Starting phenix.real_space_refine on Mon Apr 8 08:36:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on9_16983/04_2024/8on9_16983_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on9_16983/04_2024/8on9_16983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on9_16983/04_2024/8on9_16983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on9_16983/04_2024/8on9_16983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on9_16983/04_2024/8on9_16983_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on9_16983/04_2024/8on9_16983_updated.pdb" } resolution = 2.4 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= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 8289 2.51 5 N 2163 2.21 5 O 2457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 442": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13014 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4199 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 29, 'TRANS': 494} Chain breaks: 1 Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 41 Unusual residues: {'NH2': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 4} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 41 Unusual residues: {'NH2': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 4} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 41 Unusual residues: {'NH2': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 4} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4199 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 29, 'TRANS': 494} Chain breaks: 1 Chain: "C" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4199 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 29, 'TRANS': 494} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 7.03, per 1000 atoms: 0.54 Number of scatterers: 13014 At special positions: 0 Unit cell: (107.31, 108.332, 134.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2457 8.00 N 2163 7.00 C 8289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 401 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 381 " distance=2.04 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 360 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 401 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 381 " distance=2.04 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 360 " - pdb=" SG CYS C 368 " distance=2.03 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 444 " " NAG A 603 " - " ASN A 460 " " NAG B 601 " - " ASN B 392 " " NAG B 602 " - " ASN B 444 " " NAG B 603 " - " ASN B 460 " " NAG C 601 " - " ASN C 392 " " NAG C 602 " - " ASN C 444 " " NAG C 603 " - " ASN C 460 " " NAG G 1 " - " ASN A 180 " " NAG H 1 " - " ASN A 299 " " NAG I 1 " - " ASN B 180 " " NAG J 1 " - " ASN B 299 " " NAG K 1 " - " ASN C 180 " " NAG L 1 " - " ASN C 299 " Time building additional restraints: 5.20 Conformation dependent library (CDL) restraints added in 2.3 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2994 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 9 sheets defined 41.6% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 28 through 58 Processing helix chain 'A' and resid 87 through 99 Processing helix chain 'A' and resid 113 through 129 removed outlier: 3.842A pdb=" N TYR A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.084A pdb=" N LEU A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 315 through 331 Processing helix chain 'A' and resid 358 through 361 Processing helix chain 'A' and resid 366 through 391 removed outlier: 4.562A pdb=" N THR A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 399 removed outlier: 3.821A pdb=" N CYS A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 446 through 458 removed outlier: 5.979A pdb=" N GLY A 450 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 458 " --> pdb=" O PHE A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 4.399A pdb=" N LYS A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'A' and resid 513 through 529 Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 28 through 58 Processing helix chain 'B' and resid 87 through 99 Processing helix chain 'B' and resid 113 through 129 removed outlier: 3.842A pdb=" N TYR B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.084A pdb=" N LEU B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 315 through 331 Processing helix chain 'B' and resid 358 through 361 Processing helix chain 'B' and resid 366 through 391 removed outlier: 4.562A pdb=" N THR B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 399 removed outlier: 3.821A pdb=" N CYS B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'B' and resid 446 through 458 removed outlier: 5.980A pdb=" N GLY B 450 " --> pdb=" O GLY B 447 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 458 " --> pdb=" O PHE B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 removed outlier: 4.399A pdb=" N LYS B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 508 Processing helix chain 'B' and resid 513 through 529 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 28 through 58 Processing helix chain 'C' and resid 87 through 99 Processing helix chain 'C' and resid 113 through 129 removed outlier: 3.842A pdb=" N TYR C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Proline residue: C 127 - end of helix Processing helix chain 'C' and resid 137 through 143 Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.084A pdb=" N LEU C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'C' and resid 358 through 361 Processing helix chain 'C' and resid 366 through 391 removed outlier: 4.562A pdb=" N THR C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 399 removed outlier: 3.820A pdb=" N CYS C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 440 through 443 Processing helix chain 'C' and resid 446 through 458 removed outlier: 5.979A pdb=" N GLY C 450 " --> pdb=" O GLY C 447 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 458 " --> pdb=" O PHE C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 removed outlier: 4.399A pdb=" N LYS C 469 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 Processing helix chain 'C' and resid 513 through 529 Processing sheet with id= A, first strand: chain 'A' and resid 61 through 68 Processing sheet with id= B, first strand: chain 'A' and resid 185 through 189 removed outlier: 6.411A pdb=" N ASN A 195 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN A 81 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 169 through 174 removed outlier: 6.506A pdb=" N ILE A 222 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS A 172 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER A 220 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR A 174 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY A 218 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 61 through 68 Processing sheet with id= E, first strand: chain 'B' and resid 185 through 189 removed outlier: 6.411A pdb=" N ASN B 195 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN B 81 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 169 through 174 removed outlier: 6.506A pdb=" N ILE B 222 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS B 172 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER B 220 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR B 174 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY B 218 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 61 through 68 Processing sheet with id= H, first strand: chain 'C' and resid 185 through 189 removed outlier: 6.411A pdb=" N ASN C 195 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN C 81 " --> pdb=" O ASN C 195 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 169 through 174 removed outlier: 6.507A pdb=" N ILE C 222 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS C 172 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER C 220 " --> pdb=" O CYS C 172 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR C 174 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY C 218 " --> pdb=" O TYR C 174 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1593 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: 4.03 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2898 1.33 - 1.45: 3190 1.45 - 1.58: 7100 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 13344 Sorted by residual: bond pdb=" CA SER B 58 " pdb=" CB SER B 58 " ideal model delta sigma weight residual 1.534 1.481 0.053 1.71e-02 3.42e+03 9.46e+00 bond pdb=" CA SER C 58 " pdb=" CB SER C 58 " ideal model delta sigma weight residual 1.534 1.482 0.052 1.71e-02 3.42e+03 9.19e+00 bond pdb=" CA SER A 58 " pdb=" CB SER A 58 " ideal model delta sigma weight residual 1.534 1.482 0.052 1.71e-02 3.42e+03 9.19e+00 bond pdb=" N PRO C 266 " pdb=" CA PRO C 266 " ideal model delta sigma weight residual 1.465 1.431 0.034 1.15e-02 7.56e+03 8.50e+00 bond pdb=" N PRO A 266 " pdb=" CA PRO A 266 " ideal model delta sigma weight residual 1.465 1.431 0.033 1.15e-02 7.56e+03 8.40e+00 ... (remaining 13339 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.14: 400 106.14 - 113.10: 6970 113.10 - 120.06: 4818 120.06 - 127.03: 5730 127.03 - 133.99: 157 Bond angle restraints: 18075 Sorted by residual: angle pdb=" N SER B 58 " pdb=" CA SER B 58 " pdb=" C SER B 58 " ideal model delta sigma weight residual 113.38 104.51 8.87 1.23e+00 6.61e-01 5.20e+01 angle pdb=" N SER C 58 " pdb=" CA SER C 58 " pdb=" C SER C 58 " ideal model delta sigma weight residual 113.38 104.51 8.87 1.23e+00 6.61e-01 5.20e+01 angle pdb=" N SER A 58 " pdb=" CA SER A 58 " pdb=" C SER A 58 " ideal model delta sigma weight residual 113.38 104.53 8.85 1.23e+00 6.61e-01 5.18e+01 angle pdb=" CA PHE B 188 " pdb=" CB PHE B 188 " pdb=" CG PHE B 188 " ideal model delta sigma weight residual 113.80 119.09 -5.29 1.00e+00 1.00e+00 2.80e+01 angle pdb=" CA PHE C 188 " pdb=" CB PHE C 188 " pdb=" CG PHE C 188 " ideal model delta sigma weight residual 113.80 119.05 -5.25 1.00e+00 1.00e+00 2.76e+01 ... (remaining 18070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 7611 16.79 - 33.58: 522 33.58 - 50.36: 114 50.36 - 67.15: 45 67.15 - 83.94: 15 Dihedral angle restraints: 8307 sinusoidal: 3666 harmonic: 4641 Sorted by residual: dihedral pdb=" CB CYS B 80 " pdb=" SG CYS B 80 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 125.81 -32.81 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS C 80 " pdb=" SG CYS C 80 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 125.79 -32.79 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS A 80 " pdb=" SG CYS A 80 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 125.78 -32.78 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 8304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1473 0.049 - 0.099: 366 0.099 - 0.148: 123 0.148 - 0.197: 18 0.197 - 0.246: 9 Chirality restraints: 1989 Sorted by residual: 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 -2.33 -0.07 2.00e-02 2.50e+03 1.35e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.31e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.21e+01 ... (remaining 1986 not shown) Planarity restraints: 2337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 602 " 0.168 2.00e-02 2.50e+03 1.44e-01 2.60e+02 pdb=" C7 NAG C 602 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG C 602 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG C 602 " -0.238 2.00e-02 2.50e+03 pdb=" O7 NAG C 602 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.168 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" C7 NAG A 602 " -0.031 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.238 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.168 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" C7 NAG B 602 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.238 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " 0.130 2.00e-02 2.50e+03 ... (remaining 2334 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 428 2.72 - 3.26: 12979 3.26 - 3.81: 21468 3.81 - 4.35: 26561 4.35 - 4.90: 45420 Nonbonded interactions: 106856 Sorted by model distance: nonbonded pdb=" O ASP A 302 " pdb=" OD1 ASP A 302 " model vdw 2.175 3.040 nonbonded pdb=" O ASP C 302 " pdb=" OD1 ASP C 302 " model vdw 2.175 3.040 nonbonded pdb=" O ASP B 302 " pdb=" OD1 ASP B 302 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR C 192 " pdb=" O VAL C 249 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR A 192 " pdb=" O VAL A 249 " model vdw 2.283 2.440 ... (remaining 106851 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.950 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 37.200 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.005 0.053 13344 Z= 0.293 Angle : 0.744 10.458 18075 Z= 0.440 Chirality : 0.050 0.246 1989 Planarity : 0.009 0.144 2322 Dihedral : 12.861 83.940 5241 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.48 (0.22), residues: 1569 helix: 1.49 (0.21), residues: 678 sheet: 1.74 (0.30), residues: 273 loop : 0.15 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 419 HIS 0.002 0.000 HIS A 243 PHE 0.036 0.001 PHE A 188 TYR 0.013 0.001 TYR B 452 ARG 0.003 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8061 (mttt) cc_final: 0.7484 (mtmm) REVERT: A 66 GLU cc_start: 0.8307 (pt0) cc_final: 0.8028 (pt0) REVERT: A 111 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7761 (mt-10) REVERT: A 125 TYR cc_start: 0.7534 (m-80) cc_final: 0.7159 (m-80) REVERT: A 145 SER cc_start: 0.8284 (p) cc_final: 0.8025 (m) REVERT: A 156 GLU cc_start: 0.7629 (tt0) cc_final: 0.7277 (tt0) REVERT: A 166 GLU cc_start: 0.8035 (tt0) cc_final: 0.7426 (tt0) REVERT: A 232 LYS cc_start: 0.8555 (mttm) cc_final: 0.8347 (mttp) REVERT: A 235 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 289 ARG cc_start: 0.7807 (ttt180) cc_final: 0.7594 (ttt180) REVERT: A 311 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6656 (mm-30) REVERT: A 319 GLN cc_start: 0.7440 (mt0) cc_final: 0.7226 (mt0) REVERT: A 357 PRO cc_start: 0.7847 (Cg_exo) cc_final: 0.7639 (Cg_endo) REVERT: A 396 MET cc_start: 0.7595 (mmm) cc_final: 0.7284 (mmp) REVERT: A 407 GLU cc_start: 0.7759 (tt0) cc_final: 0.7539 (tt0) REVERT: A 465 GLU cc_start: 0.7874 (mp0) cc_final: 0.7614 (mp0) REVERT: A 494 ARG cc_start: 0.7035 (ttp-110) cc_final: 0.6790 (ttm110) REVERT: A 525 ASP cc_start: 0.6887 (m-30) cc_final: 0.6553 (t0) REVERT: B 15 THR cc_start: 0.6444 (p) cc_final: 0.5946 (p) REVERT: B 29 MET cc_start: 0.6947 (mmm) cc_final: 0.6638 (mmm) REVERT: B 48 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7181 (mm-40) REVERT: B 57 PHE cc_start: 0.7927 (m-80) cc_final: 0.7624 (m-80) REVERT: B 86 ASP cc_start: 0.8027 (t0) cc_final: 0.7779 (t0) REVERT: B 124 LYS cc_start: 0.7986 (mttt) cc_final: 0.7748 (mtpm) REVERT: B 145 SER cc_start: 0.8237 (p) cc_final: 0.7957 (m) REVERT: B 156 GLU cc_start: 0.7655 (tt0) cc_final: 0.7376 (tt0) REVERT: B 166 GLU cc_start: 0.8050 (tt0) cc_final: 0.7632 (tt0) REVERT: B 177 HIS cc_start: 0.7384 (m-70) cc_final: 0.7132 (m-70) REVERT: B 303 LYS cc_start: 0.8401 (ptpp) cc_final: 0.8190 (ptpp) REVERT: B 308 ASP cc_start: 0.7631 (m-30) cc_final: 0.7374 (p0) REVERT: B 311 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6548 (mm-30) REVERT: B 329 GLU cc_start: 0.7592 (tt0) cc_final: 0.7098 (mm-30) REVERT: B 357 PRO cc_start: 0.7788 (Cg_exo) cc_final: 0.7536 (Cg_endo) REVERT: B 362 PHE cc_start: 0.8246 (m-80) cc_final: 0.7952 (m-80) REVERT: B 377 ASN cc_start: 0.7654 (m-40) cc_final: 0.7389 (m110) REVERT: B 407 GLU cc_start: 0.7769 (tt0) cc_final: 0.7222 (tt0) REVERT: B 449 GLN cc_start: 0.7939 (tp40) cc_final: 0.7730 (tp40) REVERT: B 465 GLU cc_start: 0.7823 (mp0) cc_final: 0.7553 (mp0) REVERT: B 469 LYS cc_start: 0.8549 (mttt) cc_final: 0.8301 (mttm) REVERT: B 481 SER cc_start: 0.8242 (t) cc_final: 0.7950 (p) REVERT: B 511 ILE cc_start: 0.7723 (mt) cc_final: 0.7484 (mm) REVERT: B 525 ASP cc_start: 0.6820 (m-30) cc_final: 0.6550 (t70) REVERT: C 29 MET cc_start: 0.7549 (mmm) cc_final: 0.7221 (mmm) REVERT: C 49 MET cc_start: 0.7782 (tpp) cc_final: 0.7545 (tpp) REVERT: C 66 GLU cc_start: 0.8165 (pt0) cc_final: 0.7795 (pt0) REVERT: C 142 GLU cc_start: 0.7449 (tt0) cc_final: 0.7222 (tt0) REVERT: C 145 SER cc_start: 0.8200 (p) cc_final: 0.7945 (m) REVERT: C 166 GLU cc_start: 0.7994 (tt0) cc_final: 0.7582 (tt0) REVERT: C 301 SER cc_start: 0.7761 (t) cc_final: 0.7481 (p) REVERT: C 311 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6590 (mm-30) REVERT: C 329 GLU cc_start: 0.7805 (tt0) cc_final: 0.7322 (mp0) REVERT: C 407 GLU cc_start: 0.7813 (tt0) cc_final: 0.7507 (tt0) REVERT: C 465 GLU cc_start: 0.7953 (mp0) cc_final: 0.7645 (mp0) REVERT: C 480 ASP cc_start: 0.7342 (m-30) cc_final: 0.6947 (m-30) REVERT: C 481 SER cc_start: 0.8135 (t) cc_final: 0.7785 (p) REVERT: C 511 ILE cc_start: 0.7780 (mt) cc_final: 0.7531 (mm) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 1.4921 time to fit residues: 707.8896 Evaluate side-chains 373 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 400 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN B 54 GLN B 173 HIS B 286 HIS B 374 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN C 141 GLN C 286 HIS C 319 GLN C 449 GLN C 482 ASN C 495 ASN C 496 GLN C 504 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13344 Z= 0.278 Angle : 0.628 11.144 18075 Z= 0.313 Chirality : 0.047 0.250 1989 Planarity : 0.004 0.043 2322 Dihedral : 6.513 59.845 2172 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.21 % Allowed : 11.82 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.21), residues: 1569 helix: 1.33 (0.20), residues: 699 sheet: 1.63 (0.30), residues: 261 loop : 0.08 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 349 HIS 0.004 0.001 HIS B 376 PHE 0.014 0.002 PHE C 188 TYR 0.017 0.001 TYR A 414 ARG 0.009 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 399 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7971 (mtm) cc_final: 0.7751 (mtp) REVERT: A 26 LYS cc_start: 0.8173 (mttt) cc_final: 0.7568 (mtmm) REVERT: A 66 GLU cc_start: 0.8349 (pt0) cc_final: 0.8080 (pt0) REVERT: A 119 MET cc_start: 0.8171 (mmm) cc_final: 0.7525 (mmt) REVERT: A 125 TYR cc_start: 0.7501 (m-80) cc_final: 0.7240 (m-80) REVERT: A 156 GLU cc_start: 0.7660 (tt0) cc_final: 0.7339 (tt0) REVERT: A 166 GLU cc_start: 0.7976 (tt0) cc_final: 0.7716 (tt0) REVERT: A 221 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8774 (t) REVERT: A 235 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 311 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6602 (mm-30) REVERT: A 362 PHE cc_start: 0.8157 (m-80) cc_final: 0.7954 (m-80) REVERT: A 409 SER cc_start: 0.8429 (OUTLIER) cc_final: 0.8194 (p) REVERT: A 445 LYS cc_start: 0.7289 (ptpt) cc_final: 0.7075 (ptpp) REVERT: A 465 GLU cc_start: 0.7899 (mp0) cc_final: 0.7659 (mp0) REVERT: A 488 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7965 (mt-10) REVERT: A 490 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: A 494 ARG cc_start: 0.7155 (ttp-110) cc_final: 0.6922 (ttm110) REVERT: A 511 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7483 (mp) REVERT: A 525 ASP cc_start: 0.6914 (m-30) cc_final: 0.6605 (t0) REVERT: B 29 MET cc_start: 0.7024 (mmm) cc_final: 0.6628 (mmm) REVERT: B 44 MET cc_start: 0.7225 (mmm) cc_final: 0.6496 (mmm) REVERT: B 48 GLN cc_start: 0.7401 (mm-40) cc_final: 0.7147 (mm-40) REVERT: B 57 PHE cc_start: 0.8099 (m-80) cc_final: 0.7789 (m-80) REVERT: B 86 ASP cc_start: 0.7990 (t0) cc_final: 0.7740 (t0) REVERT: B 156 GLU cc_start: 0.7656 (tt0) cc_final: 0.7355 (tt0) REVERT: B 166 GLU cc_start: 0.8070 (tt0) cc_final: 0.7712 (tt0) REVERT: B 177 HIS cc_start: 0.7448 (m-70) cc_final: 0.7202 (m-70) REVERT: B 293 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7426 (pt) REVERT: B 303 LYS cc_start: 0.8445 (ptpp) cc_final: 0.8239 (ptpp) REVERT: B 311 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6484 (mm-30) REVERT: B 329 GLU cc_start: 0.7473 (tt0) cc_final: 0.6952 (mm-30) REVERT: B 357 PRO cc_start: 0.7788 (Cg_exo) cc_final: 0.7506 (Cg_endo) REVERT: B 362 PHE cc_start: 0.8234 (m-80) cc_final: 0.7908 (m-80) REVERT: B 377 ASN cc_start: 0.7611 (m-40) cc_final: 0.7347 (m110) REVERT: B 387 SER cc_start: 0.7460 (m) cc_final: 0.7162 (p) REVERT: B 388 LYS cc_start: 0.7230 (ptpt) cc_final: 0.7004 (ptpp) REVERT: B 407 GLU cc_start: 0.7881 (tt0) cc_final: 0.7363 (tt0) REVERT: B 465 GLU cc_start: 0.7804 (mp0) cc_final: 0.7591 (mp0) REVERT: B 469 LYS cc_start: 0.8583 (mttt) cc_final: 0.8352 (mttm) REVERT: B 481 SER cc_start: 0.8273 (t) cc_final: 0.7937 (p) REVERT: B 488 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 495 ASN cc_start: 0.7575 (t0) cc_final: 0.7355 (t160) REVERT: B 511 ILE cc_start: 0.7802 (mt) cc_final: 0.7525 (mm) REVERT: B 518 GLU cc_start: 0.6324 (mt-10) cc_final: 0.6078 (mt-10) REVERT: C 29 MET cc_start: 0.7552 (mmm) cc_final: 0.7113 (mmm) REVERT: C 49 MET cc_start: 0.7776 (tpp) cc_final: 0.7517 (tpp) REVERT: C 142 GLU cc_start: 0.7578 (tt0) cc_final: 0.7324 (tt0) REVERT: C 166 GLU cc_start: 0.7989 (tt0) cc_final: 0.7607 (tt0) REVERT: C 178 ARG cc_start: 0.8052 (ttm170) cc_final: 0.7758 (ttp-170) REVERT: C 301 SER cc_start: 0.7720 (t) cc_final: 0.7468 (p) REVERT: C 311 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6514 (mm-30) REVERT: C 329 GLU cc_start: 0.7638 (tt0) cc_final: 0.7420 (tt0) REVERT: C 407 GLU cc_start: 0.8016 (tt0) cc_final: 0.7745 (tt0) REVERT: C 448 THR cc_start: 0.7749 (m) cc_final: 0.7362 (t) REVERT: C 480 ASP cc_start: 0.7296 (m-30) cc_final: 0.6844 (m-30) REVERT: C 494 ARG cc_start: 0.6990 (ttp-110) cc_final: 0.6671 (ttp-110) REVERT: C 511 ILE cc_start: 0.7829 (mt) cc_final: 0.7533 (mm) REVERT: C 527 PHE cc_start: 0.7259 (t80) cc_final: 0.7020 (t80) outliers start: 45 outliers final: 18 residues processed: 415 average time/residue: 1.5253 time to fit residues: 679.5377 Evaluate side-chains 392 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 369 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 374 GLN A 400 ASN A 487 GLN A 495 ASN A 504 GLN B 54 GLN B 297 HIS B 374 GLN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN C 482 ASN C 504 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 0.035 13344 Z= 0.205 Angle : 0.588 9.425 18075 Z= 0.290 Chirality : 0.045 0.240 1989 Planarity : 0.004 0.042 2322 Dihedral : 6.202 57.584 2172 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.99 % Allowed : 12.18 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.24 (0.21), residues: 1569 helix: 1.29 (0.20), residues: 705 sheet: 1.32 (0.29), residues: 261 loop : 0.16 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 419 HIS 0.003 0.001 HIS A 260 PHE 0.014 0.001 PHE C 188 TYR 0.012 0.001 TYR A 414 ARG 0.004 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 368 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8184 (mttt) cc_final: 0.7546 (mtmm) REVERT: A 48 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7102 (mm-40) REVERT: A 66 GLU cc_start: 0.8273 (pt0) cc_final: 0.8036 (pt0) REVERT: A 125 TYR cc_start: 0.7490 (m-80) cc_final: 0.7275 (m-80) REVERT: A 156 GLU cc_start: 0.7634 (tt0) cc_final: 0.7275 (tt0) REVERT: A 166 GLU cc_start: 0.7984 (tt0) cc_final: 0.7713 (tt0) REVERT: A 235 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7511 (mt-10) REVERT: A 238 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7623 (ttm) REVERT: A 311 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6572 (mm-30) REVERT: A 409 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8311 (p) REVERT: A 465 GLU cc_start: 0.7929 (mp0) cc_final: 0.7669 (mp0) REVERT: A 488 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7990 (mt-10) REVERT: A 490 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: A 494 ARG cc_start: 0.7217 (ttp-110) cc_final: 0.6974 (ttm110) REVERT: A 518 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6336 (mt-10) REVERT: A 525 ASP cc_start: 0.6928 (m-30) cc_final: 0.6613 (t0) REVERT: B 29 MET cc_start: 0.7027 (mmm) cc_final: 0.6645 (mmm) REVERT: B 49 MET cc_start: 0.7642 (tpp) cc_final: 0.7416 (mmp) REVERT: B 86 ASP cc_start: 0.8012 (t0) cc_final: 0.7733 (t0) REVERT: B 156 GLU cc_start: 0.7661 (tt0) cc_final: 0.7354 (tt0) REVERT: B 166 GLU cc_start: 0.8073 (tt0) cc_final: 0.7686 (tt0) REVERT: B 177 HIS cc_start: 0.7475 (m-70) cc_final: 0.7231 (m-70) REVERT: B 253 GLU cc_start: 0.8389 (tt0) cc_final: 0.8104 (tt0) REVERT: B 293 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7608 (pt) REVERT: B 303 LYS cc_start: 0.8409 (ptpp) cc_final: 0.8188 (ptpp) REVERT: B 311 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6406 (mm-30) REVERT: B 316 MET cc_start: 0.7671 (mtm) cc_final: 0.7339 (mtp) REVERT: B 329 GLU cc_start: 0.7423 (tt0) cc_final: 0.7205 (tt0) REVERT: B 357 PRO cc_start: 0.7707 (Cg_exo) cc_final: 0.7494 (Cg_endo) REVERT: B 362 PHE cc_start: 0.8272 (m-80) cc_final: 0.7949 (m-80) REVERT: B 377 ASN cc_start: 0.7605 (m-40) cc_final: 0.7367 (m110) REVERT: B 388 LYS cc_start: 0.7251 (ptpt) cc_final: 0.7010 (ptpp) REVERT: B 407 GLU cc_start: 0.7916 (tt0) cc_final: 0.7575 (tt0) REVERT: B 441 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7739 (mm-30) REVERT: B 448 THR cc_start: 0.7596 (m) cc_final: 0.7129 (p) REVERT: B 465 GLU cc_start: 0.7796 (mp0) cc_final: 0.7596 (mp0) REVERT: B 469 LYS cc_start: 0.8567 (mttt) cc_final: 0.8349 (mttm) REVERT: B 488 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 525 ASP cc_start: 0.6902 (OUTLIER) cc_final: 0.6580 (t70) REVERT: C 29 MET cc_start: 0.7576 (mmm) cc_final: 0.7136 (mmm) REVERT: C 49 MET cc_start: 0.7773 (tpp) cc_final: 0.7531 (tpp) REVERT: C 121 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7506 (tppt) REVERT: C 166 GLU cc_start: 0.7972 (tt0) cc_final: 0.7613 (tt0) REVERT: C 178 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7768 (ttp-170) REVERT: C 216 GLU cc_start: 0.7758 (mp0) cc_final: 0.7504 (mp0) REVERT: C 238 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7505 (ttm) REVERT: C 311 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6447 (mm-30) REVERT: C 329 GLU cc_start: 0.7653 (tt0) cc_final: 0.7421 (tt0) REVERT: C 388 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7262 (ptpp) REVERT: C 407 GLU cc_start: 0.7985 (tt0) cc_final: 0.7727 (tt0) REVERT: C 480 ASP cc_start: 0.7311 (m-30) cc_final: 0.6851 (m-30) REVERT: C 492 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7492 (t80) REVERT: C 494 ARG cc_start: 0.7040 (ttp-110) cc_final: 0.6726 (ttp-110) REVERT: C 511 ILE cc_start: 0.7945 (mt) cc_final: 0.7636 (mm) REVERT: C 527 PHE cc_start: 0.7168 (t80) cc_final: 0.6936 (t80) outliers start: 56 outliers final: 17 residues processed: 390 average time/residue: 1.4898 time to fit residues: 624.5314 Evaluate side-chains 377 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 352 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 388 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS A 319 GLN A 324 GLN A 374 GLN A 400 ASN A 495 ASN B 374 GLN B 482 ASN C 17 HIS ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN C 482 ASN ** C 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13344 Z= 0.216 Angle : 0.592 9.532 18075 Z= 0.288 Chirality : 0.045 0.240 1989 Planarity : 0.004 0.043 2322 Dihedral : 6.164 57.876 2172 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.70 % Allowed : 13.68 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1569 helix: 1.32 (0.20), residues: 705 sheet: 1.14 (0.30), residues: 264 loop : 0.13 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 349 HIS 0.004 0.001 HIS B 376 PHE 0.014 0.001 PHE B 188 TYR 0.013 0.001 TYR A 414 ARG 0.003 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 364 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8190 (mttt) cc_final: 0.7516 (mtmm) REVERT: A 49 MET cc_start: 0.7668 (tpp) cc_final: 0.7307 (tpp) REVERT: A 66 GLU cc_start: 0.8310 (pt0) cc_final: 0.8074 (pt0) REVERT: A 156 GLU cc_start: 0.7631 (tt0) cc_final: 0.7266 (tt0) REVERT: A 166 GLU cc_start: 0.7974 (tt0) cc_final: 0.7590 (tt0) REVERT: A 235 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7497 (mt-10) REVERT: A 238 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7642 (ttm) REVERT: A 311 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6548 (mm-30) REVERT: A 396 MET cc_start: 0.7557 (mmm) cc_final: 0.7250 (mmp) REVERT: A 409 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8348 (p) REVERT: A 445 LYS cc_start: 0.7332 (ptpp) cc_final: 0.6930 (pttp) REVERT: A 465 GLU cc_start: 0.7911 (mp0) cc_final: 0.7641 (mp0) REVERT: A 488 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7948 (mt-10) REVERT: A 492 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8037 (t80) REVERT: A 494 ARG cc_start: 0.7177 (ttp-110) cc_final: 0.6971 (ttm-80) REVERT: B 29 MET cc_start: 0.7029 (mmm) cc_final: 0.6646 (mmm) REVERT: B 49 MET cc_start: 0.7540 (tpp) cc_final: 0.7338 (mmp) REVERT: B 86 ASP cc_start: 0.8076 (t0) cc_final: 0.7784 (t0) REVERT: B 156 GLU cc_start: 0.7652 (tt0) cc_final: 0.7285 (tt0) REVERT: B 166 GLU cc_start: 0.8060 (tt0) cc_final: 0.7666 (tt0) REVERT: B 177 HIS cc_start: 0.7458 (m-70) cc_final: 0.7235 (m-70) REVERT: B 293 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7645 (pt) REVERT: B 303 LYS cc_start: 0.8422 (ptpp) cc_final: 0.8196 (ptpp) REVERT: B 311 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6407 (mm-30) REVERT: B 316 MET cc_start: 0.7651 (mtm) cc_final: 0.7327 (mtp) REVERT: B 362 PHE cc_start: 0.8257 (m-80) cc_final: 0.7855 (m-80) REVERT: B 363 THR cc_start: 0.8096 (t) cc_final: 0.7840 (p) REVERT: B 366 GLU cc_start: 0.6360 (pm20) cc_final: 0.6098 (pm20) REVERT: B 377 ASN cc_start: 0.7600 (m-40) cc_final: 0.7318 (m110) REVERT: B 407 GLU cc_start: 0.7936 (tt0) cc_final: 0.7558 (tt0) REVERT: B 448 THR cc_start: 0.7575 (m) cc_final: 0.7143 (p) REVERT: B 457 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7762 (mtpp) REVERT: B 465 GLU cc_start: 0.7785 (mp0) cc_final: 0.7583 (mp0) REVERT: B 469 LYS cc_start: 0.8573 (mttt) cc_final: 0.8352 (mttm) REVERT: B 518 GLU cc_start: 0.6373 (mt-10) cc_final: 0.6058 (mt-10) REVERT: B 525 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6577 (t70) REVERT: C 29 MET cc_start: 0.7584 (mmm) cc_final: 0.7142 (mmm) REVERT: C 120 LYS cc_start: 0.7755 (mtmt) cc_final: 0.7506 (ttmm) REVERT: C 121 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7527 (tppt) REVERT: C 166 GLU cc_start: 0.7953 (tt0) cc_final: 0.7633 (tt0) REVERT: C 171 ASN cc_start: 0.8445 (t0) cc_final: 0.8018 (m-40) REVERT: C 178 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7785 (ttp-170) REVERT: C 216 GLU cc_start: 0.7759 (mp0) cc_final: 0.7480 (mp0) REVERT: C 238 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7508 (ttm) REVERT: C 311 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6441 (mm-30) REVERT: C 329 GLU cc_start: 0.7555 (tt0) cc_final: 0.7338 (tt0) REVERT: C 407 GLU cc_start: 0.7985 (tt0) cc_final: 0.7728 (tt0) REVERT: C 437 GLU cc_start: 0.7652 (tp30) cc_final: 0.7227 (tp30) REVERT: C 480 ASP cc_start: 0.7356 (m-30) cc_final: 0.6979 (m-30) REVERT: C 492 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7505 (t80) REVERT: C 494 ARG cc_start: 0.7052 (ttp-110) cc_final: 0.6749 (ttp-110) REVERT: C 496 GLN cc_start: 0.7854 (mt0) cc_final: 0.7390 (mt0) REVERT: C 511 ILE cc_start: 0.7973 (mt) cc_final: 0.7635 (mm) REVERT: C 527 PHE cc_start: 0.7221 (t80) cc_final: 0.6992 (t80) outliers start: 52 outliers final: 23 residues processed: 386 average time/residue: 1.4835 time to fit residues: 616.0273 Evaluate side-chains 392 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 362 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 128 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 374 GLN A 400 ASN A 495 ASN B 319 GLN C 106 ASN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN C 449 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13344 Z= 0.347 Angle : 0.640 10.448 18075 Z= 0.315 Chirality : 0.048 0.245 1989 Planarity : 0.004 0.045 2322 Dihedral : 6.259 58.376 2172 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.92 % Allowed : 14.32 % Favored : 81.77 % 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: 1.04 (0.21), residues: 1569 helix: 1.20 (0.20), residues: 705 sheet: 1.06 (0.29), residues: 267 loop : 0.01 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 349 HIS 0.007 0.001 HIS C 376 PHE 0.015 0.002 PHE A 188 TYR 0.016 0.002 TYR A 414 ARG 0.011 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 363 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8186 (mttt) cc_final: 0.7521 (mtmm) REVERT: A 66 GLU cc_start: 0.8327 (pt0) cc_final: 0.8090 (pt0) REVERT: A 156 GLU cc_start: 0.7634 (tt0) cc_final: 0.7273 (tt0) REVERT: A 166 GLU cc_start: 0.7952 (tt0) cc_final: 0.7572 (tt0) REVERT: A 235 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7484 (mt-10) REVERT: A 238 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7649 (ttm) REVERT: A 269 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: A 311 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6502 (mm-30) REVERT: A 396 MET cc_start: 0.7575 (mmm) cc_final: 0.7274 (mmp) REVERT: A 409 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8399 (p) REVERT: A 425 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 445 LYS cc_start: 0.7443 (ptpp) cc_final: 0.7001 (pttp) REVERT: A 465 GLU cc_start: 0.7925 (mp0) cc_final: 0.7658 (mp0) REVERT: A 488 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7928 (mt-10) REVERT: A 490 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7901 (mt-10) REVERT: A 492 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.8055 (t80) REVERT: A 521 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6591 (tm-30) REVERT: B 29 MET cc_start: 0.7032 (mmm) cc_final: 0.6657 (mmm) REVERT: B 49 MET cc_start: 0.7533 (tpp) cc_final: 0.7316 (mmp) REVERT: B 86 ASP cc_start: 0.8094 (t0) cc_final: 0.7785 (t0) REVERT: B 135 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7212 (mt-10) REVERT: B 156 GLU cc_start: 0.7705 (tt0) cc_final: 0.7351 (tt0) REVERT: B 166 GLU cc_start: 0.8051 (tt0) cc_final: 0.7642 (tt0) REVERT: B 177 HIS cc_start: 0.7496 (m-70) cc_final: 0.7276 (m-70) REVERT: B 293 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7696 (pt) REVERT: B 303 LYS cc_start: 0.8424 (ptpp) cc_final: 0.8159 (ptpp) REVERT: B 311 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6425 (mm-30) REVERT: B 316 MET cc_start: 0.7699 (mtm) cc_final: 0.7299 (mtp) REVERT: B 329 GLU cc_start: 0.7558 (tt0) cc_final: 0.7007 (mp0) REVERT: B 362 PHE cc_start: 0.8280 (m-80) cc_final: 0.7920 (m-80) REVERT: B 363 THR cc_start: 0.8127 (t) cc_final: 0.7909 (p) REVERT: B 377 ASN cc_start: 0.7614 (m-40) cc_final: 0.7362 (m110) REVERT: B 407 GLU cc_start: 0.7998 (tt0) cc_final: 0.7443 (tt0) REVERT: B 457 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7775 (mtpp) REVERT: B 469 LYS cc_start: 0.8581 (mttt) cc_final: 0.8352 (mttm) REVERT: B 488 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7797 (mt-10) REVERT: B 518 GLU cc_start: 0.6449 (mt-10) cc_final: 0.5971 (mt-10) REVERT: B 521 GLU cc_start: 0.7182 (tt0) cc_final: 0.6959 (tm-30) REVERT: B 525 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6571 (t0) REVERT: C 29 MET cc_start: 0.7603 (mmm) cc_final: 0.7174 (mmm) REVERT: C 120 LYS cc_start: 0.7731 (mtmt) cc_final: 0.7476 (ttmm) REVERT: C 166 GLU cc_start: 0.7903 (tt0) cc_final: 0.7681 (tt0) REVERT: C 171 ASN cc_start: 0.8433 (t0) cc_final: 0.8066 (m-40) REVERT: C 178 ARG cc_start: 0.8118 (ttm170) cc_final: 0.7855 (ttp-170) REVERT: C 216 GLU cc_start: 0.7741 (mp0) cc_final: 0.7454 (mp0) REVERT: C 238 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7539 (ttm) REVERT: C 311 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6738 (mm-30) REVERT: C 380 LYS cc_start: 0.7149 (mtmm) cc_final: 0.6813 (mttm) REVERT: C 437 GLU cc_start: 0.7618 (tp30) cc_final: 0.7152 (tp30) REVERT: C 448 THR cc_start: 0.7861 (m) cc_final: 0.7483 (t) REVERT: C 480 ASP cc_start: 0.7395 (m-30) cc_final: 0.7028 (m-30) REVERT: C 492 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7558 (t80) REVERT: C 494 ARG cc_start: 0.7092 (ttp-110) cc_final: 0.6818 (ttp-110) REVERT: C 496 GLN cc_start: 0.7839 (mt0) cc_final: 0.7484 (mt0) REVERT: C 511 ILE cc_start: 0.7976 (mt) cc_final: 0.7589 (mm) REVERT: C 527 PHE cc_start: 0.7231 (t80) cc_final: 0.7000 (t80) outliers start: 55 outliers final: 33 residues processed: 383 average time/residue: 1.5484 time to fit residues: 635.6360 Evaluate side-chains 396 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 355 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 0.0070 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS A 324 GLN A 374 GLN A 400 ASN A 495 ASN B 319 GLN B 495 ASN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 449 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13344 Z= 0.180 Angle : 0.586 10.683 18075 Z= 0.285 Chirality : 0.044 0.236 1989 Planarity : 0.004 0.040 2322 Dihedral : 6.070 57.899 2172 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.06 % Allowed : 15.17 % Favored : 80.77 % 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: 1.17 (0.21), residues: 1569 helix: 1.38 (0.21), residues: 702 sheet: 1.03 (0.30), residues: 267 loop : 0.06 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 419 HIS 0.004 0.001 HIS C 17 PHE 0.014 0.001 PHE B 188 TYR 0.014 0.001 TYR C 273 ARG 0.007 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 362 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8188 (mttt) cc_final: 0.7526 (mtmm) REVERT: A 66 GLU cc_start: 0.8272 (pt0) cc_final: 0.8038 (pt0) REVERT: A 156 GLU cc_start: 0.7613 (tt0) cc_final: 0.7257 (tt0) REVERT: A 166 GLU cc_start: 0.7941 (tt0) cc_final: 0.7561 (tt0) REVERT: A 235 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 238 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7652 (ttm) REVERT: A 242 LEU cc_start: 0.8272 (mt) cc_final: 0.7945 (mt) REVERT: A 269 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: A 311 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6552 (mm-30) REVERT: A 329 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: A 381 CYS cc_start: 0.5705 (m) cc_final: 0.5075 (t) REVERT: A 396 MET cc_start: 0.7582 (mmm) cc_final: 0.7273 (mmp) REVERT: A 409 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8412 (p) REVERT: A 413 SER cc_start: 0.8817 (m) cc_final: 0.8462 (p) REVERT: A 425 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7279 (mt-10) REVERT: A 445 LYS cc_start: 0.7358 (ptpp) cc_final: 0.6903 (pttp) REVERT: A 465 GLU cc_start: 0.7904 (mp0) cc_final: 0.7646 (mp0) REVERT: A 488 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7940 (mt-10) REVERT: A 490 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7850 (mt-10) REVERT: A 492 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.8061 (t80) REVERT: B 29 MET cc_start: 0.6984 (mmm) cc_final: 0.6602 (mmm) REVERT: B 86 ASP cc_start: 0.8074 (t0) cc_final: 0.7783 (t0) REVERT: B 135 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7168 (mt-10) REVERT: B 156 GLU cc_start: 0.7691 (tt0) cc_final: 0.7350 (tt0) REVERT: B 166 GLU cc_start: 0.8046 (tt0) cc_final: 0.7641 (tt0) REVERT: B 177 HIS cc_start: 0.7489 (m-70) cc_final: 0.7282 (m-70) REVERT: B 293 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7735 (pt) REVERT: B 303 LYS cc_start: 0.8410 (ptpp) cc_final: 0.8131 (ptpp) REVERT: B 311 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6470 (mm-30) REVERT: B 316 MET cc_start: 0.7516 (mtm) cc_final: 0.7159 (mtp) REVERT: B 329 GLU cc_start: 0.7519 (tt0) cc_final: 0.6999 (mp0) REVERT: B 362 PHE cc_start: 0.8259 (m-80) cc_final: 0.7874 (m-80) REVERT: B 363 THR cc_start: 0.8104 (t) cc_final: 0.7901 (p) REVERT: B 381 CYS cc_start: 0.5727 (m) cc_final: 0.4892 (t) REVERT: B 407 GLU cc_start: 0.7983 (tt0) cc_final: 0.7418 (tt0) REVERT: B 457 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7734 (mtpp) REVERT: B 469 LYS cc_start: 0.8588 (mttt) cc_final: 0.8361 (mttm) REVERT: B 518 GLU cc_start: 0.6410 (mt-10) cc_final: 0.5962 (mt-10) REVERT: B 525 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6573 (t0) REVERT: C 26 LYS cc_start: 0.8232 (mtpt) cc_final: 0.8008 (mtpt) REVERT: C 29 MET cc_start: 0.7520 (mmm) cc_final: 0.7084 (mmm) REVERT: C 120 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7476 (ttmm) REVERT: C 166 GLU cc_start: 0.7897 (tt0) cc_final: 0.7680 (tt0) REVERT: C 171 ASN cc_start: 0.8442 (t0) cc_final: 0.8073 (m-40) REVERT: C 178 ARG cc_start: 0.8064 (ttm170) cc_final: 0.7798 (ttp-170) REVERT: C 216 GLU cc_start: 0.7739 (mp0) cc_final: 0.7433 (mp0) REVERT: C 238 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7509 (ttm) REVERT: C 303 LYS cc_start: 0.8318 (ptpp) cc_final: 0.7934 (ptmm) REVERT: C 311 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6775 (mm-30) REVERT: C 329 GLU cc_start: 0.7531 (tt0) cc_final: 0.7117 (mp0) REVERT: C 386 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7389 (ttmt) REVERT: C 437 GLU cc_start: 0.7611 (tp30) cc_final: 0.7167 (tp30) REVERT: C 448 THR cc_start: 0.7826 (m) cc_final: 0.7485 (t) REVERT: C 480 ASP cc_start: 0.7355 (m-30) cc_final: 0.6887 (m-30) REVERT: C 492 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7528 (t80) REVERT: C 494 ARG cc_start: 0.7056 (ttp-110) cc_final: 0.6805 (ttp-110) REVERT: C 511 ILE cc_start: 0.7944 (mt) cc_final: 0.7538 (mm) REVERT: C 527 PHE cc_start: 0.7214 (t80) cc_final: 0.6983 (t80) outliers start: 57 outliers final: 29 residues processed: 381 average time/residue: 1.4947 time to fit residues: 611.8113 Evaluate side-chains 409 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 370 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 0.0270 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 400 ASN A 495 ASN B 319 GLN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13344 Z= 0.209 Angle : 0.592 9.531 18075 Z= 0.284 Chirality : 0.045 0.238 1989 Planarity : 0.004 0.042 2322 Dihedral : 6.027 58.104 2172 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.77 % Allowed : 15.95 % Favored : 80.27 % 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: 1.24 (0.21), residues: 1569 helix: 1.46 (0.21), residues: 702 sheet: 1.09 (0.30), residues: 267 loop : 0.05 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 419 HIS 0.005 0.001 HIS C 376 PHE 0.013 0.001 PHE B 188 TYR 0.013 0.001 TYR A 414 ARG 0.007 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 366 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8220 (mttt) cc_final: 0.7552 (mtmm) REVERT: A 66 GLU cc_start: 0.8266 (pt0) cc_final: 0.8040 (pt0) REVERT: A 154 ASP cc_start: 0.7688 (t70) cc_final: 0.7255 (t0) REVERT: A 156 GLU cc_start: 0.7626 (tt0) cc_final: 0.7207 (tt0) REVERT: A 235 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7486 (mt-10) REVERT: A 238 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7666 (ttm) REVERT: A 242 LEU cc_start: 0.8277 (mt) cc_final: 0.7953 (mt) REVERT: A 269 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: A 311 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6519 (mm-30) REVERT: A 329 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: A 396 MET cc_start: 0.7586 (mmm) cc_final: 0.7282 (mmp) REVERT: A 409 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 413 SER cc_start: 0.8811 (m) cc_final: 0.8473 (p) REVERT: A 425 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7246 (mt-10) REVERT: A 445 LYS cc_start: 0.7360 (ptpp) cc_final: 0.6901 (pttp) REVERT: A 465 GLU cc_start: 0.7920 (mp0) cc_final: 0.7648 (mp0) REVERT: A 488 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7974 (mt-10) REVERT: A 490 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 492 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7995 (t80) REVERT: B 29 MET cc_start: 0.7000 (mmm) cc_final: 0.6619 (mmm) REVERT: B 82 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7954 (mtt) REVERT: B 86 ASP cc_start: 0.8040 (t0) cc_final: 0.7729 (t0) REVERT: B 135 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7178 (mt-10) REVERT: B 141 GLN cc_start: 0.7636 (mm110) cc_final: 0.7397 (mm-40) REVERT: B 156 GLU cc_start: 0.7665 (tt0) cc_final: 0.7325 (tt0) REVERT: B 166 GLU cc_start: 0.8038 (tt0) cc_final: 0.7639 (tt0) REVERT: B 177 HIS cc_start: 0.7474 (m-70) cc_final: 0.7251 (m-70) REVERT: B 253 GLU cc_start: 0.8037 (tt0) cc_final: 0.7767 (tt0) REVERT: B 293 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7683 (pt) REVERT: B 303 LYS cc_start: 0.8411 (ptpp) cc_final: 0.8145 (ptpp) REVERT: B 311 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6451 (mm-30) REVERT: B 316 MET cc_start: 0.7514 (mtm) cc_final: 0.7173 (mtp) REVERT: B 329 GLU cc_start: 0.7522 (tt0) cc_final: 0.7001 (mp0) REVERT: B 362 PHE cc_start: 0.8273 (m-80) cc_final: 0.7934 (m-80) REVERT: B 363 THR cc_start: 0.8154 (t) cc_final: 0.7946 (p) REVERT: B 407 GLU cc_start: 0.7966 (tt0) cc_final: 0.7437 (tt0) REVERT: B 457 LYS cc_start: 0.8081 (ttmm) cc_final: 0.7751 (mtpp) REVERT: B 469 LYS cc_start: 0.8597 (mttt) cc_final: 0.8375 (mttm) REVERT: B 518 GLU cc_start: 0.6296 (mt-10) cc_final: 0.5913 (mt-10) REVERT: B 525 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6555 (t0) REVERT: C 26 LYS cc_start: 0.8229 (mtpt) cc_final: 0.8020 (mtpt) REVERT: C 29 MET cc_start: 0.7525 (mmm) cc_final: 0.7092 (mmm) REVERT: C 120 LYS cc_start: 0.7778 (mtmt) cc_final: 0.7541 (ttmm) REVERT: C 166 GLU cc_start: 0.7860 (tt0) cc_final: 0.7650 (tt0) REVERT: C 171 ASN cc_start: 0.8456 (t0) cc_final: 0.8077 (m-40) REVERT: C 178 ARG cc_start: 0.8083 (ttm170) cc_final: 0.7809 (ttp-170) REVERT: C 216 GLU cc_start: 0.7715 (mp0) cc_final: 0.7409 (mp0) REVERT: C 303 LYS cc_start: 0.8327 (ptpp) cc_final: 0.7943 (ptmm) REVERT: C 311 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6520 (mm-30) REVERT: C 386 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7393 (ttmt) REVERT: C 437 GLU cc_start: 0.7682 (tp30) cc_final: 0.7217 (tp30) REVERT: C 448 THR cc_start: 0.7853 (m) cc_final: 0.7498 (t) REVERT: C 462 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8276 (p) REVERT: C 480 ASP cc_start: 0.7368 (m-30) cc_final: 0.6903 (m-30) REVERT: C 492 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7535 (t80) REVERT: C 494 ARG cc_start: 0.7075 (ttp-110) cc_final: 0.6831 (ttp-110) REVERT: C 511 ILE cc_start: 0.8028 (mt) cc_final: 0.7592 (mm) REVERT: C 527 PHE cc_start: 0.7216 (t80) cc_final: 0.6980 (t80) outliers start: 53 outliers final: 27 residues processed: 385 average time/residue: 1.5586 time to fit residues: 645.5229 Evaluate side-chains 397 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 359 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 374 GLN A 400 ASN A 495 ASN B 374 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13344 Z= 0.247 Angle : 0.616 13.643 18075 Z= 0.298 Chirality : 0.045 0.240 1989 Planarity : 0.004 0.043 2322 Dihedral : 6.035 58.160 2172 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.77 % Allowed : 15.81 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.21), residues: 1569 helix: 1.42 (0.21), residues: 702 sheet: 1.09 (0.30), residues: 267 loop : 0.02 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 419 HIS 0.005 0.001 HIS A 376 PHE 0.014 0.001 PHE C 188 TYR 0.013 0.001 TYR A 414 ARG 0.006 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 367 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8239 (mttt) cc_final: 0.7563 (mtmm) REVERT: A 49 MET cc_start: 0.7615 (mmm) cc_final: 0.7354 (tpp) REVERT: A 66 GLU cc_start: 0.8261 (pt0) cc_final: 0.8034 (pt0) REVERT: A 154 ASP cc_start: 0.7691 (t70) cc_final: 0.7254 (t0) REVERT: A 156 GLU cc_start: 0.7614 (tt0) cc_final: 0.7215 (tt0) REVERT: A 235 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 238 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7665 (ttm) REVERT: A 242 LEU cc_start: 0.8291 (mt) cc_final: 0.7949 (mt) REVERT: A 269 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: A 311 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6509 (mm-30) REVERT: A 329 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: A 381 CYS cc_start: 0.5651 (m) cc_final: 0.5047 (t) REVERT: A 396 MET cc_start: 0.7589 (mmm) cc_final: 0.7284 (mmp) REVERT: A 409 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8413 (p) REVERT: A 413 SER cc_start: 0.8804 (m) cc_final: 0.8468 (p) REVERT: A 425 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7175 (mt-10) REVERT: A 445 LYS cc_start: 0.7422 (ptpp) cc_final: 0.7015 (pttp) REVERT: A 465 GLU cc_start: 0.7900 (mp0) cc_final: 0.7648 (mp0) REVERT: A 488 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7985 (mt-10) REVERT: A 490 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 492 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8041 (t80) REVERT: B 29 MET cc_start: 0.7010 (mmm) cc_final: 0.6630 (mmm) REVERT: B 82 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7929 (mtt) REVERT: B 86 ASP cc_start: 0.8042 (t0) cc_final: 0.7747 (t0) REVERT: B 135 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7218 (mt-10) REVERT: B 156 GLU cc_start: 0.7659 (tt0) cc_final: 0.7320 (tt0) REVERT: B 166 GLU cc_start: 0.8032 (tt0) cc_final: 0.7634 (tt0) REVERT: B 177 HIS cc_start: 0.7474 (m-70) cc_final: 0.7249 (m-70) REVERT: B 253 GLU cc_start: 0.8061 (tt0) cc_final: 0.7761 (tt0) REVERT: B 293 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7314 (pt) REVERT: B 303 LYS cc_start: 0.8405 (ptpp) cc_final: 0.8158 (ptpp) REVERT: B 311 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6449 (mm-30) REVERT: B 316 MET cc_start: 0.7551 (mtm) cc_final: 0.7168 (mtp) REVERT: B 329 GLU cc_start: 0.7515 (tt0) cc_final: 0.7005 (mp0) REVERT: B 362 PHE cc_start: 0.8260 (m-80) cc_final: 0.7930 (m-80) REVERT: B 381 CYS cc_start: 0.5516 (m) cc_final: 0.4538 (t) REVERT: B 407 GLU cc_start: 0.7961 (tt0) cc_final: 0.7417 (tt0) REVERT: B 457 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7840 (ttmm) REVERT: B 469 LYS cc_start: 0.8598 (mttt) cc_final: 0.8378 (mttm) REVERT: B 518 GLU cc_start: 0.6336 (mt-10) cc_final: 0.5983 (mt-10) REVERT: B 525 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6557 (t0) REVERT: C 29 MET cc_start: 0.7542 (mmm) cc_final: 0.7106 (mmm) REVERT: C 120 LYS cc_start: 0.7682 (mtmt) cc_final: 0.7415 (ttmm) REVERT: C 166 GLU cc_start: 0.7849 (tt0) cc_final: 0.7639 (tt0) REVERT: C 171 ASN cc_start: 0.8463 (t0) cc_final: 0.8106 (m-40) REVERT: C 178 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7819 (ttp-170) REVERT: C 216 GLU cc_start: 0.7724 (mp0) cc_final: 0.7424 (mp0) REVERT: C 253 GLU cc_start: 0.8458 (tt0) cc_final: 0.8200 (tt0) REVERT: C 311 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6515 (mm-30) REVERT: C 329 GLU cc_start: 0.7544 (tt0) cc_final: 0.7072 (mp0) REVERT: C 386 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7428 (ttmt) REVERT: C 437 GLU cc_start: 0.7618 (tp30) cc_final: 0.7142 (tp30) REVERT: C 448 THR cc_start: 0.7838 (m) cc_final: 0.7483 (t) REVERT: C 462 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8270 (p) REVERT: C 480 ASP cc_start: 0.7379 (m-30) cc_final: 0.6921 (m-30) REVERT: C 492 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7442 (t80) REVERT: C 494 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6841 (ttp-110) REVERT: C 511 ILE cc_start: 0.8037 (mt) cc_final: 0.7589 (mm) REVERT: C 527 PHE cc_start: 0.7218 (t80) cc_final: 0.6980 (t80) outliers start: 53 outliers final: 35 residues processed: 383 average time/residue: 1.5118 time to fit residues: 621.3371 Evaluate side-chains 402 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 356 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 400 ASN A 495 ASN B 319 GLN B 374 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13344 Z= 0.240 Angle : 0.618 12.556 18075 Z= 0.298 Chirality : 0.045 0.240 1989 Planarity : 0.004 0.042 2322 Dihedral : 6.041 58.132 2172 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.42 % Allowed : 16.38 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1569 helix: 1.43 (0.21), residues: 702 sheet: 1.07 (0.30), residues: 267 loop : 0.00 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 419 HIS 0.004 0.001 HIS C 376 PHE 0.014 0.001 PHE B 188 TYR 0.013 0.001 TYR A 414 ARG 0.005 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 366 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8229 (mttt) cc_final: 0.7557 (mtmm) REVERT: A 66 GLU cc_start: 0.8255 (pt0) cc_final: 0.8033 (pt0) REVERT: A 119 MET cc_start: 0.8092 (mmt) cc_final: 0.7826 (mmm) REVERT: A 154 ASP cc_start: 0.7694 (t70) cc_final: 0.7237 (t0) REVERT: A 156 GLU cc_start: 0.7610 (tt0) cc_final: 0.7207 (tt0) REVERT: A 235 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 238 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7667 (ttm) REVERT: A 242 LEU cc_start: 0.8295 (mt) cc_final: 0.7947 (mt) REVERT: A 269 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: A 311 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6495 (mm-30) REVERT: A 329 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: A 381 CYS cc_start: 0.5617 (m) cc_final: 0.5021 (t) REVERT: A 391 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8162 (mmtm) REVERT: A 396 MET cc_start: 0.7591 (mmm) cc_final: 0.7287 (mmp) REVERT: A 413 SER cc_start: 0.8803 (m) cc_final: 0.8467 (p) REVERT: A 465 GLU cc_start: 0.7898 (mp0) cc_final: 0.7651 (mp0) REVERT: A 488 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7977 (mt-10) REVERT: A 490 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 492 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8047 (t80) REVERT: B 29 MET cc_start: 0.7005 (mmm) cc_final: 0.6623 (mmm) REVERT: B 86 ASP cc_start: 0.8042 (t0) cc_final: 0.7748 (t0) REVERT: B 135 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7211 (mt-10) REVERT: B 156 GLU cc_start: 0.7625 (tt0) cc_final: 0.7318 (tt0) REVERT: B 166 GLU cc_start: 0.8023 (tt0) cc_final: 0.7624 (tt0) REVERT: B 177 HIS cc_start: 0.7477 (m-70) cc_final: 0.7249 (m-70) REVERT: B 293 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7509 (pt) REVERT: B 303 LYS cc_start: 0.8386 (ptpp) cc_final: 0.8137 (ptpp) REVERT: B 311 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6453 (mm-30) REVERT: B 316 MET cc_start: 0.7537 (mtm) cc_final: 0.7177 (mtp) REVERT: B 329 GLU cc_start: 0.7508 (tt0) cc_final: 0.6985 (mp0) REVERT: B 362 PHE cc_start: 0.8218 (m-80) cc_final: 0.7910 (m-80) REVERT: B 407 GLU cc_start: 0.7951 (tt0) cc_final: 0.7428 (tt0) REVERT: B 457 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7863 (ttmm) REVERT: B 469 LYS cc_start: 0.8588 (mttt) cc_final: 0.8364 (mttm) REVERT: B 518 GLU cc_start: 0.6345 (mt-10) cc_final: 0.5981 (mt-10) REVERT: B 525 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6559 (t0) REVERT: C 28 SER cc_start: 0.6881 (m) cc_final: 0.6590 (t) REVERT: C 29 MET cc_start: 0.7529 (mmm) cc_final: 0.7202 (mmm) REVERT: C 120 LYS cc_start: 0.7727 (mtmt) cc_final: 0.7462 (ttmm) REVERT: C 166 GLU cc_start: 0.7830 (tt0) cc_final: 0.7615 (tt0) REVERT: C 171 ASN cc_start: 0.8482 (t0) cc_final: 0.8117 (m-40) REVERT: C 178 ARG cc_start: 0.8092 (ttm170) cc_final: 0.7812 (ttp-170) REVERT: C 216 GLU cc_start: 0.7718 (mp0) cc_final: 0.7411 (mp0) REVERT: C 311 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6533 (mm-30) REVERT: C 316 MET cc_start: 0.7781 (mtp) cc_final: 0.7563 (mtm) REVERT: C 386 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7409 (ttmt) REVERT: C 437 GLU cc_start: 0.7620 (tp30) cc_final: 0.7138 (tp30) REVERT: C 448 THR cc_start: 0.7834 (m) cc_final: 0.7481 (t) REVERT: C 462 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8271 (p) REVERT: C 480 ASP cc_start: 0.7393 (m-30) cc_final: 0.6936 (m-30) REVERT: C 492 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7446 (t80) REVERT: C 494 ARG cc_start: 0.7097 (ttp-110) cc_final: 0.6834 (ttp-110) REVERT: C 527 PHE cc_start: 0.7210 (t80) cc_final: 0.6970 (t80) outliers start: 48 outliers final: 31 residues processed: 381 average time/residue: 1.5343 time to fit residues: 626.5832 Evaluate side-chains 400 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 359 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 70 optimal weight: 0.0270 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 0.0770 chunk 98 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 374 GLN A 400 ASN A 495 ASN B 319 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13344 Z= 0.180 Angle : 0.609 11.520 18075 Z= 0.291 Chirality : 0.044 0.239 1989 Planarity : 0.004 0.042 2322 Dihedral : 5.953 57.918 2172 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.21 % Allowed : 17.31 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1569 helix: 1.48 (0.21), residues: 702 sheet: 1.07 (0.30), residues: 267 loop : 0.00 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 419 HIS 0.005 0.001 HIS C 17 PHE 0.013 0.001 PHE B 188 TYR 0.011 0.001 TYR C 414 ARG 0.012 0.000 ARG B 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 366 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8228 (mttt) cc_final: 0.7554 (mtmm) REVERT: A 154 ASP cc_start: 0.7708 (t70) cc_final: 0.7268 (t0) REVERT: A 156 GLU cc_start: 0.7593 (tt0) cc_final: 0.7186 (tt0) REVERT: A 166 GLU cc_start: 0.7961 (tt0) cc_final: 0.7581 (tt0) REVERT: A 235 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 238 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7673 (ttm) REVERT: A 242 LEU cc_start: 0.8269 (mt) cc_final: 0.7907 (mt) REVERT: A 311 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6521 (mm-30) REVERT: A 329 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: A 391 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8161 (mmtm) REVERT: A 396 MET cc_start: 0.7600 (mmm) cc_final: 0.7302 (mmp) REVERT: A 413 SER cc_start: 0.8815 (m) cc_final: 0.8492 (p) REVERT: A 465 GLU cc_start: 0.7903 (mp0) cc_final: 0.7646 (mp0) REVERT: A 488 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7937 (mt-10) REVERT: A 490 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7876 (mt-10) REVERT: A 492 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.8040 (t80) REVERT: A 511 ILE cc_start: 0.7873 (mt) cc_final: 0.7650 (pt) REVERT: B 29 MET cc_start: 0.6976 (mmm) cc_final: 0.6584 (mmm) REVERT: B 86 ASP cc_start: 0.8034 (t0) cc_final: 0.7741 (t0) REVERT: B 135 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7169 (mt-10) REVERT: B 138 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6875 (mp0) REVERT: B 156 GLU cc_start: 0.7619 (tt0) cc_final: 0.7317 (tt0) REVERT: B 166 GLU cc_start: 0.8015 (tt0) cc_final: 0.7602 (tt0) REVERT: B 177 HIS cc_start: 0.7478 (m-70) cc_final: 0.7249 (m-70) REVERT: B 293 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7454 (pt) REVERT: B 303 LYS cc_start: 0.8367 (ptpp) cc_final: 0.8103 (ptpp) REVERT: B 311 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6469 (mm-30) REVERT: B 316 MET cc_start: 0.7470 (mtm) cc_final: 0.7143 (mtp) REVERT: B 329 GLU cc_start: 0.7471 (tt0) cc_final: 0.6987 (mp0) REVERT: B 362 PHE cc_start: 0.8225 (m-80) cc_final: 0.7908 (m-80) REVERT: B 381 CYS cc_start: 0.5302 (m) cc_final: 0.4672 (t) REVERT: B 407 GLU cc_start: 0.7931 (tt0) cc_final: 0.7401 (tt0) REVERT: B 448 THR cc_start: 0.7582 (OUTLIER) cc_final: 0.7206 (p) REVERT: B 457 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7861 (ttmm) REVERT: B 469 LYS cc_start: 0.8626 (mttt) cc_final: 0.8402 (mttm) REVERT: B 518 GLU cc_start: 0.6319 (mt-10) cc_final: 0.5994 (mt-10) REVERT: B 525 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6567 (t0) REVERT: C 7 MET cc_start: 0.6929 (mmm) cc_final: 0.6605 (mpp) REVERT: C 28 SER cc_start: 0.6869 (m) cc_final: 0.6572 (t) REVERT: C 29 MET cc_start: 0.7527 (mmm) cc_final: 0.7197 (mmm) REVERT: C 49 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7134 (mpp) REVERT: C 120 LYS cc_start: 0.7698 (mtmt) cc_final: 0.7449 (ttmm) REVERT: C 166 GLU cc_start: 0.7827 (tt0) cc_final: 0.7611 (tt0) REVERT: C 178 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7791 (ttp-170) REVERT: C 216 GLU cc_start: 0.7721 (mp0) cc_final: 0.7420 (mp0) REVERT: C 311 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6548 (mm-30) REVERT: C 316 MET cc_start: 0.7730 (mtp) cc_final: 0.7513 (mtm) REVERT: C 329 GLU cc_start: 0.7612 (tt0) cc_final: 0.7162 (mp0) REVERT: C 386 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7363 (ttmt) REVERT: C 437 GLU cc_start: 0.7631 (tp30) cc_final: 0.7158 (tp30) REVERT: C 448 THR cc_start: 0.7826 (m) cc_final: 0.7470 (t) REVERT: C 480 ASP cc_start: 0.7378 (m-30) cc_final: 0.6928 (m-30) REVERT: C 492 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7465 (t80) REVERT: C 494 ARG cc_start: 0.7075 (ttp-110) cc_final: 0.6817 (ttp-110) REVERT: C 527 PHE cc_start: 0.7207 (t80) cc_final: 0.6968 (t80) outliers start: 45 outliers final: 27 residues processed: 380 average time/residue: 1.5409 time to fit residues: 628.0729 Evaluate side-chains 393 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 356 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 15 optimal weight: 0.0050 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 400 ASN A 495 ASN B 319 GLN B 504 GLN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.132474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.121301 restraints weight = 17094.765| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.62 r_work: 0.3616 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13344 Z= 0.199 Angle : 0.608 11.074 18075 Z= 0.293 Chirality : 0.045 0.240 1989 Planarity : 0.004 0.047 2322 Dihedral : 5.979 57.996 2172 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.92 % Allowed : 17.31 % Favored : 79.77 % 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: 1.24 (0.21), residues: 1569 helix: 1.49 (0.21), residues: 702 sheet: 1.09 (0.30), residues: 267 loop : 0.00 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 419 HIS 0.007 0.001 HIS C 17 PHE 0.016 0.001 PHE C 45 TYR 0.012 0.001 TYR C 414 ARG 0.011 0.000 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8519.91 seconds wall clock time: 151 minutes 31.21 seconds (9091.21 seconds total)