5 N 2338 2.21 5 O 2914 1.98 5 H 13833 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28223 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3485 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain: "B" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3485 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain: "C" Number of atoms: 3486 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 3485 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Conformer: "B" Number of residues, atoms: 221, 3485 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} bond proxies already assigned to first conformer: 3518 Chain: "D" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3485 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain: "E" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3485 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain: "F" Number of atoms: 3500 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 3485 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Conformer: "B" Number of residues, atoms: 221, 3485 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} bond proxies already assigned to first conformer: 3502 Chain: "G" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3485 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain: "H" Number of atoms: 3500 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 3485 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Conformer: "B" Number of residues, atoms: 221, 3485 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} bond proxies already assigned to first conformer: 3502 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APRO F 328 " occ=0.76 ... (26 atoms not shown) pdb=" HD3BPRO F 328 " occ=0.24 residue: pdb=" N APRO H 328 " occ=0.74 ... (26 atoms not shown) pdb=" HD3BPRO H 328 " occ=0.26 Time building chain proxies: 6.45, per 1000 atoms: 0.23 Number of scatterers: 28223 At special positions: 0 Unit cell: (71.82, 170.145, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 2914 8.00 N 2338 7.00 C 9058 6.00 H 13833 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 341 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 294 " distance=2.04 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 244 " - pdb=" SG CYS C 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 341 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS D 244 " - pdb=" SG CYS D 294 " distance=2.03 Simple disulfide: pdb=" SG CYS D 341 " - pdb=" SG CYS D 407 " distance=2.04 Simple disulfide: pdb=" SG CYS E 244 " - pdb=" SG CYS E 294 " distance=2.03 Simple disulfide: pdb=" SG CYS E 341 " - pdb=" SG CYS E 407 " distance=2.04 Simple disulfide: pdb=" SG CYS F 244 " - pdb=" SG CYS F 294 " distance=2.03 Simple disulfide: pdb=" SG CYS F 341 " - pdb=" SG CYS F 407 " distance=2.03 Simple disulfide: pdb=" SG CYS G 244 " - pdb=" SG CYS G 294 " distance=2.04 Simple disulfide: pdb=" SG CYS G 341 " - pdb=" SG CYS G 407 " distance=2.05 Simple disulfide: pdb=" SG CYS H 244 " - pdb=" SG CYS H 294 " distance=2.03 Simple disulfide: pdb=" SG CYS H 341 " - pdb=" SG CYS H 407 " distance=2.04 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 BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG I 1 " - " ASN A 374 " " NAG J 1 " - " ASN B 374 " " NAG K 1 " - " ASN C 374 " " NAG L 1 " - " ASN D 374 " " NAG M 1 " - " ASN E 374 " " NAG O 1 " - " ASN G 374 " " NAG P 1 " - " ASN H 374 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 941.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3412 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 38 sheets defined 12.6% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 300 through 304 removed outlier: 4.269A pdb=" N GLY A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 283 through 289 Processing helix chain 'B' and resid 300 through 304 removed outlier: 4.281A pdb=" N GLY B 303 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.555A pdb=" N MET B 414 " --> pdb=" O HIS B 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 300 through 304 removed outlier: 4.277A pdb=" N GLY C 303 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 283 through 289 Processing helix chain 'D' and resid 300 through 304 removed outlier: 4.283A pdb=" N GLY D 303 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 removed outlier: 4.157A pdb=" N THR D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 361 through 366' Processing helix chain 'D' and resid 395 through 399 Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 283 through 289 Processing helix chain 'E' and resid 300 through 304 removed outlier: 4.231A pdb=" N GLY E 303 " --> pdb=" O GLU E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 395 through 400 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 283 through 289 Processing helix chain 'F' and resid 300 through 304 removed outlier: 4.231A pdb=" N GLY F 303 " --> pdb=" O GLU F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 365 removed outlier: 4.079A pdb=" N THR F 365 " --> pdb=" O VAL F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 401 removed outlier: 3.623A pdb=" N LYS F 399 " --> pdb=" O ASN F 395 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 415 removed outlier: 3.662A pdb=" N ILE F 415 " --> pdb=" O GLU F 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 412 through 415' Processing helix chain 'G' and resid 231 through 236 Processing helix chain 'G' and resid 283 through 289 Processing helix chain 'G' and resid 300 through 304 removed outlier: 4.283A pdb=" N GLY G 303 " --> pdb=" O GLU G 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 369 No H-bonds generated for 'chain 'G' and resid 367 through 369' Processing helix chain 'G' and resid 394 through 400 Processing helix chain 'H' and resid 231 through 236 Processing helix chain 'H' and resid 283 through 289 Processing helix chain 'H' and resid 300 through 304 removed outlier: 4.265A pdb=" N GLY H 303 " --> pdb=" O GLU H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 228 removed outlier: 4.245A pdb=" N VAL A 243 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 259 Processing sheet with id=AA3, first strand: chain 'A' and resid 323 through 325 removed outlier: 3.708A pdb=" N THR A 338 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 325 Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 357 removed outlier: 4.254A pdb=" N ASN C 433 " --> pdb=" O PRO A 432 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASN B 433 " --> pdb=" O LEU C 434 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ASN C 436 " --> pdb=" O ASN B 433 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 435 " --> pdb=" O ASN C 436 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N SER C 438 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 437 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ASN C 440 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 439 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 228 removed outlier: 4.157A pdb=" N VAL B 243 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 256 through 259 removed outlier: 3.902A pdb=" N PHE B 292 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 326 removed outlier: 3.725A pdb=" N THR B 340 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TYR B 385 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AB1, first strand: chain 'C' and resid 226 through 228 removed outlier: 3.618A pdb=" N GLU C 228 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 243 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 256 through 260 Processing sheet with id=AB3, first strand: chain 'C' and resid 322 through 326 removed outlier: 3.557A pdb=" N LYS C 344 " --> pdb=" O SER C 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 322 through 326 removed outlier: 3.557A pdb=" N LYS C 344 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 381 " --> pdb=" O THR C 384 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AB6, first strand: chain 'D' and resid 226 through 228 removed outlier: 3.514A pdb=" N GLU D 228 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL D 243 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 240 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 281 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 256 through 259 removed outlier: 3.761A pdb=" N PHE D 292 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 323 through 325 removed outlier: 3.506A pdb=" N ASP D 345 " --> pdb=" O TYR D 385 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR D 385 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 329 through 331 removed outlier: 3.506A pdb=" N ASP D 345 " --> pdb=" O TYR D 385 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR D 385 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 351 through 356 Processing sheet with id=AC2, first strand: chain 'E' and resid 226 through 227 removed outlier: 3.585A pdb=" N ALA E 240 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 281 " --> pdb=" O ALA E 240 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 256 through 259 Processing sheet with id=AC4, first strand: chain 'E' and resid 324 through 325 removed outlier: 3.520A pdb=" N VAL E 387 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR E 385 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 324 through 325 removed outlier: 3.520A pdb=" N VAL E 387 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR E 385 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 351 through 356 Processing sheet with id=AC7, first strand: chain 'E' and resid 434 through 437 removed outlier: 6.043A pdb=" N VAL E 435 " --> pdb=" O ASN G 436 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER G 438 " --> pdb=" O VAL E 435 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU E 437 " --> pdb=" O SER G 438 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ASN G 440 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN F 433 " --> pdb=" O PRO H 432 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU H 434 " --> pdb=" O ASN F 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 226 through 228 removed outlier: 3.542A pdb=" N GLU F 228 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL F 243 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 256 through 260 Processing sheet with id=AD1, first strand: chain 'F' and resid 322 through 326 removed outlier: 3.521A pdb=" N ASN F 374 " --> pdb=" O GLN F 390 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 352 through 356 Processing sheet with id=AD3, first strand: chain 'G' and resid 226 through 228 removed outlier: 4.337A pdb=" N VAL G 243 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 256 through 259 removed outlier: 4.138A pdb=" N PHE G 292 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL G 296 " --> pdb=" O VAL G 306 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL G 306 " --> pdb=" O VAL G 296 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 322 through 326 removed outlier: 5.765A pdb=" N TYR G 385 " --> pdb=" O ASP G 345 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 322 through 326 removed outlier: 5.765A pdb=" N TYR G 385 " --> pdb=" O ASP G 345 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 360 through 361 Processing sheet with id=AD8, first strand: chain 'H' and resid 226 through 228 removed outlier: 4.273A pdb=" N VAL H 243 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 256 through 259 removed outlier: 3.850A pdb=" N PHE H 292 " --> pdb=" O TYR H 310 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 323 through 325 Processing sheet with id=AE2, first strand: chain 'H' and resid 323 through 325 520 hydrogen bonds defined for protein. 1329 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: 6.03 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 13825 1.02 - 1.22: 35 1.22 - 1.42: 5934 1.42 - 1.62: 8585 1.62 - 1.83: 120 Bond restraints: 28499 Sorted by residual: bond pdb=" ND2 ASN C 374 " pdb="HD21 ASN C 374 " ideal model delta sigma weight residual 0.860 1.003 -0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" ND2 ASN B 374 " pdb="HD21 ASN B 374 " ideal model delta sigma weight residual 0.860 1.003 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" ND2 ASN H 374 " pdb="HD22 ASN H 374 " ideal model delta sigma weight residual 0.860 1.003 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" ND2 ASN A 374 " pdb="HD21 ASN A 374 " ideal model delta sigma weight residual 0.860 1.002 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" ND2 ASN G 374 " pdb="HD21 ASN G 374 " ideal model delta sigma weight residual 0.860 1.002 -0.142 2.00e-02 2.50e+03 5.05e+01 ... (remaining 28494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 49493 1.39 - 2.78: 1616 2.78 - 4.18: 217 4.18 - 5.57: 47 5.57 - 6.96: 11 Bond angle restraints: 51384 Sorted by residual: angle pdb=" N LYS H 344 " pdb=" CA LYS H 344 " pdb=" C LYS H 344 " ideal model delta sigma weight residual 112.45 119.40 -6.95 1.39e+00 5.18e-01 2.50e+01 angle pdb=" N ASP H 345 " pdb=" CA ASP H 345 " pdb=" C ASP H 345 " ideal model delta sigma weight residual 107.61 114.57 -6.96 1.74e+00 3.30e-01 1.60e+01 angle pdb=" N GLU H 402 " pdb=" CA GLU H 402 " pdb=" C GLU H 402 " ideal model delta sigma weight residual 107.23 113.87 -6.64 1.67e+00 3.59e-01 1.58e+01 angle pdb=" N VAL E 441 " pdb=" CA VAL E 441 " pdb=" C VAL E 441 " ideal model delta sigma weight residual 108.15 112.03 -3.88 9.90e-01 1.02e+00 1.53e+01 angle pdb=" N ASN A 440 " pdb=" CA ASN A 440 " pdb=" C ASN A 440 " ideal model delta sigma weight residual 112.88 108.21 4.67 1.29e+00 6.01e-01 1.31e+01 ... (remaining 51379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.42: 12784 21.42 - 42.83: 784 42.83 - 64.25: 205 64.25 - 85.67: 56 85.67 - 107.09: 35 Dihedral angle restraints: 13864 sinusoidal: 7808 harmonic: 6056 Sorted by residual: dihedral pdb=" CB CYS H 341 " pdb=" SG CYS H 341 " pdb=" SG CYS H 407 " pdb=" CB CYS H 407 " ideal model delta sinusoidal sigma weight residual 93.00 -178.10 -88.90 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS E 341 " pdb=" SG CYS E 341 " pdb=" SG CYS E 407 " pdb=" CB CYS E 407 " ideal model delta sinusoidal sigma weight residual 93.00 46.37 46.63 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CB CYS B 341 " pdb=" SG CYS B 341 " pdb=" SG CYS B 407 " pdb=" CB CYS B 407 " ideal model delta sinusoidal sigma weight residual 93.00 50.95 42.05 1 1.00e+01 1.00e-02 2.47e+01 ... (remaining 13861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2367 0.137 - 0.274: 30 0.274 - 0.412: 3 0.412 - 0.549: 0 0.549 - 0.686: 1 Chirality restraints: 2401 Sorted by residual: chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-02 2.50e+03 1.18e+03 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-02 2.50e+03 3.95e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 2398 not shown) Planarity restraints: 4208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 443 " -0.174 2.00e-02 2.50e+03 2.01e-01 6.09e+02 pdb=" CD GLN C 443 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN C 443 " 0.174 2.00e-02 2.50e+03 pdb=" NE2 GLN C 443 " -0.008 2.00e-02 2.50e+03 pdb="HE21 GLN C 443 " 0.302 2.00e-02 2.50e+03 pdb="HE22 GLN C 443 " -0.302 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 443 " -0.168 2.00e-02 2.50e+03 1.93e-01 5.58e+02 pdb=" CD GLN G 443 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN G 443 " 0.166 2.00e-02 2.50e+03 pdb=" NE2 GLN G 443 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN G 443 " 0.288 2.00e-02 2.50e+03 pdb="HE22 GLN G 443 " -0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 374 " 0.102 2.00e-02 2.50e+03 1.55e-01 2.99e+02 pdb=" CG ASN F 374 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN F 374 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN F 374 " -0.249 2.00e-02 2.50e+03 pdb="HD21 ASN F 374 " 0.209 2.00e-02 2.50e+03 ... (remaining 4205 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 539 2.12 - 2.74: 50975 2.74 - 3.36: 75152 3.36 - 3.98: 98263 3.98 - 4.60: 149578 Nonbonded interactions: 374507 Sorted by model distance: nonbonded pdb=" OE1 GLU G 284 " pdb=" H GLU G 284 " model vdw 1.501 2.450 nonbonded pdb=" OE1 GLU D 284 " pdb=" H GLU D 284 " model vdw 1.578 2.450 nonbonded pdb=" OE1 GLU B 284 " pdb=" H GLU B 284 " model vdw 1.597 2.450 nonbonded pdb=" OE1 GLU A 232 " pdb=" H GLU A 232 " model vdw 1.618 2.450 nonbonded pdb=" OE1 GLU C 284 " pdb=" H GLU C 284 " model vdw 1.644 2.450 ... (remaining 374502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 225 through 327 or resid 330 through 445)) selection = (chain 'B' and (resid 225 through 327 or resid 330 through 445)) selection = (chain 'C' and (resid 225 through 327 or resid 330 through 445)) selection = (chain 'D' and (resid 225 through 327 or resid 330 through 445)) selection = (chain 'E' and (resid 225 through 327 or resid 330 through 445)) selection = (chain 'F' and (resid 225 through 327 or resid 330 through 445)) selection = (chain 'G' and (resid 225 through 327 or resid 330 through 445)) selection = (chain 'H' and (resid 225 through 327 or resid 330 through 445)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.460 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14705 Z= 0.221 Angle : 0.735 6.990 20075 Z= 0.390 Chirality : 0.052 0.686 2401 Planarity : 0.006 0.080 2510 Dihedral : 17.884 107.087 5778 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 1.28 % Allowed : 18.39 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.19), residues: 1758 helix: -2.48 (0.31), residues: 192 sheet: -0.75 (0.18), residues: 710 loop : -2.13 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 427 TYR 0.022 0.001 TYR H 388 PHE 0.013 0.001 PHE G 373 TRP 0.013 0.001 TRP D 398 HIS 0.005 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00401 (14666) covalent geometry : angle 0.71910 (19974) SS BOND : bond 0.00729 ( 16) SS BOND : angle 1.55819 ( 32) hydrogen bonds : bond 0.17077 ( 470) hydrogen bonds : angle 8.26815 ( 1329) link_BETA1-4 : bond 0.00417 ( 16) link_BETA1-4 : angle 1.59759 ( 48) link_NAG-ASN : bond 0.02216 ( 7) link_NAG-ASN : angle 3.80369 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 GLN cc_start: 0.8122 (mp10) cc_final: 0.7432 (mm-40) REVERT: C 234 MET cc_start: 0.8366 (mtp) cc_final: 0.8068 (tpp) REVERT: D 377 SER cc_start: 0.8830 (m) cc_final: 0.8581 (p) REVERT: E 414 MET cc_start: 0.8129 (tpt) cc_final: 0.7894 (tpt) REVERT: H 422 MET cc_start: 0.8455 (mtp) cc_final: 0.8186 (mtp) outliers start: 21 outliers final: 8 residues processed: 215 average time/residue: 1.2460 time to fit residues: 293.0228 Evaluate side-chains 153 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 443 GLN Chi-restraints excluded: chain H residue 406 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN C 443 GLN F 395 ASN F 443 GLN G 443 GLN H 335 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.146683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.085560 restraints weight = 105186.652| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 4.26 r_work: 0.3040 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14705 Z= 0.192 Angle : 0.665 8.341 20075 Z= 0.340 Chirality : 0.048 0.189 2401 Planarity : 0.004 0.048 2510 Dihedral : 10.399 72.145 2407 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.86 % Rotamer: Outliers : 1.83 % Allowed : 19.73 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.19), residues: 1758 helix: -2.28 (0.30), residues: 192 sheet: -0.52 (0.18), residues: 714 loop : -2.03 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 427 TYR 0.017 0.001 TYR A 347 PHE 0.011 0.001 PHE E 393 TRP 0.010 0.001 TRP F 398 HIS 0.002 0.001 HIS G 298 Details of bonding type rmsd covalent geometry : bond 0.00458 (14666) covalent geometry : angle 0.65103 (19974) SS BOND : bond 0.00962 ( 16) SS BOND : angle 1.62152 ( 32) hydrogen bonds : bond 0.05102 ( 470) hydrogen bonds : angle 6.53599 ( 1329) link_BETA1-4 : bond 0.00524 ( 16) link_BETA1-4 : angle 2.45905 ( 48) link_NAG-ASN : bond 0.00310 ( 7) link_NAG-ASN : angle 1.50426 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 GLN cc_start: 0.7925 (mp10) cc_final: 0.7317 (mm-40) REVERT: C 319 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8797 (tt0) REVERT: C 331 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8269 (mp10) REVERT: D 377 SER cc_start: 0.8800 (m) cc_final: 0.8520 (p) REVERT: D 401 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: D 427 ARG cc_start: 0.7831 (tpt-90) cc_final: 0.7470 (tpt-90) REVERT: E 414 MET cc_start: 0.8164 (tpt) cc_final: 0.7961 (tpt) REVERT: G 244 CYS cc_start: 0.3921 (p) cc_final: 0.2569 (p) REVERT: G 412 GLU cc_start: 0.8870 (tt0) cc_final: 0.8581 (tt0) outliers start: 30 outliers final: 14 residues processed: 181 average time/residue: 1.1054 time to fit residues: 220.9481 Evaluate side-chains 153 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 406 SER Chi-restraints excluded: chain H residue 420 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** H 443 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 = 0.4208 r_free = 0.4208 target = 0.151813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.094277 restraints weight = 102530.408| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.48 r_work: 0.3036 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14705 Z= 0.122 Angle : 0.603 8.441 20075 Z= 0.305 Chirality : 0.046 0.183 2401 Planarity : 0.004 0.039 2510 Dihedral : 7.301 64.187 2400 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.52 % Allowed : 20.28 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.19), residues: 1758 helix: -2.12 (0.31), residues: 194 sheet: -0.31 (0.18), residues: 726 loop : -1.78 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 444 TYR 0.014 0.001 TYR A 347 PHE 0.007 0.001 PHE G 346 TRP 0.012 0.001 TRP G 258 HIS 0.002 0.001 HIS H 411 Details of bonding type rmsd covalent geometry : bond 0.00293 (14666) covalent geometry : angle 0.59138 (19974) SS BOND : bond 0.00682 ( 16) SS BOND : angle 1.33854 ( 32) hydrogen bonds : bond 0.04288 ( 470) hydrogen bonds : angle 6.00975 ( 1329) link_BETA1-4 : bond 0.00501 ( 16) link_BETA1-4 : angle 2.20922 ( 48) link_NAG-ASN : bond 0.00314 ( 7) link_NAG-ASN : angle 1.16531 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 GLN cc_start: 0.7881 (mp10) cc_final: 0.7245 (mm-40) REVERT: B 244 CYS cc_start: 0.4536 (p) cc_final: 0.3342 (p) REVERT: B 286 TRP cc_start: 0.7515 (t60) cc_final: 0.7141 (t60) REVERT: C 231 LEU cc_start: 0.8282 (tp) cc_final: 0.7738 (tp) REVERT: C 234 MET cc_start: 0.8612 (mtp) cc_final: 0.8252 (mpp) REVERT: C 319 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8763 (tt0) REVERT: C 331 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8274 (mp10) REVERT: D 377 SER cc_start: 0.8804 (m) cc_final: 0.8492 (p) REVERT: D 401 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8318 (mt-10) REVERT: E 230 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8398 (t) REVERT: E 414 MET cc_start: 0.8239 (tpt) cc_final: 0.8023 (tpt) REVERT: F 234 MET cc_start: 0.8604 (mmt) cc_final: 0.8398 (mmm) REVERT: G 234 MET cc_start: 0.8666 (mmm) cc_final: 0.7900 (tpt) REVERT: G 412 GLU cc_start: 0.8849 (tt0) cc_final: 0.8607 (tt0) outliers start: 25 outliers final: 15 residues processed: 170 average time/residue: 1.1209 time to fit residues: 210.0491 Evaluate side-chains 154 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain H residue 406 SER Chi-restraints excluded: chain H residue 420 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 16 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 ASN ** H 443 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 = 0.4195 r_free = 0.4195 target = 0.151932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094599 restraints weight = 90159.599| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.96 r_work: 0.3057 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14705 Z= 0.148 Angle : 0.603 7.455 20075 Z= 0.307 Chirality : 0.045 0.170 2401 Planarity : 0.004 0.044 2510 Dihedral : 6.237 59.887 2400 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.77 % Allowed : 20.34 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.19), residues: 1758 helix: -2.18 (0.31), residues: 196 sheet: -0.18 (0.18), residues: 722 loop : -1.71 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 444 TYR 0.015 0.001 TYR A 347 PHE 0.009 0.001 PHE G 346 TRP 0.010 0.001 TRP B 258 HIS 0.002 0.001 HIS H 298 Details of bonding type rmsd covalent geometry : bond 0.00359 (14666) covalent geometry : angle 0.59223 (19974) SS BOND : bond 0.00654 ( 16) SS BOND : angle 1.38560 ( 32) hydrogen bonds : bond 0.04088 ( 470) hydrogen bonds : angle 5.77543 ( 1329) link_BETA1-4 : bond 0.00400 ( 16) link_BETA1-4 : angle 2.07834 ( 48) link_NAG-ASN : bond 0.00309 ( 7) link_NAG-ASN : angle 1.11554 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 GLN cc_start: 0.8003 (mp10) cc_final: 0.7379 (mm-40) REVERT: B 286 TRP cc_start: 0.7493 (t60) cc_final: 0.7290 (t60) REVERT: C 234 MET cc_start: 0.8671 (mtp) cc_final: 0.8411 (mpp) REVERT: C 319 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8795 (tt0) REVERT: C 331 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8249 (mp10) REVERT: D 377 SER cc_start: 0.8803 (m) cc_final: 0.8485 (p) REVERT: D 401 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: E 414 MET cc_start: 0.8250 (tpt) cc_final: 0.8032 (tpt) REVERT: F 234 MET cc_start: 0.8633 (mmt) cc_final: 0.8412 (mmm) REVERT: G 234 MET cc_start: 0.8609 (mmm) cc_final: 0.7777 (tpt) REVERT: G 412 GLU cc_start: 0.8878 (tt0) cc_final: 0.8629 (tt0) outliers start: 29 outliers final: 19 residues processed: 165 average time/residue: 1.1223 time to fit residues: 204.1624 Evaluate side-chains 154 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 400 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 406 SER Chi-restraints excluded: chain H residue 420 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 130 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 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 = 0.4197 r_free = 0.4197 target = 0.151783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093664 restraints weight = 112867.939| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.37 r_work: 0.3035 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14705 Z= 0.125 Angle : 0.585 7.947 20075 Z= 0.297 Chirality : 0.045 0.170 2401 Planarity : 0.003 0.040 2510 Dihedral : 5.835 59.526 2400 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.40 % Allowed : 20.95 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.19), residues: 1758 helix: -2.20 (0.33), residues: 184 sheet: -0.03 (0.18), residues: 718 loop : -1.55 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 269 TYR 0.014 0.001 TYR A 347 PHE 0.007 0.001 PHE G 346 TRP 0.008 0.001 TRP B 258 HIS 0.002 0.001 HIS H 298 Details of bonding type rmsd covalent geometry : bond 0.00304 (14666) covalent geometry : angle 0.57705 (19974) SS BOND : bond 0.00625 ( 16) SS BOND : angle 1.25301 ( 32) hydrogen bonds : bond 0.03822 ( 470) hydrogen bonds : angle 5.57850 ( 1329) link_BETA1-4 : bond 0.00390 ( 16) link_BETA1-4 : angle 1.82324 ( 48) link_NAG-ASN : bond 0.00337 ( 7) link_NAG-ASN : angle 0.94355 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.7887 (tpt) cc_final: 0.7683 (tpt) REVERT: B 234 MET cc_start: 0.8699 (mmm) cc_final: 0.8400 (mpp) REVERT: B 241 GLN cc_start: 0.8009 (mp10) cc_final: 0.7391 (mm-40) REVERT: B 286 TRP cc_start: 0.7481 (t60) cc_final: 0.7184 (t60) REVERT: C 231 LEU cc_start: 0.8378 (tp) cc_final: 0.7687 (tp) REVERT: C 234 MET cc_start: 0.8670 (mtp) cc_final: 0.8304 (mpp) REVERT: C 319 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8787 (tt0) REVERT: C 331 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8209 (mp10) REVERT: D 377 SER cc_start: 0.8814 (m) cc_final: 0.8491 (p) REVERT: D 401 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: E 414 MET cc_start: 0.8265 (tpt) cc_final: 0.8055 (tpt) REVERT: F 234 MET cc_start: 0.8626 (mmt) cc_final: 0.8405 (mmm) REVERT: G 234 MET cc_start: 0.8571 (mmm) cc_final: 0.7745 (tpt) REVERT: G 412 GLU cc_start: 0.8895 (tt0) cc_final: 0.8661 (tt0) REVERT: H 269 ARG cc_start: 0.7332 (tpp80) cc_final: 0.7129 (tpp80) outliers start: 23 outliers final: 21 residues processed: 154 average time/residue: 1.1790 time to fit residues: 201.4064 Evaluate side-chains 154 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 406 SER Chi-restraints excluded: chain H residue 420 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 161 optimal weight: 40.0000 chunk 166 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.146912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088553 restraints weight = 102739.353| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.53 r_work: 0.2976 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14705 Z= 0.179 Angle : 0.608 8.210 20075 Z= 0.312 Chirality : 0.045 0.158 2401 Planarity : 0.003 0.050 2510 Dihedral : 5.870 59.921 2399 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.83 % Allowed : 20.34 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.19), residues: 1758 helix: -2.22 (0.33), residues: 184 sheet: -0.01 (0.19), residues: 718 loop : -1.55 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 269 TYR 0.016 0.001 TYR A 347 PHE 0.012 0.001 PHE E 292 TRP 0.011 0.001 TRP H 258 HIS 0.003 0.001 HIS H 298 Details of bonding type rmsd covalent geometry : bond 0.00435 (14666) covalent geometry : angle 0.59977 (19974) SS BOND : bond 0.00706 ( 16) SS BOND : angle 1.45522 ( 32) hydrogen bonds : bond 0.04172 ( 470) hydrogen bonds : angle 5.59320 ( 1329) link_BETA1-4 : bond 0.00394 ( 16) link_BETA1-4 : angle 1.72325 ( 48) link_NAG-ASN : bond 0.00244 ( 7) link_NAG-ASN : angle 1.07951 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 LEU cc_start: 0.8477 (tp) cc_final: 0.8022 (tp) REVERT: B 236 MET cc_start: 0.7793 (mmt) cc_final: 0.7556 (mpt) REVERT: B 241 GLN cc_start: 0.8112 (mp10) cc_final: 0.7547 (mm-40) REVERT: B 286 TRP cc_start: 0.7683 (t60) cc_final: 0.7353 (t60) REVERT: C 234 MET cc_start: 0.8655 (mtp) cc_final: 0.8360 (mpp) REVERT: C 319 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8735 (tt0) REVERT: D 401 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: E 230 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8392 (t) REVERT: F 234 MET cc_start: 0.8605 (mmt) cc_final: 0.8388 (mmm) REVERT: G 234 MET cc_start: 0.8579 (mmm) cc_final: 0.7737 (tpt) outliers start: 30 outliers final: 19 residues processed: 157 average time/residue: 0.9711 time to fit residues: 170.1860 Evaluate side-chains 149 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 400 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 395 ASN Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 406 SER Chi-restraints excluded: chain H residue 420 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.148209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090324 restraints weight = 96427.046| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 4.43 r_work: 0.3010 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14705 Z= 0.110 Angle : 0.572 6.668 20075 Z= 0.293 Chirality : 0.045 0.169 2401 Planarity : 0.003 0.047 2510 Dihedral : 5.602 59.416 2399 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.40 % Allowed : 20.77 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.19), residues: 1758 helix: -2.10 (0.34), residues: 184 sheet: 0.09 (0.19), residues: 714 loop : -1.49 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 269 TYR 0.014 0.001 TYR A 347 PHE 0.008 0.001 PHE D 292 TRP 0.013 0.001 TRP H 258 HIS 0.002 0.001 HIS G 298 Details of bonding type rmsd covalent geometry : bond 0.00262 (14666) covalent geometry : angle 0.56634 (19974) SS BOND : bond 0.00777 ( 16) SS BOND : angle 1.17436 ( 32) hydrogen bonds : bond 0.03644 ( 470) hydrogen bonds : angle 5.41187 ( 1329) link_BETA1-4 : bond 0.00399 ( 16) link_BETA1-4 : angle 1.50009 ( 48) link_NAG-ASN : bond 0.00397 ( 7) link_NAG-ASN : angle 0.75469 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 LEU cc_start: 0.8373 (tp) cc_final: 0.7966 (tp) REVERT: B 236 MET cc_start: 0.7779 (mmt) cc_final: 0.7533 (mpt) REVERT: B 241 GLN cc_start: 0.8120 (mp10) cc_final: 0.7570 (mm-40) REVERT: B 286 TRP cc_start: 0.7469 (t60) cc_final: 0.7239 (t60) REVERT: C 231 LEU cc_start: 0.8241 (tp) cc_final: 0.7566 (tp) REVERT: C 234 MET cc_start: 0.8611 (mtp) cc_final: 0.8243 (mpp) REVERT: C 319 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8705 (tt0) REVERT: C 331 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8078 (mp10) REVERT: D 401 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: E 230 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8414 (t) REVERT: F 234 MET cc_start: 0.8573 (mmt) cc_final: 0.8363 (mmm) REVERT: G 234 MET cc_start: 0.8552 (mmm) cc_final: 0.7614 (tpp) outliers start: 23 outliers final: 23 residues processed: 152 average time/residue: 1.0022 time to fit residues: 168.8288 Evaluate side-chains 155 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 406 SER Chi-restraints excluded: chain H residue 420 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 172 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 395 ASN H 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.147551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.089605 restraints weight = 98641.441| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 4.44 r_work: 0.3004 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14705 Z= 0.137 Angle : 0.582 10.106 20075 Z= 0.296 Chirality : 0.045 0.165 2401 Planarity : 0.003 0.044 2510 Dihedral : 5.516 59.379 2399 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.40 % Allowed : 20.95 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.19), residues: 1758 helix: -2.13 (0.33), residues: 184 sheet: 0.13 (0.19), residues: 714 loop : -1.46 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 269 TYR 0.014 0.001 TYR A 347 PHE 0.012 0.001 PHE D 292 TRP 0.017 0.001 TRP H 258 HIS 0.002 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00335 (14666) covalent geometry : angle 0.57564 (19974) SS BOND : bond 0.00619 ( 16) SS BOND : angle 1.33392 ( 32) hydrogen bonds : bond 0.03787 ( 470) hydrogen bonds : angle 5.38433 ( 1329) link_BETA1-4 : bond 0.00361 ( 16) link_BETA1-4 : angle 1.50017 ( 48) link_NAG-ASN : bond 0.00309 ( 7) link_NAG-ASN : angle 0.89190 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 LEU cc_start: 0.8433 (tp) cc_final: 0.8072 (tp) REVERT: B 241 GLN cc_start: 0.8147 (mp10) cc_final: 0.7618 (mm-40) REVERT: C 231 LEU cc_start: 0.8355 (tp) cc_final: 0.7633 (tp) REVERT: C 234 MET cc_start: 0.8645 (mtp) cc_final: 0.8290 (mpp) REVERT: C 319 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8772 (tt0) REVERT: C 331 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8058 (mp10) REVERT: D 401 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8375 (mt-10) REVERT: E 230 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8424 (t) REVERT: F 234 MET cc_start: 0.8624 (mmt) cc_final: 0.8388 (mmm) REVERT: G 234 MET cc_start: 0.8566 (mmm) cc_final: 0.7626 (tpp) outliers start: 23 outliers final: 22 residues processed: 151 average time/residue: 1.0095 time to fit residues: 170.2383 Evaluate side-chains 153 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 406 SER Chi-restraints excluded: chain H residue 420 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 92 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 2 optimal weight: 40.0000 chunk 22 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.148126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090192 restraints weight = 101369.912| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 4.47 r_work: 0.3023 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14705 Z= 0.111 Angle : 0.570 7.696 20075 Z= 0.291 Chirality : 0.044 0.167 2401 Planarity : 0.003 0.044 2510 Dihedral : 5.378 58.941 2399 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.40 % Allowed : 21.07 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.19), residues: 1758 helix: -2.08 (0.34), residues: 184 sheet: 0.17 (0.19), residues: 718 loop : -1.42 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 269 TYR 0.014 0.001 TYR A 347 PHE 0.009 0.001 PHE D 292 TRP 0.022 0.001 TRP H 258 HIS 0.001 0.001 HIS H 298 Details of bonding type rmsd covalent geometry : bond 0.00270 (14666) covalent geometry : angle 0.56486 (19974) SS BOND : bond 0.00584 ( 16) SS BOND : angle 1.07427 ( 32) hydrogen bonds : bond 0.03556 ( 470) hydrogen bonds : angle 5.28738 ( 1329) link_BETA1-4 : bond 0.00424 ( 16) link_BETA1-4 : angle 1.43527 ( 48) link_NAG-ASN : bond 0.00377 ( 7) link_NAG-ASN : angle 0.76546 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8141 (tpt) cc_final: 0.7718 (tpt) REVERT: A 414 MET cc_start: 0.7401 (tpt) cc_final: 0.7134 (tpt) REVERT: B 234 MET cc_start: 0.8678 (mmm) cc_final: 0.8296 (tpt) REVERT: B 241 GLN cc_start: 0.8178 (mp10) cc_final: 0.7433 (mm-40) REVERT: C 231 LEU cc_start: 0.8384 (tp) cc_final: 0.7677 (tp) REVERT: C 234 MET cc_start: 0.8638 (mtp) cc_final: 0.8277 (mpp) REVERT: C 319 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8764 (tt0) REVERT: C 331 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8082 (mp10) REVERT: D 401 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: E 230 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8426 (t) REVERT: G 234 MET cc_start: 0.8565 (mmm) cc_final: 0.7605 (tpp) REVERT: G 331 GLN cc_start: 0.7857 (pm20) cc_final: 0.7655 (mp10) outliers start: 23 outliers final: 21 residues processed: 152 average time/residue: 1.0642 time to fit residues: 179.8913 Evaluate side-chains 153 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 406 SER Chi-restraints excluded: chain H residue 420 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 109 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 139 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.146777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088730 restraints weight = 98993.061| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 4.40 r_work: 0.2977 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14705 Z= 0.187 Angle : 0.612 9.830 20075 Z= 0.313 Chirality : 0.045 0.157 2401 Planarity : 0.003 0.045 2510 Dihedral : 5.565 59.269 2399 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.28 % Allowed : 21.32 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.19), residues: 1758 helix: -2.16 (0.33), residues: 184 sheet: 0.08 (0.19), residues: 722 loop : -1.42 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 269 TYR 0.013 0.001 TYR A 347 PHE 0.016 0.001 PHE D 292 TRP 0.027 0.002 TRP B 286 HIS 0.002 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00458 (14666) covalent geometry : angle 0.60566 (19974) SS BOND : bond 0.00666 ( 16) SS BOND : angle 1.43950 ( 32) hydrogen bonds : bond 0.04047 ( 470) hydrogen bonds : angle 5.41162 ( 1329) link_BETA1-4 : bond 0.00354 ( 16) link_BETA1-4 : angle 1.51908 ( 48) link_NAG-ASN : bond 0.00248 ( 7) link_NAG-ASN : angle 0.99614 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8169 (tpt) cc_final: 0.7586 (tpt) REVERT: B 234 MET cc_start: 0.8668 (mmm) cc_final: 0.8160 (tpt) REVERT: B 236 MET cc_start: 0.7771 (mmt) cc_final: 0.7537 (mpt) REVERT: B 241 GLN cc_start: 0.8031 (mp10) cc_final: 0.7546 (mm-40) REVERT: C 231 LEU cc_start: 0.8354 (tp) cc_final: 0.7686 (tp) REVERT: C 234 MET cc_start: 0.8649 (mtp) cc_final: 0.8286 (mpp) REVERT: C 319 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8778 (tt0) REVERT: C 331 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8021 (mp10) REVERT: D 401 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8333 (mt-10) REVERT: E 230 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8443 (t) REVERT: F 234 MET cc_start: 0.8634 (mmm) cc_final: 0.8360 (mmt) REVERT: G 234 MET cc_start: 0.8559 (mmm) cc_final: 0.7605 (tpp) REVERT: H 431 GLN cc_start: 0.8440 (tp40) cc_final: 0.7825 (mp10) outliers start: 21 outliers final: 18 residues processed: 150 average time/residue: 1.1321 time to fit residues: 188.9152 Evaluate side-chains 149 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 406 SER Chi-restraints excluded: chain H residue 420 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 116 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.148094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090349 restraints weight = 96409.520| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 4.35 r_work: 0.3002 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14705 Z= 0.112 Angle : 0.573 9.036 20075 Z= 0.293 Chirality : 0.045 0.167 2401 Planarity : 0.003 0.045 2510 Dihedral : 5.385 58.542 2399 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.34 % Allowed : 21.62 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.20), residues: 1758 helix: -2.05 (0.35), residues: 184 sheet: 0.17 (0.19), residues: 718 loop : -1.37 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 269 TYR 0.014 0.001 TYR A 347 PHE 0.008 0.001 PHE D 292 TRP 0.031 0.001 TRP A 258 HIS 0.001 0.001 HIS D 298 Details of bonding type rmsd covalent geometry : bond 0.00269 (14666) covalent geometry : angle 0.56868 (19974) SS BOND : bond 0.00708 ( 16) SS BOND : angle 1.07995 ( 32) hydrogen bonds : bond 0.03571 ( 470) hydrogen bonds : angle 5.25483 ( 1329) link_BETA1-4 : bond 0.00390 ( 16) link_BETA1-4 : angle 1.39295 ( 48) link_NAG-ASN : bond 0.00414 ( 7) link_NAG-ASN : angle 0.72522 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9768.45 seconds wall clock time: 165 minutes 45.75 seconds (9945.75 seconds total)