Starting phenix.real_space_refine on Tue Feb 20 15:58:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghz_40054/02_2024/8ghz_40054_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghz_40054/02_2024/8ghz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghz_40054/02_2024/8ghz_40054.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghz_40054/02_2024/8ghz_40054.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghz_40054/02_2024/8ghz_40054_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghz_40054/02_2024/8ghz_40054_trim.pdb" } 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 Residue "A ARG 444": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 16.29, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 24.63 Conformation dependent library (CDL) restraints added in 5.5 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: 2.59 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: 10.21 Time building geometry restraints manager: 25.42 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: 100.24 - 107.03: 568 107.03 - 113.82: 34569 113.82 - 120.61: 8585 120.61 - 127.40: 7518 127.40 - 134.18: 144 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 1.850 nonbonded pdb=" OE1 GLU D 284 " pdb=" H GLU D 284 " model vdw 1.578 1.850 nonbonded pdb=" OE1 GLU B 284 " pdb=" H GLU B 284 " model vdw 1.597 1.850 nonbonded pdb=" OE1 GLU A 232 " pdb=" H GLU A 232 " model vdw 1.618 1.850 nonbonded pdb=" OE1 GLU C 284 " pdb=" H GLU C 284 " model vdw 1.644 1.850 ... (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 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: 2.870 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: 0.400 Extract box with map and model: 10.650 Check model and map are aligned: 0.420 Set scattering table: 0.280 Process input model: 97.800 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.390 ------------------------------------------------------------------------------- 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 14666 Z= 0.259 Angle : 0.719 6.962 19974 Z= 0.387 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 *********************** 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 fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 2.365 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: 2.6853 time to fit residues: 633.2977 Evaluate side-chains 153 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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: 1.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 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: 0.8182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14666 Z= 0.187 Angle : 0.600 7.659 19974 Z= 0.310 Chirality : 0.046 0.181 2401 Planarity : 0.004 0.047 2510 Dihedral : 11.383 78.261 2407 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 1.58 % Allowed : 20.10 % 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: -2.04 (0.19), residues: 1758 helix: -2.11 (0.32), residues: 192 sheet: -0.43 (0.19), residues: 702 loop : -1.96 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 398 HIS 0.001 0.001 HIS G 298 PHE 0.010 0.001 PHE E 393 TYR 0.014 0.001 TYR A 347 ARG 0.005 0.000 ARG D 427 *********************** 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 180 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 2.314 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 364 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6526 (mmp80) REVERT: B 241 GLN cc_start: 0.8278 (mp10) cc_final: 0.7523 (mm-40) REVERT: C 231 LEU cc_start: 0.8366 (tp) cc_final: 0.7924 (tp) REVERT: C 319 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8844 (tt0) REVERT: C 331 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8282 (mp10) REVERT: D 377 SER cc_start: 0.8791 (m) cc_final: 0.8552 (p) REVERT: D 401 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8431 (mt-10) REVERT: G 412 GLU cc_start: 0.8619 (tt0) cc_final: 0.8382 (tt0) outliers start: 26 outliers final: 11 residues processed: 173 average time/residue: 2.6567 time to fit residues: 512.4088 Evaluate side-chains 158 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 418 THR 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 88 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.0070 chunk 44 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- 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** ** C 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14666 Z= 0.208 Angle : 0.586 8.420 19974 Z= 0.300 Chirality : 0.046 0.178 2401 Planarity : 0.004 0.060 2510 Dihedral : 7.802 71.135 2400 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.83 % Allowed : 19.79 % Favored : 78.38 % 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: -1.80 (0.19), residues: 1758 helix: -2.00 (0.32), residues: 192 sheet: -0.31 (0.18), residues: 726 loop : -1.78 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 258 HIS 0.002 0.001 HIS G 298 PHE 0.008 0.001 PHE G 346 TYR 0.014 0.001 TYR A 347 ARG 0.003 0.000 ARG C 444 *********************** 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 183 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 2.491 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 364 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6595 (mmp80) REVERT: B 241 GLN cc_start: 0.8226 (mp10) cc_final: 0.7513 (mm-40) REVERT: B 244 CYS cc_start: 0.4491 (p) cc_final: 0.3408 (p) REVERT: B 286 TRP cc_start: 0.8225 (t60) cc_final: 0.7455 (t60) REVERT: C 234 MET cc_start: 0.8585 (mpp) cc_final: 0.8350 (mpp) REVERT: C 319 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8858 (tt0) REVERT: C 331 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8311 (mp10) REVERT: D 377 SER cc_start: 0.8825 (m) cc_final: 0.8551 (p) REVERT: D 401 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: E 230 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8491 (t) REVERT: F 234 MET cc_start: 0.8592 (mmt) cc_final: 0.8353 (mmm) REVERT: G 244 CYS cc_start: 0.3985 (p) cc_final: 0.2946 (p) REVERT: G 412 GLU cc_start: 0.8642 (tt0) cc_final: 0.8409 (tt0) outliers start: 30 outliers final: 16 residues processed: 175 average time/residue: 2.5593 time to fit residues: 494.5574 Evaluate side-chains 155 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 2.483 ------------------------------------------------------------------------------- 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 364 ARG Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 285 ASP 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 230 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 406 SER Chi-restraints excluded: chain H residue 420 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 141 optimal weight: 0.0050 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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** ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14666 Z= 0.187 Angle : 0.570 8.117 19974 Z= 0.292 Chirality : 0.045 0.168 2401 Planarity : 0.004 0.051 2510 Dihedral : 6.413 64.680 2400 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.01 % Allowed : 20.34 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.64 (0.19), residues: 1758 helix: -2.01 (0.32), residues: 194 sheet: -0.21 (0.18), residues: 732 loop : -1.63 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 286 HIS 0.002 0.001 HIS B 298 PHE 0.009 0.001 PHE E 292 TYR 0.014 0.001 TYR A 347 ARG 0.004 0.000 ARG G 312 *********************** 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 173 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 2.525 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: B 241 GLN cc_start: 0.8240 (mp10) cc_final: 0.7560 (mm-40) REVERT: B 286 TRP cc_start: 0.7817 (t60) cc_final: 0.7595 (t60) REVERT: C 319 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8835 (tt0) REVERT: C 331 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8300 (mp10) REVERT: D 377 SER cc_start: 0.8835 (m) cc_final: 0.8547 (p) REVERT: D 401 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8420 (mt-10) REVERT: E 414 MET cc_start: 0.8186 (tpt) cc_final: 0.7975 (tpt) REVERT: F 234 MET cc_start: 0.8594 (mmt) cc_final: 0.8359 (mmm) REVERT: G 234 MET cc_start: 0.8561 (mmm) cc_final: 0.7918 (tpt) REVERT: G 412 GLU cc_start: 0.8648 (tt0) cc_final: 0.8444 (tt0) outliers start: 33 outliers final: 20 residues processed: 165 average time/residue: 2.4474 time to fit residues: 447.9511 Evaluate side-chains 157 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 285 ASP 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 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 E residue 400 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 236 MET 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 96 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 145 optimal weight: 0.2980 chunk 117 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 ASN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14666 Z= 0.176 Angle : 0.560 7.774 19974 Z= 0.287 Chirality : 0.045 0.167 2401 Planarity : 0.003 0.046 2510 Dihedral : 5.861 59.453 2399 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.01 % Allowed : 20.71 % Favored : 77.28 % 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: -1.52 (0.19), residues: 1758 helix: -2.02 (0.32), residues: 196 sheet: -0.12 (0.18), residues: 736 loop : -1.55 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 258 HIS 0.003 0.001 HIS G 298 PHE 0.007 0.001 PHE G 346 TYR 0.013 0.001 TYR A 347 ARG 0.005 0.000 ARG G 312 *********************** 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 170 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 2.090 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: B 241 GLN cc_start: 0.8251 (mp10) cc_final: 0.7584 (mm-40) REVERT: B 286 TRP cc_start: 0.7821 (t60) cc_final: 0.7497 (t60) REVERT: C 319 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8824 (tt0) REVERT: C 331 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8235 (mp10) REVERT: D 377 SER cc_start: 0.8840 (m) cc_final: 0.8544 (p) REVERT: D 401 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8451 (mt-10) REVERT: D 427 ARG cc_start: 0.8339 (tmt170) cc_final: 0.7937 (tmt170) REVERT: E 230 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8487 (t) REVERT: F 234 MET cc_start: 0.8594 (mmt) cc_final: 0.8363 (mmm) REVERT: G 234 MET cc_start: 0.8498 (mmm) cc_final: 0.7909 (tpt) REVERT: G 412 GLU cc_start: 0.8657 (tt0) cc_final: 0.8383 (tt0) outliers start: 33 outliers final: 25 residues processed: 161 average time/residue: 2.5746 time to fit residues: 462.7670 Evaluate side-chains 159 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 285 ASP 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 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 400 ASN Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 236 MET Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 406 SER Chi-restraints excluded: chain H residue 420 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14666 Z= 0.166 Angle : 0.553 8.817 19974 Z= 0.282 Chirality : 0.045 0.166 2401 Planarity : 0.003 0.046 2510 Dihedral : 5.540 59.291 2398 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.95 % Allowed : 20.71 % Favored : 77.34 % 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: -2.01 (0.32), residues: 200 sheet: 0.01 (0.19), residues: 722 loop : -1.50 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 258 HIS 0.001 0.000 HIS B 411 PHE 0.010 0.001 PHE D 292 TYR 0.012 0.001 TYR A 347 ARG 0.007 0.000 ARG E 269 *********************** 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 167 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 2.404 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 236 MET cc_start: 0.7683 (mmt) cc_final: 0.7434 (mpt) REVERT: B 241 GLN cc_start: 0.8271 (mp10) cc_final: 0.7369 (mm-40) REVERT: B 286 TRP cc_start: 0.7792 (t60) cc_final: 0.7477 (t60) REVERT: C 234 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8109 (mpp) REVERT: C 319 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8811 (tt0) REVERT: C 331 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8202 (mp10) REVERT: D 377 SER cc_start: 0.8859 (m) cc_final: 0.8550 (p) REVERT: D 401 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: D 427 ARG cc_start: 0.8372 (tmt170) cc_final: 0.7975 (tmt170) REVERT: E 230 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8485 (t) REVERT: F 234 MET cc_start: 0.8604 (mmt) cc_final: 0.8342 (mmm) REVERT: G 234 MET cc_start: 0.8487 (mmm) cc_final: 0.7805 (tpp) outliers start: 32 outliers final: 24 residues processed: 160 average time/residue: 2.4325 time to fit residues: 435.0446 Evaluate side-chains 157 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 234 MET 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 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 F residue 260 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 236 MET 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 19 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 169 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14666 Z= 0.171 Angle : 0.550 9.702 19974 Z= 0.282 Chirality : 0.044 0.164 2401 Planarity : 0.003 0.047 2510 Dihedral : 5.390 59.064 2398 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.58 % Allowed : 20.77 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.19), residues: 1758 helix: -1.96 (0.32), residues: 200 sheet: 0.01 (0.19), residues: 728 loop : -1.45 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 258 HIS 0.001 0.001 HIS G 411 PHE 0.008 0.001 PHE E 292 TYR 0.013 0.001 TYR A 347 ARG 0.008 0.000 ARG E 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.7687 (tpt) cc_final: 0.7402 (tpt) REVERT: B 241 GLN cc_start: 0.8223 (mp10) cc_final: 0.7640 (mm-40) REVERT: B 286 TRP cc_start: 0.7833 (t60) cc_final: 0.7443 (t60) REVERT: C 319 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8803 (tt0) REVERT: C 331 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8176 (mp10) REVERT: D 377 SER cc_start: 0.8854 (m) cc_final: 0.8547 (p) REVERT: D 401 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8489 (mt-10) REVERT: D 427 ARG cc_start: 0.8369 (tmt170) cc_final: 0.7965 (tmt170) REVERT: E 230 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8488 (t) REVERT: F 234 MET cc_start: 0.8610 (mmt) cc_final: 0.8346 (mmm) REVERT: G 236 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7142 (mpt) outliers start: 26 outliers final: 22 residues processed: 150 average time/residue: 2.2974 time to fit residues: 385.7896 Evaluate side-chains 152 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 420 ILE 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 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 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 400 ASN Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain G residue 260 ASN 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 67 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14666 Z= 0.218 Angle : 0.564 10.070 19974 Z= 0.290 Chirality : 0.045 0.168 2401 Planarity : 0.003 0.048 2510 Dihedral : 5.529 59.188 2398 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.77 % Allowed : 21.13 % Favored : 77.10 % 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: -1.35 (0.19), residues: 1758 helix: -1.89 (0.33), residues: 200 sheet: 0.04 (0.19), residues: 728 loop : -1.47 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 258 HIS 0.002 0.001 HIS B 411 PHE 0.014 0.001 PHE E 292 TYR 0.013 0.001 TYR A 347 ARG 0.007 0.000 ARG E 269 *********************** 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 158 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 2.349 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: 0.7461 (tpt) cc_final: 0.7218 (tpt) REVERT: B 241 GLN cc_start: 0.8323 (mp10) cc_final: 0.7778 (mm-40) REVERT: B 286 TRP cc_start: 0.7889 (t60) cc_final: 0.7528 (t60) REVERT: C 319 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8834 (tt0) REVERT: D 401 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: D 427 ARG cc_start: 0.8374 (tmt170) cc_final: 0.7978 (tmt170) REVERT: E 230 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8497 (t) REVERT: F 234 MET cc_start: 0.8631 (mmt) cc_final: 0.8419 (mmm) outliers start: 29 outliers final: 24 residues processed: 151 average time/residue: 2.2754 time to fit residues: 387.3231 Evaluate side-chains 153 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 226 ILE 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 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 400 ASN Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain G residue 260 ASN 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 162 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 157 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14666 Z= 0.247 Angle : 0.582 11.077 19974 Z= 0.298 Chirality : 0.045 0.158 2401 Planarity : 0.003 0.046 2510 Dihedral : 5.642 59.012 2398 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.95 % Allowed : 21.25 % Favored : 76.80 % 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: -1.30 (0.19), residues: 1758 helix: -1.75 (0.35), residues: 174 sheet: -0.05 (0.19), residues: 738 loop : -1.37 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 258 HIS 0.002 0.001 HIS B 411 PHE 0.009 0.001 PHE G 346 TYR 0.013 0.001 TYR A 347 ARG 0.007 0.000 ARG E 269 *********************** 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 158 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.7764 (tpt) cc_final: 0.7556 (tpt) REVERT: B 241 GLN cc_start: 0.8350 (mp10) cc_final: 0.7813 (mm-40) REVERT: B 286 TRP cc_start: 0.7950 (t60) cc_final: 0.7661 (t60) REVERT: C 234 MET cc_start: 0.8274 (mpp) cc_final: 0.7971 (pmm) REVERT: C 319 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8827 (tt0) REVERT: C 331 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8076 (mp10) REVERT: D 401 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8494 (mt-10) REVERT: D 427 ARG cc_start: 0.8385 (tmt170) cc_final: 0.8005 (tmt170) REVERT: E 230 SER cc_start: 0.9014 (OUTLIER) cc_final: 0.8526 (t) REVERT: E 414 MET cc_start: 0.8169 (tpt) cc_final: 0.7969 (tpt) REVERT: F 234 MET cc_start: 0.8630 (mmt) cc_final: 0.8374 (mmm) outliers start: 32 outliers final: 26 residues processed: 151 average time/residue: 2.1999 time to fit residues: 373.4589 Evaluate side-chains 153 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 243 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 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 400 ASN Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain G residue 260 ASN 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 167 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 116 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 161 optimal weight: 40.0000 chunk 139 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14666 Z= 0.184 Angle : 0.565 11.253 19974 Z= 0.289 Chirality : 0.045 0.159 2401 Planarity : 0.003 0.046 2510 Dihedral : 5.566 58.588 2398 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.64 % Allowed : 21.80 % Favored : 76.55 % 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: -1.22 (0.19), residues: 1758 helix: -1.67 (0.36), residues: 174 sheet: 0.05 (0.19), residues: 730 loop : -1.36 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 258 HIS 0.002 0.001 HIS D 298 PHE 0.016 0.001 PHE E 292 TYR 0.014 0.001 TYR A 347 ARG 0.006 0.000 ARG E 269 ********************** 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 152 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 2.299 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: B 241 GLN cc_start: 0.8365 (mp10) cc_final: 0.7836 (mm-40) REVERT: B 286 TRP cc_start: 0.7854 (t60) cc_final: 0.7568 (t60) REVERT: C 234 MET cc_start: 0.8252 (mpp) cc_final: 0.7986 (pmm) REVERT: C 319 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8785 (tt0) REVERT: C 331 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8025 (mp10) REVERT: D 401 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8511 (mt-10) REVERT: D 427 ARG cc_start: 0.8384 (tmt170) cc_final: 0.8003 (tmt170) REVERT: E 230 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8504 (t) REVERT: F 234 MET cc_start: 0.8617 (mmt) cc_final: 0.8408 (mmm) outliers start: 27 outliers final: 23 residues processed: 147 average time/residue: 2.2393 time to fit residues: 369.7918 Evaluate side-chains 150 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 235 LEU 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 266 LEU 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 400 ASN Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 260 ASN 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 148 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.147743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.090216 restraints weight = 85005.825| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.97 r_work: 0.3037 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- 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: 24 | |-----------------------------------------------------------------------------| |-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: 24 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14666 Z= 0.229 Angle : 0.579 11.054 19974 Z= 0.297 Chirality : 0.045 0.158 2401 Planarity : 0.003 0.044 2510 Dihedral : 5.624 59.172 2398 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.64 % Allowed : 22.05 % Favored : 76.31 % 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: -1.25 (0.19), residues: 1758 helix: -1.73 (0.36), residues: 174 sheet: 0.04 (0.19), residues: 726 loop : -1.38 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 258 HIS 0.003 0.001 HIS H 298 PHE 0.008 0.001 PHE E 346 TYR 0.013 0.001 TYR A 347 ARG 0.006 0.000 ARG E 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9378.70 seconds wall clock time: 165 minutes 43.75 seconds (9943.75 seconds total)