Starting phenix.real_space_refine on Tue Jun 24 17:29:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghz_40054/06_2025/8ghz_40054_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghz_40054/06_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_40054/06_2025/8ghz_40054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghz_40054/06_2025/8ghz_40054.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghz_40054/06_2025/8ghz_40054_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghz_40054/06_2025/8ghz_40054_trim.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.73, per 1000 atoms: 0.66 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: 7.84 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.90 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: 10.28 Time building geometry restraints manager: 9.40 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.490 Extract box with map and model: 1.080 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 65.450 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 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:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (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 TRP 0.013 0.001 TRP D 398 HIS 0.005 0.001 HIS C 411 PHE 0.013 0.001 PHE G 373 TYR 0.022 0.001 TYR H 388 ARG 0.004 0.001 ARG E 427 Details of bonding type rmsd link_NAG-ASN : bond 0.02216 ( 7) link_NAG-ASN : angle 3.80369 ( 21) link_BETA1-4 : bond 0.00417 ( 16) link_BETA1-4 : angle 1.59759 ( 48) hydrogen bonds : bond 0.17077 ( 470) hydrogen bonds : angle 8.26815 ( 1329) SS BOND : bond 0.00729 ( 16) SS BOND : angle 1.55819 ( 32) covalent geometry : bond 0.00401 (14666) covalent geometry : angle 0.71910 (19974) *********************** 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 : 2.180 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: 0.8122 (mp10) cc_final: 0.7432 (mm-40) 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: 2.6835 time to fit residues: 633.7666 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 : 2.092 ------------------------------------------------------------------------------- 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 148 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 71 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 159 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** C 443 GLN ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.148930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088566 restraints weight = 95187.416| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.44 r_work: 0.3090 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14705 Z= 0.122 Angle : 0.621 8.203 20075 Z= 0.316 Chirality : 0.047 0.199 2401 Planarity : 0.004 0.050 2510 Dihedral : 10.763 76.517 2407 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.34 % Favored : 95.61 % Rotamer: Outliers : 1.52 % Allowed : 19.67 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.19), residues: 1758 helix: -2.15 (0.32), residues: 192 sheet: -0.39 (0.18), residues: 700 loop : -1.93 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 398 HIS 0.001 0.001 HIS B 298 PHE 0.009 0.001 PHE E 393 TYR 0.013 0.001 TYR A 347 ARG 0.004 0.000 ARG D 427 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 7) link_NAG-ASN : angle 1.48312 ( 21) link_BETA1-4 : bond 0.00617 ( 16) link_BETA1-4 : angle 2.37390 ( 48) hydrogen bonds : bond 0.04903 ( 470) hydrogen bonds : angle 6.47110 ( 1329) SS BOND : bond 0.00677 ( 16) SS BOND : angle 1.29402 ( 32) covalent geometry : bond 0.00278 (14666) covalent geometry : angle 0.60790 (19974) *********************** 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 182 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 2.207 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: 0.7956 (mp10) cc_final: 0.7307 (mm-40) REVERT: C 231 LEU cc_start: 0.8144 (tp) cc_final: 0.7774 (tp) REVERT: C 234 MET cc_start: 0.8567 (mtp) cc_final: 0.8325 (mpp) REVERT: C 319 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8801 (tt0) REVERT: C 331 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8271 (mp10) REVERT: D 377 SER cc_start: 0.8741 (m) cc_final: 0.8484 (p) REVERT: D 401 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: F 234 MET cc_start: 0.8481 (mmm) cc_final: 0.8242 (mmt) REVERT: G 244 CYS cc_start: 0.3815 (p) cc_final: 0.2503 (p) REVERT: G 412 GLU cc_start: 0.8865 (tt0) cc_final: 0.8585 (tt0) REVERT: H 422 MET cc_start: 0.8412 (mtp) cc_final: 0.8150 (mtp) outliers start: 25 outliers final: 9 residues processed: 177 average time/residue: 2.7052 time to fit residues: 528.9361 Evaluate side-chains 153 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL 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 386 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 434 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 163 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 0.0870 chunk 104 optimal weight: 0.5980 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 ASN ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.154585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097180 restraints weight = 99825.916| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 4.18 r_work: 0.3028 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1744 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= 0.111 Angle : 0.589 8.428 20075 Z= 0.296 Chirality : 0.046 0.185 2401 Planarity : 0.004 0.040 2510 Dihedral : 7.505 70.298 2400 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.22 % Allowed : 19.98 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.19), residues: 1758 helix: -2.05 (0.32), residues: 194 sheet: -0.22 (0.18), residues: 714 loop : -1.73 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 286 HIS 0.002 0.001 HIS B 298 PHE 0.006 0.001 PHE G 346 TYR 0.013 0.001 TYR A 347 ARG 0.003 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 7) link_NAG-ASN : angle 1.27203 ( 21) link_BETA1-4 : bond 0.00445 ( 16) link_BETA1-4 : angle 2.14555 ( 48) hydrogen bonds : bond 0.04132 ( 470) hydrogen bonds : angle 5.94993 ( 1329) SS BOND : bond 0.00835 ( 16) SS BOND : angle 1.20459 ( 32) covalent geometry : bond 0.00262 (14666) covalent geometry : angle 0.57740 (19974) *********************** 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 168 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 2.186 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: 0.7869 (mp10) cc_final: 0.7227 (mm-40) REVERT: B 244 CYS cc_start: 0.4884 (p) cc_final: 0.3692 (p) REVERT: B 286 TRP cc_start: 0.7454 (t60) cc_final: 0.7082 (t60) REVERT: C 231 LEU cc_start: 0.8080 (tp) cc_final: 0.7820 (tp) REVERT: C 234 MET cc_start: 0.8573 (mtp) cc_final: 0.8318 (mpp) REVERT: C 319 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: C 331 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8265 (mp10) REVERT: C 439 LEU cc_start: 0.8967 (tp) cc_final: 0.8701 (tm) REVERT: D 377 SER cc_start: 0.8723 (m) cc_final: 0.8429 (p) REVERT: D 401 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: D 427 ARG cc_start: 0.8278 (tmt170) cc_final: 0.7761 (tpt-90) REVERT: F 234 MET cc_start: 0.8482 (mmm) cc_final: 0.8276 (mmt) REVERT: G 234 MET cc_start: 0.8634 (mmm) cc_final: 0.7868 (tpt) REVERT: G 412 GLU cc_start: 0.8896 (tt0) cc_final: 0.8603 (tt0) REVERT: H 422 MET cc_start: 0.8366 (mtp) cc_final: 0.8115 (mtp) outliers start: 20 outliers final: 12 residues processed: 165 average time/residue: 2.6577 time to fit residues: 482.9305 Evaluate side-chains 148 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 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 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 266 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain H residue 266 LEU 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 43 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN B 288 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.149012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.091242 restraints weight = 102286.606| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.22 r_work: 0.2992 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14705 Z= 0.150 Angle : 0.596 7.870 20075 Z= 0.303 Chirality : 0.045 0.166 2401 Planarity : 0.004 0.066 2510 Dihedral : 6.211 60.726 2399 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.34 % Allowed : 20.04 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.19), residues: 1758 helix: -2.25 (0.31), residues: 196 sheet: -0.20 (0.18), residues: 726 loop : -1.69 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 286 HIS 0.002 0.001 HIS H 298 PHE 0.009 0.001 PHE G 346 TYR 0.014 0.001 TYR A 347 ARG 0.007 0.000 ARG A 312 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 7) link_NAG-ASN : angle 1.19486 ( 21) link_BETA1-4 : bond 0.00390 ( 16) link_BETA1-4 : angle 2.06528 ( 48) hydrogen bonds : bond 0.04089 ( 470) hydrogen bonds : angle 5.75669 ( 1329) SS BOND : bond 0.00653 ( 16) SS BOND : angle 1.39234 ( 32) covalent geometry : bond 0.00362 (14666) covalent geometry : angle 0.58514 (19974) *********************** 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 161 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 2.267 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 236 MET cc_start: 0.7816 (mmt) cc_final: 0.7588 (mpt) REVERT: B 241 GLN cc_start: 0.7895 (mp10) cc_final: 0.7294 (mm-40) REVERT: B 286 TRP cc_start: 0.7429 (t60) cc_final: 0.7187 (t60) REVERT: C 231 LEU cc_start: 0.8102 (tp) cc_final: 0.7783 (tp) REVERT: C 234 MET cc_start: 0.8628 (mtp) cc_final: 0.8368 (mpp) REVERT: C 319 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8713 (tt0) REVERT: C 331 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8203 (mp10) REVERT: C 439 LEU cc_start: 0.8949 (tp) cc_final: 0.8677 (tm) REVERT: D 377 SER cc_start: 0.8793 (m) cc_final: 0.8458 (p) REVERT: D 401 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8261 (mt-10) REVERT: E 230 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8356 (t) REVERT: F 234 MET cc_start: 0.8476 (mmm) cc_final: 0.8266 (mmt) REVERT: G 234 MET cc_start: 0.8549 (mmm) cc_final: 0.7860 (tpt) REVERT: G 412 GLU cc_start: 0.8849 (tt0) cc_final: 0.8577 (tt0) outliers start: 22 outliers final: 13 residues processed: 157 average time/residue: 2.4798 time to fit residues: 431.1067 Evaluate side-chains 147 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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 420 ILE 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 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 420 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 95 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 76 optimal weight: 0.2980 chunk 155 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** G 430 ASN ** 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 = 0.4201 r_free = 0.4201 target = 0.151754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094508 restraints weight = 87548.609| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.99 r_work: 0.3056 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2301 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= 0.134 Angle : 0.589 9.139 20075 Z= 0.299 Chirality : 0.045 0.182 2401 Planarity : 0.003 0.043 2510 Dihedral : 5.784 59.546 2398 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.40 % Allowed : 20.28 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1758 helix: -2.19 (0.32), residues: 198 sheet: -0.02 (0.19), residues: 718 loop : -1.61 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 258 HIS 0.001 0.001 HIS A 411 PHE 0.008 0.001 PHE G 346 TYR 0.014 0.001 TYR A 347 ARG 0.004 0.000 ARG A 312 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 7) link_NAG-ASN : angle 1.00432 ( 21) link_BETA1-4 : bond 0.00382 ( 16) link_BETA1-4 : angle 1.83034 ( 48) hydrogen bonds : bond 0.03874 ( 470) hydrogen bonds : angle 5.56680 ( 1329) SS BOND : bond 0.00652 ( 16) SS BOND : angle 1.33825 ( 32) covalent geometry : bond 0.00324 (14666) covalent geometry : angle 0.58001 (19974) *********************** 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 160 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 2.092 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 241 GLN cc_start: 0.7981 (mp10) cc_final: 0.7376 (mm-40) REVERT: C 231 LEU cc_start: 0.8339 (tp) cc_final: 0.7949 (tp) REVERT: C 234 MET cc_start: 0.8627 (mtp) cc_final: 0.8377 (mpp) REVERT: C 319 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8796 (tt0) REVERT: C 331 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8203 (mp10) REVERT: C 439 LEU cc_start: 0.9056 (tp) cc_final: 0.8823 (tm) REVERT: D 377 SER cc_start: 0.8832 (m) cc_final: 0.8519 (p) REVERT: D 401 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: D 427 ARG cc_start: 0.8303 (tmt170) cc_final: 0.7887 (tmt170) REVERT: E 230 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8432 (t) REVERT: G 234 MET cc_start: 0.8572 (mmm) cc_final: 0.7936 (tpt) REVERT: G 412 GLU cc_start: 0.8891 (tt0) cc_final: 0.8648 (tt0) REVERT: H 269 ARG cc_start: 0.7261 (tpp80) cc_final: 0.7053 (tpp80) outliers start: 23 outliers final: 18 residues processed: 156 average time/residue: 2.5170 time to fit residues: 441.0538 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 : 2.226 ------------------------------------------------------------------------------- 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 420 ILE Chi-restraints excluded: chain C residue 434 LEU 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 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 420 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 50 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 29 optimal weight: 30.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.148182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090229 restraints weight = 102193.031| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 4.20 r_work: 0.3047 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14705 Z= 0.153 Angle : 0.592 8.617 20075 Z= 0.301 Chirality : 0.045 0.162 2401 Planarity : 0.003 0.044 2510 Dihedral : 5.724 59.560 2398 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.52 % Allowed : 20.22 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1758 helix: -2.23 (0.33), residues: 186 sheet: 0.06 (0.19), residues: 714 loop : -1.53 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 286 HIS 0.003 0.001 HIS H 298 PHE 0.009 0.001 PHE E 292 TYR 0.014 0.001 TYR A 347 ARG 0.006 0.000 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 7) link_NAG-ASN : angle 1.02436 ( 21) link_BETA1-4 : bond 0.00366 ( 16) link_BETA1-4 : angle 1.77443 ( 48) hydrogen bonds : bond 0.03945 ( 470) hydrogen bonds : angle 5.51809 ( 1329) SS BOND : bond 0.00667 ( 16) SS BOND : angle 1.37494 ( 32) covalent geometry : bond 0.00373 (14666) covalent geometry : angle 0.58394 (19974) *********************** 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 156 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 2.097 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: B 231 LEU cc_start: 0.8504 (tp) cc_final: 0.8034 (tp) REVERT: B 236 MET cc_start: 0.7800 (mmt) cc_final: 0.7541 (mpt) REVERT: B 241 GLN cc_start: 0.8120 (mp10) cc_final: 0.7500 (mm-40) REVERT: C 231 LEU cc_start: 0.8372 (tp) cc_final: 0.7984 (tp) REVERT: C 234 MET cc_start: 0.8634 (mtp) cc_final: 0.8390 (mpp) REVERT: C 319 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8798 (tt0) REVERT: C 439 LEU cc_start: 0.9059 (tp) cc_final: 0.8826 (tm) REVERT: D 401 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: D 427 ARG cc_start: 0.8335 (tmt170) cc_final: 0.7923 (tmt170) REVERT: E 230 SER cc_start: 0.8928 (OUTLIER) cc_final: 0.8425 (t) REVERT: F 234 MET cc_start: 0.8607 (mmt) cc_final: 0.8374 (mmm) REVERT: G 234 MET cc_start: 0.8595 (mmm) cc_final: 0.7941 (tpt) REVERT: G 412 GLU cc_start: 0.8917 (tt0) cc_final: 0.8688 (tt0) outliers start: 25 outliers final: 20 residues processed: 153 average time/residue: 2.3671 time to fit residues: 402.9261 Evaluate side-chains 152 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 2.143 ------------------------------------------------------------------------------- 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 420 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 420 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 9.9990 chunk 161 optimal weight: 50.0000 chunk 152 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 ASN F 288 ASN H 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.147533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.089280 restraints weight = 104886.109| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 4.26 r_work: 0.3005 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14705 Z= 0.161 Angle : 0.597 9.221 20075 Z= 0.305 Chirality : 0.045 0.171 2401 Planarity : 0.003 0.044 2510 Dihedral : 5.661 59.370 2398 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.52 % Allowed : 20.40 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.19), residues: 1758 helix: -2.22 (0.33), residues: 186 sheet: 0.07 (0.19), residues: 718 loop : -1.51 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 258 HIS 0.002 0.001 HIS B 411 PHE 0.009 0.001 PHE E 346 TYR 0.015 0.001 TYR A 347 ARG 0.006 0.000 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 7) link_NAG-ASN : angle 0.98331 ( 21) link_BETA1-4 : bond 0.00366 ( 16) link_BETA1-4 : angle 1.60248 ( 48) hydrogen bonds : bond 0.03995 ( 470) hydrogen bonds : angle 5.48110 ( 1329) SS BOND : bond 0.00741 ( 16) SS BOND : angle 1.41140 ( 32) covalent geometry : bond 0.00393 (14666) covalent geometry : angle 0.59013 (19974) *********************** 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 157 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 2.190 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: A 234 MET cc_start: 0.7774 (tpt) cc_final: 0.7552 (tpt) REVERT: A 414 MET cc_start: 0.7620 (tpt) cc_final: 0.7410 (tpt) REVERT: A 431 GLN cc_start: 0.8162 (mp10) cc_final: 0.7939 (mp10) REVERT: B 231 LEU cc_start: 0.8433 (tp) cc_final: 0.8047 (tp) REVERT: B 241 GLN cc_start: 0.8082 (mp10) cc_final: 0.7317 (mm-40) REVERT: B 286 TRP cc_start: 0.8076 (t60) cc_final: 0.7423 (t60) REVERT: C 231 LEU cc_start: 0.8336 (tp) cc_final: 0.7931 (tp) REVERT: C 234 MET cc_start: 0.8637 (mtp) cc_final: 0.8375 (mpp) REVERT: C 319 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8752 (tt0) REVERT: C 331 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8104 (mp10) REVERT: C 439 LEU cc_start: 0.9050 (tp) cc_final: 0.8805 (tm) REVERT: D 401 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: D 427 ARG cc_start: 0.8327 (tmt170) cc_final: 0.7907 (tmt170) REVERT: E 230 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8409 (t) REVERT: G 234 MET cc_start: 0.8597 (mmm) cc_final: 0.7934 (tpt) REVERT: H 234 MET cc_start: 0.7613 (tpt) cc_final: 0.7103 (tpt) outliers start: 25 outliers final: 20 residues processed: 153 average time/residue: 2.4059 time to fit residues: 409.2795 Evaluate side-chains 151 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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 420 ILE Chi-restraints excluded: chain C residue 434 LEU 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 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 58 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 41 optimal weight: 0.0670 chunk 168 optimal weight: 3.9990 chunk 142 optimal weight: 0.0070 chunk 6 optimal weight: 10.0000 chunk 114 optimal weight: 0.0370 chunk 132 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.0218 ------------------------------------------------------------------------------- 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 = 0.147918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.089896 restraints weight = 97417.251| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.42 r_work: 0.2950 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14705 Z= 0.124 Angle : 0.576 9.850 20075 Z= 0.294 Chirality : 0.045 0.165 2401 Planarity : 0.003 0.051 2510 Dihedral : 5.487 59.108 2398 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.40 % Allowed : 20.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.19), residues: 1758 helix: -2.15 (0.33), residues: 186 sheet: 0.14 (0.19), residues: 714 loop : -1.46 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 258 HIS 0.002 0.001 HIS H 298 PHE 0.013 0.001 PHE D 292 TYR 0.014 0.001 TYR A 347 ARG 0.009 0.000 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 7) link_NAG-ASN : angle 0.83736 ( 21) link_BETA1-4 : bond 0.00360 ( 16) link_BETA1-4 : angle 1.48385 ( 48) hydrogen bonds : bond 0.03717 ( 470) hydrogen bonds : angle 5.36543 ( 1329) SS BOND : bond 0.00644 ( 16) SS BOND : angle 1.44029 ( 32) covalent geometry : bond 0.00302 (14666) covalent geometry : angle 0.56951 (19974) *********************** 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 : 2.107 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: A 414 MET cc_start: 0.7542 (tpt) cc_final: 0.7341 (tpt) REVERT: B 231 LEU cc_start: 0.8340 (tp) cc_final: 0.7992 (tp) REVERT: B 241 GLN cc_start: 0.7935 (mp10) cc_final: 0.7456 (mm-40) REVERT: B 286 TRP cc_start: 0.7812 (t60) cc_final: 0.7318 (t60) REVERT: C 234 MET cc_start: 0.8594 (mtp) cc_final: 0.8249 (mpp) REVERT: C 319 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: C 331 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8023 (mp10) REVERT: C 439 LEU cc_start: 0.9028 (tp) cc_final: 0.8762 (tm) REVERT: D 401 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: D 427 ARG cc_start: 0.8310 (tmt170) cc_final: 0.7884 (tmt170) REVERT: E 230 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8405 (t) REVERT: G 234 MET cc_start: 0.8603 (mmm) cc_final: 0.7914 (tpt) REVERT: H 269 ARG cc_start: 0.7028 (mmm160) cc_final: 0.6647 (tpp80) outliers start: 23 outliers final: 22 residues processed: 150 average time/residue: 2.4246 time to fit residues: 406.9651 Evaluate side-chains 154 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 2.807 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 434 LEU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 141 optimal weight: 0.0370 chunk 40 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.148625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090759 restraints weight = 93923.060| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.10 r_work: 0.3056 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- 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: 39 | |-----------------------------------------------------------------------------| |-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: 39 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14705 Z= 0.106 Angle : 0.582 11.253 20075 Z= 0.293 Chirality : 0.044 0.168 2401 Planarity : 0.003 0.051 2510 Dihedral : 5.260 58.598 2398 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.22 % Allowed : 20.65 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.19), residues: 1758 helix: -2.09 (0.33), residues: 188 sheet: 0.13 (0.19), residues: 722 loop : -1.39 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 258 HIS 0.002 0.001 HIS H 298 PHE 0.009 0.001 PHE D 292 TYR 0.014 0.001 TYR A 347 ARG 0.008 0.000 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 7) link_NAG-ASN : angle 0.75301 ( 21) link_BETA1-4 : bond 0.00428 ( 16) link_BETA1-4 : angle 1.42402 ( 48) hydrogen bonds : bond 0.03467 ( 470) hydrogen bonds : angle 5.21878 ( 1329) SS BOND : bond 0.00618 ( 16) SS BOND : angle 1.30405 ( 32) covalent geometry : bond 0.00255 (14666) covalent geometry : angle 0.57633 (19974) *********************** 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 149 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 2.318 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: A 414 MET cc_start: 0.7480 (tpt) cc_final: 0.7277 (tpt) REVERT: B 231 LEU cc_start: 0.8410 (tp) cc_final: 0.8017 (tp) REVERT: B 241 GLN cc_start: 0.7992 (mp10) cc_final: 0.7509 (mm-40) REVERT: C 234 MET cc_start: 0.8631 (mtp) cc_final: 0.8334 (mpp) REVERT: C 319 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8745 (tt0) REVERT: C 331 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8066 (mp10) REVERT: C 439 LEU cc_start: 0.9033 (tp) cc_final: 0.8813 (tm) REVERT: D 401 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: D 427 ARG cc_start: 0.8337 (tmt170) cc_final: 0.7916 (tmt170) REVERT: E 230 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8423 (t) REVERT: G 234 MET cc_start: 0.8614 (mmm) cc_final: 0.7938 (tpt) REVERT: G 331 GLN cc_start: 0.7866 (pm20) cc_final: 0.7630 (mp10) REVERT: H 269 ARG cc_start: 0.7166 (mmm160) cc_final: 0.6774 (tpp80) REVERT: H 431 GLN cc_start: 0.8485 (tp40) cc_final: 0.7841 (mp10) outliers start: 20 outliers final: 19 residues processed: 146 average time/residue: 2.3947 time to fit residues: 390.0264 Evaluate side-chains 150 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 2.427 ------------------------------------------------------------------------------- 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 C residue 226 ILE Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 434 LEU 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 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 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.148684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.090353 restraints weight = 118174.890| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.85 r_work: 0.3061 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- 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: 39 | |-----------------------------------------------------------------------------| |-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: 39 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2863 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= 0.112 Angle : 0.587 13.872 20075 Z= 0.294 Chirality : 0.044 0.166 2401 Planarity : 0.003 0.052 2510 Dihedral : 5.209 58.459 2398 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.22 % Allowed : 20.77 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.19), residues: 1758 helix: -2.08 (0.34), residues: 188 sheet: 0.18 (0.19), residues: 718 loop : -1.37 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 286 HIS 0.006 0.001 HIS A 298 PHE 0.016 0.001 PHE D 292 TYR 0.013 0.001 TYR A 347 ARG 0.008 0.000 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 7) link_NAG-ASN : angle 0.78755 ( 21) link_BETA1-4 : bond 0.00388 ( 16) link_BETA1-4 : angle 1.41262 ( 48) hydrogen bonds : bond 0.03492 ( 470) hydrogen bonds : angle 5.19082 ( 1329) SS BOND : bond 0.00636 ( 16) SS BOND : angle 1.16677 ( 32) covalent geometry : bond 0.00271 (14666) covalent geometry : angle 0.58169 (19974) ********************** 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 149 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 2.331 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: A 269 ARG cc_start: 0.6997 (tpp80) cc_final: 0.6675 (mpp-170) REVERT: B 234 MET cc_start: 0.8639 (mmm) cc_final: 0.8346 (tpt) REVERT: B 241 GLN cc_start: 0.8011 (mp10) cc_final: 0.7530 (mm-40) REVERT: C 234 MET cc_start: 0.8681 (mtp) cc_final: 0.8401 (mpp) REVERT: C 319 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8828 (tt0) REVERT: C 331 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8122 (mp10) REVERT: D 401 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8463 (mt-10) REVERT: D 427 ARG cc_start: 0.8358 (tmt170) cc_final: 0.7953 (tmt170) REVERT: E 230 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8465 (t) REVERT: G 234 MET cc_start: 0.8673 (mmm) cc_final: 0.8002 (tpt) REVERT: H 234 MET cc_start: 0.7611 (tpt) cc_final: 0.7116 (tpt) REVERT: H 269 ARG cc_start: 0.7205 (mmm160) cc_final: 0.6799 (tpp80) REVERT: H 431 GLN cc_start: 0.8554 (tp40) cc_final: 0.7900 (mp10) outliers start: 20 outliers final: 16 residues processed: 147 average time/residue: 2.4139 time to fit residues: 394.9193 Evaluate side-chains 144 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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 C residue 226 ILE Chi-restraints excluded: chain C residue 319 GLN 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 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 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 42 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 119 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.147339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089273 restraints weight = 91916.996| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.06 r_work: 0.3035 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2946 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= 0.168 Angle : 0.620 13.491 20075 Z= 0.312 Chirality : 0.045 0.157 2401 Planarity : 0.003 0.052 2510 Dihedral : 5.239 55.224 2397 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.22 % Allowed : 20.77 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1758 helix: -2.21 (0.33), residues: 188 sheet: 0.09 (0.19), residues: 722 loop : -1.39 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 286 HIS 0.006 0.001 HIS F 298 PHE 0.009 0.001 PHE E 346 TYR 0.013 0.001 TYR A 347 ARG 0.007 0.000 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 7) link_NAG-ASN : angle 0.96485 ( 21) link_BETA1-4 : bond 0.00374 ( 16) link_BETA1-4 : angle 1.47539 ( 48) hydrogen bonds : bond 0.03923 ( 470) hydrogen bonds : angle 5.30325 ( 1329) SS BOND : bond 0.00662 ( 16) SS BOND : angle 1.36227 ( 32) covalent geometry : bond 0.00410 (14666) covalent geometry : angle 0.61401 (19974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21892.29 seconds wall clock time: 371 minutes 49.60 seconds (22309.60 seconds total)