Starting phenix.real_space_refine on Mon Dec 30 11:08:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8on9_16983/12_2024/8on9_16983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8on9_16983/12_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/cci-nas-00/data/ceres_data/8on9_16983/12_2024/8on9_16983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8on9_16983/12_2024/8on9_16983.map" model { file = "/net/cci-nas-00/data/ceres_data/8on9_16983/12_2024/8on9_16983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8on9_16983/12_2024/8on9_16983.cif" } 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. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13014 Number of models: 1 Model: "" Number of chains: 18 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Link IDs: {'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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Link IDs: {'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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Link IDs: {'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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 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: 7.93, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, 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 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.7 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... Secondary structure from input PDB file: 63 helices and 9 sheets defined 46.0% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 27 through 57 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.665A pdb=" N PHE A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 removed outlier: 3.952A pdb=" N PHE A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.565A pdb=" N CYS A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 365 through 390 removed outlier: 4.562A pdb=" N THR A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 398 Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.506A pdb=" N ASN A 444 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'A' and resid 514 through 530 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 18 through 25 Processing helix chain 'B' and resid 27 through 57 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 136 through 144 removed outlier: 3.665A pdb=" N PHE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 removed outlier: 3.952A pdb=" N PHE B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.564A pdb=" N CYS B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 365 through 390 removed outlier: 4.562A pdb=" N THR B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 398 Processing helix chain 'B' and resid 423 through 435 Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.506A pdb=" N ASN B 444 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 493 through 509 Processing helix chain 'B' and resid 514 through 530 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 27 through 57 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 136 through 144 removed outlier: 3.665A pdb=" N PHE C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.952A pdb=" N PHE C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 314 through 332 removed outlier: 3.565A pdb=" N CYS C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 365 through 390 removed outlier: 4.562A pdb=" N THR C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 398 Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.506A pdb=" N ASN C 444 " --> pdb=" O GLU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 493 through 509 Processing helix chain 'C' and resid 514 through 530 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 removed outlier: 9.246A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLU A 490 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A 279 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 171 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 224 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL A 169 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 68 removed outlier: 9.246A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLU A 490 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, first strand: chain 'B' and resid 61 through 68 removed outlier: 9.247A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLU B 490 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE B 279 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 171 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU B 224 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 169 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 68 removed outlier: 9.247A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLU B 490 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AA6, 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=AA7, first strand: chain 'C' and resid 61 through 68 removed outlier: 9.246A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLU C 490 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE C 279 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN C 171 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU C 224 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL C 169 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 68 removed outlier: 9.246A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLU C 490 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AA9, 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) 661 hydrogen bonds defined for protein. 1884 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: 4.38 Time building geometry restraints manager: 3.89 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: 2896 1.33 - 1.45: 3189 1.45 - 1.58: 7100 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 13341 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 13336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 17550 2.09 - 4.18: 438 4.18 - 6.27: 69 6.27 - 8.37: 6 8.37 - 10.46: 6 Bond angle restraints: 18069 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 18064 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: 2334 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 2331 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 425 2.72 - 3.26: 12904 3.26 - 3.81: 21443 3.81 - 4.35: 26422 4.35 - 4.90: 45406 Nonbonded interactions: 106600 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 3.040 nonbonded pdb=" OH TYR A 192 " pdb=" O VAL A 249 " model vdw 2.283 3.040 ... (remaining 106595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.450 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 31.430 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 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:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.750 ------------------------------------------------------------------------------- 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 13341 Z= 0.292 Angle : 0.744 10.458 18069 Z= 0.441 Chirality : 0.050 0.246 1989 Planarity : 0.009 0.144 2319 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 to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 1.541 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: 1.4546 time to fit residues: 690.7343 Evaluate side-chains 373 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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: 1.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 449 GLN C 482 ASN C 495 ASN C 496 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13341 Z= 0.231 Angle : 0.628 11.558 18069 Z= 0.314 Chirality : 0.046 0.247 1989 Planarity : 0.004 0.041 2319 Dihedral : 6.482 59.866 2172 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.06 % Allowed : 11.61 % Favored : 85.33 % 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: 1.43 (0.21), residues: 1569 helix: 1.45 (0.20), residues: 705 sheet: 1.46 (0.29), residues: 273 loop : 0.21 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 419 HIS 0.003 0.001 HIS B 376 PHE 0.015 0.001 PHE C 439 TYR 0.013 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 442 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 399 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7604 (mtp) REVERT: A 26 LYS cc_start: 0.8201 (mttt) cc_final: 0.7563 (mtmm) REVERT: A 66 GLU cc_start: 0.8351 (pt0) cc_final: 0.8095 (pt0) REVERT: A 82 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8356 (mtt) REVERT: A 145 SER cc_start: 0.8276 (p) cc_final: 0.8074 (m) REVERT: A 156 GLU cc_start: 0.7693 (tt0) cc_final: 0.7363 (tt0) REVERT: A 166 GLU cc_start: 0.7984 (tt0) cc_final: 0.7479 (tt0) REVERT: A 235 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 242 LEU cc_start: 0.8367 (mm) cc_final: 0.8165 (mt) REVERT: A 293 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7708 (pt) REVERT: A 311 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6624 (mm-30) REVERT: A 357 PRO cc_start: 0.7650 (Cg_exo) cc_final: 0.7447 (Cg_endo) REVERT: A 396 MET cc_start: 0.7612 (mmm) cc_final: 0.7288 (mmp) REVERT: A 407 GLU cc_start: 0.8015 (tt0) cc_final: 0.7744 (tt0) REVERT: A 445 LYS cc_start: 0.7222 (ptpt) cc_final: 0.7002 (ptpp) REVERT: A 465 GLU cc_start: 0.7907 (mp0) cc_final: 0.7674 (mp0) REVERT: A 488 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7992 (mt-10) REVERT: A 494 ARG cc_start: 0.7053 (ttp-110) cc_final: 0.6812 (ttm110) REVERT: A 511 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7538 (mp) REVERT: A 525 ASP cc_start: 0.6907 (m-30) cc_final: 0.6601 (t0) REVERT: B 29 MET cc_start: 0.7031 (mmm) cc_final: 0.6634 (mmm) REVERT: B 44 MET cc_start: 0.7219 (mmm) cc_final: 0.6490 (mmm) REVERT: B 48 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7171 (mm-40) REVERT: B 57 PHE cc_start: 0.8060 (m-80) cc_final: 0.7759 (m-80) REVERT: B 86 ASP cc_start: 0.7916 (t0) cc_final: 0.7641 (t0) REVERT: B 124 LYS cc_start: 0.8022 (mttt) cc_final: 0.7808 (mttp) REVERT: B 145 SER cc_start: 0.8145 (p) cc_final: 0.7936 (m) REVERT: B 156 GLU cc_start: 0.7753 (tt0) cc_final: 0.7429 (tt0) REVERT: B 166 GLU cc_start: 0.8071 (tt0) cc_final: 0.7694 (tt0) REVERT: B 177 HIS cc_start: 0.7386 (m-70) cc_final: 0.7151 (m-70) REVERT: B 293 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7427 (pt) REVERT: B 303 LYS cc_start: 0.8418 (ptpp) cc_final: 0.8209 (ptpp) REVERT: B 311 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6508 (mm-30) REVERT: B 329 GLU cc_start: 0.7477 (tt0) cc_final: 0.6995 (mm-30) REVERT: B 357 PRO cc_start: 0.7550 (Cg_exo) cc_final: 0.7258 (Cg_endo) REVERT: B 362 PHE cc_start: 0.8178 (m-80) cc_final: 0.7913 (m-80) REVERT: B 377 ASN cc_start: 0.7597 (m-40) cc_final: 0.7323 (m110) REVERT: B 407 GLU cc_start: 0.7852 (tt0) cc_final: 0.7337 (tt0) REVERT: B 465 GLU cc_start: 0.7826 (mp0) cc_final: 0.7588 (mp0) REVERT: B 469 LYS cc_start: 0.8584 (mttt) cc_final: 0.8362 (mttm) REVERT: B 481 SER cc_start: 0.8261 (t) cc_final: 0.7912 (p) REVERT: B 490 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: B 495 ASN cc_start: 0.7573 (t0) cc_final: 0.7337 (t160) REVERT: B 511 ILE cc_start: 0.7889 (mt) cc_final: 0.7613 (mm) REVERT: B 518 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6458 (mt-10) REVERT: C 28 SER cc_start: 0.6878 (m) cc_final: 0.6631 (t) REVERT: C 29 MET cc_start: 0.7542 (mmm) cc_final: 0.7197 (mmm) REVERT: C 49 MET cc_start: 0.7766 (tpp) cc_final: 0.7500 (tpp) REVERT: C 116 ARG cc_start: 0.7584 (mtp180) cc_final: 0.7384 (mtp85) REVERT: C 141 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7558 (mm110) REVERT: C 142 GLU cc_start: 0.7546 (tt0) cc_final: 0.7294 (tt0) REVERT: C 166 GLU cc_start: 0.8000 (tt0) cc_final: 0.7608 (tt0) REVERT: C 178 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7767 (ttp-170) REVERT: C 301 SER cc_start: 0.7656 (t) cc_final: 0.7441 (p) REVERT: C 311 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6564 (mm-30) REVERT: C 329 GLU cc_start: 0.7713 (tt0) cc_final: 0.7486 (tt0) REVERT: C 357 PRO cc_start: 0.7621 (Cg_exo) cc_final: 0.7419 (Cg_endo) REVERT: C 407 GLU cc_start: 0.8020 (tt0) cc_final: 0.7733 (tt0) REVERT: C 465 GLU cc_start: 0.7946 (mp0) cc_final: 0.7738 (mp0) REVERT: C 480 ASP cc_start: 0.7380 (m-30) cc_final: 0.7060 (m-30) REVERT: C 511 ILE cc_start: 0.7891 (mt) cc_final: 0.7582 (mm) outliers start: 43 outliers final: 13 residues processed: 414 average time/residue: 1.4658 time to fit residues: 652.9054 Evaluate side-chains 378 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 359 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 82 MET 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 511 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 293 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 124 LYS 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: 0.9980 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 319 GLN A 324 GLN A 374 GLN A 400 ASN A 487 GLN A 495 ASN B 374 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 496 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13341 Z= 0.212 Angle : 0.601 9.451 18069 Z= 0.296 Chirality : 0.046 0.247 1989 Planarity : 0.004 0.043 2319 Dihedral : 6.249 57.561 2172 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.63 % Allowed : 12.39 % Favored : 83.97 % 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: 1.43 (0.21), residues: 1569 helix: 1.49 (0.20), residues: 711 sheet: 1.28 (0.29), residues: 273 loop : 0.24 (0.25), residues: 585 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 A 188 TYR 0.012 0.001 TYR A 414 ARG 0.005 0.000 ARG C 246 *********************** 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 420 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 369 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8191 (mttt) cc_final: 0.7503 (mtmm) REVERT: A 48 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7303 (mm-40) REVERT: A 66 GLU cc_start: 0.8321 (pt0) cc_final: 0.8065 (pt0) REVERT: A 156 GLU cc_start: 0.7650 (tt0) cc_final: 0.7290 (tt0) REVERT: A 166 GLU cc_start: 0.7988 (tt0) cc_final: 0.7702 (tt0) REVERT: A 235 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 288 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7693 (mtp180) REVERT: A 311 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6591 (mm-30) REVERT: A 351 ARG cc_start: 0.7638 (mtt90) cc_final: 0.7422 (mtt-85) REVERT: A 357 PRO cc_start: 0.7537 (Cg_exo) cc_final: 0.7326 (Cg_endo) REVERT: A 396 MET cc_start: 0.7581 (mmm) cc_final: 0.7308 (mmp) REVERT: A 409 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8296 (p) REVERT: A 441 GLU cc_start: 0.8152 (mp0) cc_final: 0.7948 (mm-30) REVERT: A 445 LYS cc_start: 0.7378 (ptpt) cc_final: 0.7123 (ptpp) REVERT: A 465 GLU cc_start: 0.7894 (mp0) cc_final: 0.7655 (mp0) REVERT: A 488 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8005 (mt-10) REVERT: A 490 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: A 494 ARG cc_start: 0.7035 (ttp-110) cc_final: 0.6814 (ttm-80) REVERT: A 511 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7588 (mp) REVERT: A 525 ASP cc_start: 0.6848 (m-30) cc_final: 0.6574 (t0) REVERT: B 29 MET cc_start: 0.7037 (mmm) cc_final: 0.6656 (mmm) REVERT: B 48 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7205 (mm-40) REVERT: B 49 MET cc_start: 0.7549 (tpp) cc_final: 0.7346 (mmp) REVERT: B 57 PHE cc_start: 0.8068 (m-80) cc_final: 0.7807 (m-80) REVERT: B 86 ASP cc_start: 0.8001 (t0) cc_final: 0.7702 (t0) REVERT: B 124 LYS cc_start: 0.8061 (mttt) cc_final: 0.7838 (mttp) REVERT: B 138 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6911 (mp0) REVERT: B 141 GLN cc_start: 0.7744 (mm110) cc_final: 0.7524 (mm-40) REVERT: B 145 SER cc_start: 0.8303 (p) cc_final: 0.8046 (m) REVERT: B 156 GLU cc_start: 0.7754 (tt0) cc_final: 0.7429 (tt0) REVERT: B 166 GLU cc_start: 0.8086 (tt0) cc_final: 0.7754 (tt0) REVERT: B 177 HIS cc_start: 0.7387 (m-70) cc_final: 0.7142 (m-70) REVERT: B 213 GLU cc_start: 0.7581 (pt0) cc_final: 0.7332 (pt0) REVERT: B 253 GLU cc_start: 0.8392 (tt0) cc_final: 0.8125 (tt0) REVERT: B 293 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7681 (pt) REVERT: B 303 LYS cc_start: 0.8405 (ptpp) cc_final: 0.8179 (ptpp) REVERT: B 311 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6408 (mm-30) REVERT: B 329 GLU cc_start: 0.7452 (tt0) cc_final: 0.6966 (mm-30) REVERT: B 357 PRO cc_start: 0.7531 (Cg_exo) cc_final: 0.7240 (Cg_endo) REVERT: B 362 PHE cc_start: 0.8185 (m-80) cc_final: 0.7881 (m-80) REVERT: B 363 THR cc_start: 0.7923 (t) cc_final: 0.7674 (p) REVERT: B 377 ASN cc_start: 0.7588 (m-40) cc_final: 0.7341 (m110) REVERT: B 407 GLU cc_start: 0.7911 (tt0) cc_final: 0.7396 (tt0) REVERT: B 465 GLU cc_start: 0.7820 (mp0) cc_final: 0.7589 (mp0) REVERT: B 469 LYS cc_start: 0.8584 (mttt) cc_final: 0.8331 (mttm) REVERT: B 480 ASP cc_start: 0.7414 (m-30) cc_final: 0.7182 (m-30) REVERT: B 495 ASN cc_start: 0.7501 (t0) cc_final: 0.7271 (t160) REVERT: B 511 ILE cc_start: 0.7964 (mt) cc_final: 0.7628 (mm) REVERT: B 518 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6404 (mt-10) REVERT: C 29 MET cc_start: 0.7626 (mmm) cc_final: 0.7176 (mmm) REVERT: C 49 MET cc_start: 0.7790 (tpp) cc_final: 0.7480 (tpp) REVERT: C 116 ARG cc_start: 0.7586 (mtp180) cc_final: 0.7379 (mtp85) REVERT: C 121 LYS cc_start: 0.7851 (ttmm) cc_final: 0.7511 (tppt) REVERT: C 166 GLU cc_start: 0.7990 (tt0) cc_final: 0.7618 (tt0) REVERT: C 178 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7765 (ttp-170) REVERT: C 246 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7969 (mtt180) REVERT: C 301 SER cc_start: 0.7660 (t) cc_final: 0.7446 (p) REVERT: C 311 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6445 (mm-30) REVERT: C 329 GLU cc_start: 0.7674 (tt0) cc_final: 0.7437 (tt0) REVERT: C 357 PRO cc_start: 0.7488 (Cg_exo) cc_final: 0.7276 (Cg_endo) REVERT: C 388 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7239 (ptpp) REVERT: C 407 GLU cc_start: 0.7988 (tt0) cc_final: 0.7726 (tt0) REVERT: C 480 ASP cc_start: 0.7430 (m-30) cc_final: 0.7085 (m-30) REVERT: C 494 ARG cc_start: 0.6988 (ttp-110) cc_final: 0.6683 (ttp-110) REVERT: C 495 ASN cc_start: 0.7565 (t0) cc_final: 0.7134 (t0) REVERT: C 511 ILE cc_start: 0.8024 (mt) cc_final: 0.7682 (mm) REVERT: C 527 PHE cc_start: 0.7249 (t80) cc_final: 0.7021 (t80) outliers start: 51 outliers final: 18 residues processed: 392 average time/residue: 1.4747 time to fit residues: 621.1606 Evaluate side-chains 380 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 356 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 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 A residue 511 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 99 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 246 ARG 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 490 GLU 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: 1.9990 chunk 106 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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 286 HIS A 319 GLN A 324 GLN A 374 GLN A 400 ASN A 495 ASN B 297 HIS B 374 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 496 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13341 Z= 0.224 Angle : 0.597 9.544 18069 Z= 0.295 Chirality : 0.046 0.240 1989 Planarity : 0.004 0.044 2319 Dihedral : 6.203 57.876 2172 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.99 % Allowed : 12.54 % Favored : 83.48 % 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: 1.34 (0.21), residues: 1569 helix: 1.49 (0.20), residues: 711 sheet: 1.11 (0.30), residues: 264 loop : 0.18 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 419 HIS 0.003 0.001 HIS B 376 PHE 0.015 0.001 PHE B 188 TYR 0.012 0.001 TYR A 414 ARG 0.006 0.000 ARG C 246 *********************** 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 427 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 371 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8202 (mttt) cc_final: 0.7520 (mtmm) REVERT: A 66 GLU cc_start: 0.8339 (pt0) cc_final: 0.8090 (pt0) REVERT: A 156 GLU cc_start: 0.7653 (tt0) cc_final: 0.7288 (tt0) REVERT: A 166 GLU cc_start: 0.7991 (tt0) cc_final: 0.7404 (tt0) REVERT: A 235 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 311 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6551 (mm-30) REVERT: A 396 MET cc_start: 0.7585 (mmm) cc_final: 0.7307 (mmp) REVERT: A 409 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8330 (p) REVERT: A 441 GLU cc_start: 0.8126 (mp0) cc_final: 0.7921 (mm-30) REVERT: A 445 LYS cc_start: 0.7535 (ptpt) cc_final: 0.7086 (pttp) REVERT: A 465 GLU cc_start: 0.7905 (mp0) cc_final: 0.7659 (mp0) REVERT: A 488 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8000 (mt-10) REVERT: A 490 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: A 494 ARG cc_start: 0.7038 (ttp-110) cc_final: 0.6822 (ttm-80) REVERT: A 525 ASP cc_start: 0.6852 (m-30) cc_final: 0.6591 (t0) REVERT: B 29 MET cc_start: 0.7037 (mmm) cc_final: 0.6661 (mmm) REVERT: B 49 MET cc_start: 0.7491 (tpp) cc_final: 0.7284 (mmp) REVERT: B 86 ASP cc_start: 0.7976 (t0) cc_final: 0.7669 (t0) REVERT: B 124 LYS cc_start: 0.8102 (mttt) cc_final: 0.7870 (mttp) REVERT: B 141 GLN cc_start: 0.7757 (mm110) cc_final: 0.7526 (mm-40) REVERT: B 145 SER cc_start: 0.8285 (p) cc_final: 0.8058 (m) REVERT: B 156 GLU cc_start: 0.7732 (tt0) cc_final: 0.7412 (tt0) REVERT: B 166 GLU cc_start: 0.8063 (tt0) cc_final: 0.7674 (tt0) REVERT: B 177 HIS cc_start: 0.7377 (m-70) cc_final: 0.7131 (m-70) REVERT: B 213 GLU cc_start: 0.7640 (pt0) cc_final: 0.7438 (pt0) REVERT: B 253 GLU cc_start: 0.8273 (tt0) cc_final: 0.8040 (tt0) REVERT: B 303 LYS cc_start: 0.8416 (ptpp) cc_final: 0.8185 (ptpp) REVERT: B 311 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6400 (mm-30) REVERT: B 329 GLU cc_start: 0.7474 (tt0) cc_final: 0.6993 (mp0) REVERT: B 357 PRO cc_start: 0.7521 (Cg_exo) cc_final: 0.7229 (Cg_endo) REVERT: B 362 PHE cc_start: 0.8181 (m-80) cc_final: 0.7884 (m-80) REVERT: B 363 THR cc_start: 0.7939 (t) cc_final: 0.7707 (p) REVERT: B 377 ASN cc_start: 0.7598 (m-40) cc_final: 0.7317 (m110) REVERT: B 407 GLU cc_start: 0.7938 (tt0) cc_final: 0.7416 (tt0) REVERT: B 413 SER cc_start: 0.8818 (m) cc_final: 0.8527 (p) REVERT: B 465 GLU cc_start: 0.7824 (mp0) cc_final: 0.7592 (mp0) REVERT: B 469 LYS cc_start: 0.8583 (mttt) cc_final: 0.8330 (mttm) REVERT: B 480 ASP cc_start: 0.7503 (m-30) cc_final: 0.7279 (m-30) REVERT: B 495 ASN cc_start: 0.7464 (t0) cc_final: 0.7232 (t160) REVERT: B 511 ILE cc_start: 0.8032 (mt) cc_final: 0.7659 (mm) REVERT: B 518 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6325 (mt-10) REVERT: C 29 MET cc_start: 0.7597 (mmm) cc_final: 0.7160 (mmm) REVERT: C 116 ARG cc_start: 0.7579 (mtp180) cc_final: 0.7343 (mtp85) REVERT: C 121 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7590 (tppt) REVERT: C 166 GLU cc_start: 0.8029 (tt0) cc_final: 0.7670 (tt0) REVERT: C 178 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7815 (ttp-170) REVERT: C 238 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7309 (ttp) REVERT: C 246 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7962 (mtt180) REVERT: C 301 SER cc_start: 0.7664 (t) cc_final: 0.7423 (p) REVERT: C 311 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6444 (mm-30) REVERT: C 329 GLU cc_start: 0.7574 (tt0) cc_final: 0.7072 (mp0) REVERT: C 357 PRO cc_start: 0.7540 (Cg_exo) cc_final: 0.7321 (Cg_endo) REVERT: C 407 GLU cc_start: 0.7991 (tt0) cc_final: 0.7721 (tt0) REVERT: C 417 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8490 (p) REVERT: C 437 GLU cc_start: 0.7590 (tp30) cc_final: 0.7192 (tp30) REVERT: C 480 ASP cc_start: 0.7429 (m-30) cc_final: 0.7078 (m-30) REVERT: C 494 ARG cc_start: 0.7015 (ttp-110) cc_final: 0.6721 (ttp-110) REVERT: C 511 ILE cc_start: 0.8097 (mt) cc_final: 0.7725 (mm) REVERT: C 527 PHE cc_start: 0.7228 (t80) cc_final: 0.6998 (t80) outliers start: 56 outliers final: 25 residues processed: 393 average time/residue: 1.4635 time to fit residues: 618.6077 Evaluate side-chains 392 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 362 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 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 409 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 527 PHE 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 462 SER 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 246 ARG Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 513 LEU 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: 2.9990 chunk 2 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 128 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- 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 319 GLN A 374 GLN A 400 ASN A 495 ASN B 374 GLN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN C 475 ASN C 482 ASN C 496 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13341 Z= 0.224 Angle : 0.592 9.542 18069 Z= 0.291 Chirality : 0.045 0.242 1989 Planarity : 0.004 0.044 2319 Dihedral : 6.125 58.013 2172 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.42 % Allowed : 13.32 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.21), residues: 1569 helix: 1.50 (0.20), residues: 711 sheet: 1.17 (0.29), residues: 261 loop : 0.22 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 419 HIS 0.004 0.001 HIS A 376 PHE 0.014 0.001 PHE B 188 TYR 0.013 0.001 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 428 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 366 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8212 (mttt) cc_final: 0.7531 (mtmm) REVERT: A 66 GLU cc_start: 0.8309 (pt0) cc_final: 0.8070 (pt0) REVERT: A 101 ASP cc_start: 0.7960 (p0) cc_final: 0.7750 (p0) REVERT: A 156 GLU cc_start: 0.7653 (tt0) cc_final: 0.7285 (tt0) REVERT: A 166 GLU cc_start: 0.7981 (tt0) cc_final: 0.7600 (tt0) REVERT: A 235 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 311 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6543 (mm-30) REVERT: A 396 MET cc_start: 0.7599 (mmm) cc_final: 0.7318 (mmp) REVERT: A 409 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8373 (p) REVERT: A 413 SER cc_start: 0.8818 (m) cc_final: 0.8443 (p) REVERT: A 425 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7309 (mt-10) REVERT: A 445 LYS cc_start: 0.7638 (ptpt) cc_final: 0.7213 (pttp) REVERT: A 465 GLU cc_start: 0.7968 (mp0) cc_final: 0.7672 (mp0) REVERT: A 490 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: A 518 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: A 525 ASP cc_start: 0.6856 (m-30) cc_final: 0.6571 (t0) REVERT: B 21 LYS cc_start: 0.6935 (mmtt) cc_final: 0.6727 (mmtm) REVERT: B 29 MET cc_start: 0.7022 (mmm) cc_final: 0.6649 (mmm) REVERT: B 86 ASP cc_start: 0.7974 (t0) cc_final: 0.7663 (t0) REVERT: B 141 GLN cc_start: 0.7766 (mm110) cc_final: 0.7543 (mm-40) REVERT: B 145 SER cc_start: 0.8308 (p) cc_final: 0.8092 (m) REVERT: B 156 GLU cc_start: 0.7652 (tt0) cc_final: 0.7284 (tt0) REVERT: B 166 GLU cc_start: 0.8067 (tt0) cc_final: 0.7641 (tt0) REVERT: B 177 HIS cc_start: 0.7367 (m-70) cc_final: 0.7111 (m-70) REVERT: B 178 ARG cc_start: 0.8015 (ttm170) cc_final: 0.7743 (ttm170) REVERT: B 213 GLU cc_start: 0.7628 (pt0) cc_final: 0.7345 (pt0) REVERT: B 253 GLU cc_start: 0.8184 (tt0) cc_final: 0.7908 (tt0) REVERT: B 303 LYS cc_start: 0.8408 (ptpp) cc_final: 0.8178 (ptpp) REVERT: B 311 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6389 (mm-30) REVERT: B 316 MET cc_start: 0.7626 (mtm) cc_final: 0.7286 (mtp) REVERT: B 329 GLU cc_start: 0.7468 (tt0) cc_final: 0.6953 (mp0) REVERT: B 357 PRO cc_start: 0.7516 (Cg_exo) cc_final: 0.7206 (Cg_endo) REVERT: B 362 PHE cc_start: 0.8168 (m-80) cc_final: 0.7874 (m-80) REVERT: B 363 THR cc_start: 0.7934 (t) cc_final: 0.7714 (p) REVERT: B 377 ASN cc_start: 0.7588 (m-40) cc_final: 0.7360 (m110) REVERT: B 407 GLU cc_start: 0.7976 (tt0) cc_final: 0.7448 (tt0) REVERT: B 413 SER cc_start: 0.8827 (m) cc_final: 0.8572 (p) REVERT: B 465 GLU cc_start: 0.7824 (mp0) cc_final: 0.7598 (mp0) REVERT: B 469 LYS cc_start: 0.8584 (mttt) cc_final: 0.8336 (mttm) REVERT: B 480 ASP cc_start: 0.7462 (m-30) cc_final: 0.7262 (m-30) REVERT: B 518 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6356 (mt-10) REVERT: B 525 ASP cc_start: 0.6856 (t0) cc_final: 0.6562 (t0) REVERT: C 29 MET cc_start: 0.7602 (mmm) cc_final: 0.7169 (mmm) REVERT: C 116 ARG cc_start: 0.7610 (mtp180) cc_final: 0.7347 (mtp85) REVERT: C 121 LYS cc_start: 0.7862 (ttmm) cc_final: 0.7650 (tppt) REVERT: C 166 GLU cc_start: 0.7981 (tt0) cc_final: 0.7655 (tt0) REVERT: C 238 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7273 (ttp) REVERT: C 311 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6431 (mm-30) REVERT: C 329 GLU cc_start: 0.7641 (tt0) cc_final: 0.7440 (tt0) REVERT: C 357 PRO cc_start: 0.7524 (Cg_exo) cc_final: 0.7275 (Cg_endo) REVERT: C 407 GLU cc_start: 0.7996 (tt0) cc_final: 0.7748 (tt0) REVERT: C 437 GLU cc_start: 0.7614 (tp30) cc_final: 0.7183 (tp30) REVERT: C 475 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8182 (t0) REVERT: C 480 ASP cc_start: 0.7430 (m-30) cc_final: 0.7073 (m-30) REVERT: C 494 ARG cc_start: 0.7017 (ttp-110) cc_final: 0.6741 (ttp-110) REVERT: C 511 ILE cc_start: 0.8169 (mt) cc_final: 0.7789 (mm) REVERT: C 527 PHE cc_start: 0.7260 (t80) cc_final: 0.7032 (t80) outliers start: 62 outliers final: 29 residues processed: 387 average time/residue: 1.5240 time to fit residues: 632.8869 Evaluate side-chains 394 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 360 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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 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 461 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain B residue 28 SER 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 249 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 513 LEU 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 244 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 448 THR 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 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: 1.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 319 GLN A 374 GLN A 400 ASN A 495 ASN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 482 ASN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN C 482 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 13341 Z= 0.228 Angle : 0.607 10.826 18069 Z= 0.296 Chirality : 0.045 0.239 1989 Planarity : 0.004 0.044 2319 Dihedral : 6.095 58.049 2172 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.28 % Allowed : 14.89 % Favored : 81.84 % 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: 1.38 (0.21), residues: 1569 helix: 1.50 (0.20), residues: 711 sheet: 1.15 (0.30), residues: 261 loop : 0.22 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 419 HIS 0.004 0.001 HIS C 376 PHE 0.014 0.001 PHE B 188 TYR 0.012 0.001 TYR A 414 ARG 0.008 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 413 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 367 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7438 (mmtt) cc_final: 0.7024 (mmtp) REVERT: A 26 LYS cc_start: 0.8238 (mttt) cc_final: 0.7555 (mtmm) REVERT: A 29 MET cc_start: 0.7235 (mmm) cc_final: 0.6846 (mmm) REVERT: A 49 MET cc_start: 0.7676 (tpp) cc_final: 0.7312 (tpp) REVERT: A 66 GLU cc_start: 0.8306 (pt0) cc_final: 0.8067 (pt0) REVERT: A 156 GLU cc_start: 0.7651 (tt0) cc_final: 0.7287 (tt0) REVERT: A 166 GLU cc_start: 0.7974 (tt0) cc_final: 0.7599 (tt0) REVERT: A 235 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7498 (mt-10) REVERT: A 242 LEU cc_start: 0.8530 (mt) cc_final: 0.8165 (mt) REVERT: A 311 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6535 (mm-30) REVERT: A 329 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: A 380 LYS cc_start: 0.6608 (mtmt) cc_final: 0.6374 (mttp) REVERT: A 396 MET cc_start: 0.7599 (mmm) cc_final: 0.7320 (mmp) REVERT: A 409 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 413 SER cc_start: 0.8814 (m) cc_final: 0.8457 (p) REVERT: A 465 GLU cc_start: 0.7969 (mp0) cc_final: 0.7667 (mp0) REVERT: A 488 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 490 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: B 29 MET cc_start: 0.7031 (mmm) cc_final: 0.6659 (mmm) REVERT: B 49 MET cc_start: 0.7510 (tpp) cc_final: 0.7282 (mmp) REVERT: B 86 ASP cc_start: 0.7958 (t0) cc_final: 0.7699 (t0) REVERT: B 141 GLN cc_start: 0.7768 (mm110) cc_final: 0.7458 (mm-40) REVERT: B 145 SER cc_start: 0.8316 (p) cc_final: 0.8098 (m) REVERT: B 156 GLU cc_start: 0.7700 (tt0) cc_final: 0.7335 (tt0) REVERT: B 166 GLU cc_start: 0.8061 (tt0) cc_final: 0.7638 (tt0) REVERT: B 177 HIS cc_start: 0.7369 (m-70) cc_final: 0.7109 (m-70) REVERT: B 178 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7722 (ttm170) REVERT: B 213 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7364 (pt0) REVERT: B 253 GLU cc_start: 0.8150 (tt0) cc_final: 0.7870 (tt0) REVERT: B 303 LYS cc_start: 0.8407 (ptpp) cc_final: 0.8184 (ptpp) REVERT: B 311 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6459 (mm-30) REVERT: B 316 MET cc_start: 0.7620 (mtm) cc_final: 0.7230 (mtp) REVERT: B 329 GLU cc_start: 0.7471 (tt0) cc_final: 0.6967 (mp0) REVERT: B 357 PRO cc_start: 0.7505 (Cg_exo) cc_final: 0.7216 (Cg_endo) REVERT: B 362 PHE cc_start: 0.8160 (m-80) cc_final: 0.7871 (m-80) REVERT: B 363 THR cc_start: 0.7929 (t) cc_final: 0.7717 (p) REVERT: B 407 GLU cc_start: 0.7970 (tt0) cc_final: 0.7443 (tt0) REVERT: B 413 SER cc_start: 0.8819 (m) cc_final: 0.8581 (p) REVERT: B 465 GLU cc_start: 0.7834 (mp0) cc_final: 0.7601 (mp0) REVERT: B 469 LYS cc_start: 0.8585 (mttt) cc_final: 0.8336 (mttm) REVERT: B 481 SER cc_start: 0.8053 (t) cc_final: 0.7776 (p) REVERT: B 518 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6346 (mt-10) REVERT: B 525 ASP cc_start: 0.6855 (t0) cc_final: 0.6561 (t0) REVERT: C 29 MET cc_start: 0.7581 (mmm) cc_final: 0.7157 (mmm) REVERT: C 116 ARG cc_start: 0.7605 (mtp180) cc_final: 0.7351 (mtp85) REVERT: C 120 LYS cc_start: 0.7657 (ttmt) cc_final: 0.7450 (ttmm) REVERT: C 166 GLU cc_start: 0.7972 (tt0) cc_final: 0.7661 (tt0) REVERT: C 178 ARG cc_start: 0.8096 (ttm170) cc_final: 0.7888 (ttp-170) REVERT: C 238 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7272 (ttp) REVERT: C 303 LYS cc_start: 0.8317 (ptpp) cc_final: 0.7902 (ptmm) REVERT: C 311 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6447 (mm-30) REVERT: C 321 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6581 (mtt) REVERT: C 329 GLU cc_start: 0.7563 (tt0) cc_final: 0.7081 (mp0) REVERT: C 357 PRO cc_start: 0.7499 (Cg_exo) cc_final: 0.7272 (Cg_endo) REVERT: C 380 LYS cc_start: 0.6936 (mtmm) cc_final: 0.6698 (mttp) REVERT: C 388 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7140 (ptpp) REVERT: C 407 GLU cc_start: 0.7979 (tt0) cc_final: 0.7718 (tt0) REVERT: C 437 GLU cc_start: 0.7614 (tp30) cc_final: 0.7167 (tp30) REVERT: C 480 ASP cc_start: 0.7433 (m-30) cc_final: 0.7074 (m-30) REVERT: C 494 ARG cc_start: 0.7013 (ttp-110) cc_final: 0.6742 (ttp-110) REVERT: C 511 ILE cc_start: 0.8173 (mt) cc_final: 0.7752 (mm) REVERT: C 527 PHE cc_start: 0.7257 (t80) cc_final: 0.7025 (t80) outliers start: 46 outliers final: 26 residues processed: 379 average time/residue: 1.5300 time to fit residues: 621.8583 Evaluate side-chains 397 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 364 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 269 PHE 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 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 526 LEU 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 249 VAL Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 388 LYS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 513 LEU 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: 0.2980 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 319 GLN A 324 GLN A 374 GLN A 400 ASN A 495 ASN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 374 GLN B 495 ASN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 374 GLN C 475 ASN C 482 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13341 Z= 0.203 Angle : 0.602 13.034 18069 Z= 0.291 Chirality : 0.045 0.239 1989 Planarity : 0.004 0.042 2319 Dihedral : 6.059 58.025 2172 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.56 % Allowed : 14.67 % 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: 1.43 (0.21), residues: 1569 helix: 1.58 (0.20), residues: 711 sheet: 1.16 (0.30), residues: 261 loop : 0.19 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 419 HIS 0.003 0.001 HIS A 376 PHE 0.014 0.001 PHE B 188 TYR 0.011 0.001 TYR A 414 ARG 0.006 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 425 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 375 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7414 (mmtt) cc_final: 0.7031 (mmtp) REVERT: A 26 LYS cc_start: 0.8238 (mttt) cc_final: 0.7556 (mtmm) REVERT: A 66 GLU cc_start: 0.8282 (pt0) cc_final: 0.8056 (pt0) REVERT: A 95 ARG cc_start: 0.7881 (mtt180) cc_final: 0.7409 (mtt-85) REVERT: A 156 GLU cc_start: 0.7642 (tt0) cc_final: 0.7288 (tt0) REVERT: A 166 GLU cc_start: 0.7976 (tt0) cc_final: 0.7598 (tt0) REVERT: A 235 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7487 (mt-10) REVERT: A 242 LEU cc_start: 0.8520 (mt) cc_final: 0.8147 (mt) REVERT: A 311 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6536 (mm-30) REVERT: A 329 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: A 381 CYS cc_start: 0.5588 (m) cc_final: 0.4987 (t) REVERT: A 391 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8101 (mttt) REVERT: A 396 MET cc_start: 0.7592 (mmm) cc_final: 0.7326 (mmp) REVERT: A 409 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8423 (p) REVERT: A 413 SER cc_start: 0.8811 (m) cc_final: 0.8471 (p) REVERT: A 465 GLU cc_start: 0.7965 (mp0) cc_final: 0.7671 (mp0) REVERT: A 490 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: B 29 MET cc_start: 0.7026 (mmm) cc_final: 0.6647 (mmm) REVERT: B 86 ASP cc_start: 0.7954 (t0) cc_final: 0.7691 (t0) REVERT: B 135 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7184 (mt-10) REVERT: B 141 GLN cc_start: 0.7764 (mm110) cc_final: 0.7444 (mm-40) REVERT: B 145 SER cc_start: 0.8331 (p) cc_final: 0.8105 (m) REVERT: B 156 GLU cc_start: 0.7683 (tt0) cc_final: 0.7343 (tt0) REVERT: B 166 GLU cc_start: 0.8057 (tt0) cc_final: 0.7634 (tt0) REVERT: B 177 HIS cc_start: 0.7380 (m-70) cc_final: 0.7121 (m-70) REVERT: B 178 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7639 (ttm170) REVERT: B 213 GLU cc_start: 0.7692 (pt0) cc_final: 0.7250 (pt0) REVERT: B 252 SER cc_start: 0.8165 (p) cc_final: 0.7933 (t) REVERT: B 253 GLU cc_start: 0.8061 (tt0) cc_final: 0.7721 (tt0) REVERT: B 303 LYS cc_start: 0.8397 (ptpp) cc_final: 0.8182 (ptpp) REVERT: B 311 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6465 (mm-30) REVERT: B 316 MET cc_start: 0.7603 (mtm) cc_final: 0.7247 (mtp) REVERT: B 329 GLU cc_start: 0.7467 (tt0) cc_final: 0.6933 (mp0) REVERT: B 357 PRO cc_start: 0.7532 (Cg_exo) cc_final: 0.7247 (Cg_endo) REVERT: B 362 PHE cc_start: 0.8126 (m-80) cc_final: 0.7831 (m-80) REVERT: B 363 THR cc_start: 0.7948 (t) cc_final: 0.7741 (p) REVERT: B 393 THR cc_start: 0.7450 (p) cc_final: 0.7195 (m) REVERT: B 407 GLU cc_start: 0.7957 (tt0) cc_final: 0.7411 (tt0) REVERT: B 413 SER cc_start: 0.8807 (m) cc_final: 0.8585 (p) REVERT: B 480 ASP cc_start: 0.7411 (m-30) cc_final: 0.7168 (m-30) REVERT: B 518 GLU cc_start: 0.6658 (mt-10) cc_final: 0.6287 (mt-10) REVERT: B 525 ASP cc_start: 0.6856 (t0) cc_final: 0.6554 (t0) REVERT: C 29 MET cc_start: 0.7560 (mmm) cc_final: 0.7145 (mmm) REVERT: C 99 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: C 116 ARG cc_start: 0.7585 (mtp180) cc_final: 0.7325 (mtp85) REVERT: C 120 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7467 (ttmm) REVERT: C 166 GLU cc_start: 0.7968 (tt0) cc_final: 0.7729 (tt0) REVERT: C 178 ARG cc_start: 0.8109 (ttm170) cc_final: 0.7890 (ttp-170) REVERT: C 238 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7265 (ttp) REVERT: C 303 LYS cc_start: 0.8334 (ptpp) cc_final: 0.7984 (ptmm) REVERT: C 311 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6680 (mm-30) REVERT: C 321 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6557 (mtt) REVERT: C 329 GLU cc_start: 0.7636 (tt0) cc_final: 0.7430 (tt0) REVERT: C 380 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6798 (mttp) REVERT: C 407 GLU cc_start: 0.7987 (tt0) cc_final: 0.7730 (tt0) REVERT: C 437 GLU cc_start: 0.7618 (tp30) cc_final: 0.7171 (tp30) REVERT: C 480 ASP cc_start: 0.7430 (m-30) cc_final: 0.7072 (m-30) REVERT: C 494 ARG cc_start: 0.6966 (ttp-110) cc_final: 0.6729 (ttp-110) REVERT: C 527 PHE cc_start: 0.7197 (t80) cc_final: 0.6970 (t80) outliers start: 50 outliers final: 27 residues processed: 388 average time/residue: 1.5395 time to fit residues: 641.2076 Evaluate side-chains 401 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 366 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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 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 490 GLU 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 120 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 513 LEU 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 143 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 405 CYS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 513 LEU 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: 1.9990 chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 0.0370 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 324 GLN A 374 GLN A 400 ASN A 495 ASN B 319 GLN B 374 GLN B 482 ASN B 495 ASN C 106 ASN C 319 GLN C 374 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13341 Z= 0.214 Angle : 0.609 12.185 18069 Z= 0.297 Chirality : 0.045 0.239 1989 Planarity : 0.004 0.043 2319 Dihedral : 6.043 57.993 2172 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.49 % Allowed : 15.38 % Favored : 81.13 % 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: 1.39 (0.21), residues: 1569 helix: 1.54 (0.20), residues: 711 sheet: 1.26 (0.30), residues: 264 loop : 0.11 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 419 HIS 0.004 0.001 HIS A 376 PHE 0.014 0.001 PHE B 188 TYR 0.012 0.001 TYR A 414 ARG 0.005 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 423 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 374 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7433 (mmtt) cc_final: 0.7026 (mmtp) REVERT: A 26 LYS cc_start: 0.8237 (mttt) cc_final: 0.7552 (mtmm) REVERT: A 66 GLU cc_start: 0.8283 (pt0) cc_final: 0.8063 (pt0) REVERT: A 95 ARG cc_start: 0.7882 (mtt180) cc_final: 0.7409 (mtt-85) REVERT: A 156 GLU cc_start: 0.7637 (tt0) cc_final: 0.7290 (tt0) REVERT: A 235 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 242 LEU cc_start: 0.8529 (mt) cc_final: 0.8124 (mt) REVERT: A 311 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6517 (mm-30) REVERT: A 329 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: A 381 CYS cc_start: 0.5532 (m) cc_final: 0.4968 (t) REVERT: A 391 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8084 (mttt) REVERT: A 396 MET cc_start: 0.7591 (mmm) cc_final: 0.7326 (mmp) REVERT: A 409 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8436 (p) REVERT: A 413 SER cc_start: 0.8816 (m) cc_final: 0.8473 (p) REVERT: A 465 GLU cc_start: 0.7966 (mp0) cc_final: 0.7672 (mp0) REVERT: A 490 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: B 29 MET cc_start: 0.7025 (mmm) cc_final: 0.6647 (mmm) REVERT: B 86 ASP cc_start: 0.7958 (t0) cc_final: 0.7681 (t0) REVERT: B 135 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7191 (mt-10) REVERT: B 141 GLN cc_start: 0.7736 (mm110) cc_final: 0.7439 (mm-40) REVERT: B 145 SER cc_start: 0.8338 (p) cc_final: 0.8105 (m) REVERT: B 156 GLU cc_start: 0.7669 (tt0) cc_final: 0.7345 (tt0) REVERT: B 166 GLU cc_start: 0.8054 (tt0) cc_final: 0.7643 (tt0) REVERT: B 177 HIS cc_start: 0.7371 (m-70) cc_final: 0.7109 (m-70) REVERT: B 178 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7751 (ttm170) REVERT: B 213 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: B 242 LEU cc_start: 0.8486 (mm) cc_final: 0.8273 (mp) REVERT: B 252 SER cc_start: 0.8150 (p) cc_final: 0.7928 (t) REVERT: B 253 GLU cc_start: 0.8050 (tt0) cc_final: 0.7708 (tt0) REVERT: B 303 LYS cc_start: 0.8410 (ptpp) cc_final: 0.8127 (ptpp) REVERT: B 311 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6460 (mm-30) REVERT: B 316 MET cc_start: 0.7613 (mtm) cc_final: 0.7227 (mtp) REVERT: B 329 GLU cc_start: 0.7458 (tt0) cc_final: 0.6916 (mp0) REVERT: B 362 PHE cc_start: 0.8143 (m-80) cc_final: 0.7842 (m-80) REVERT: B 363 THR cc_start: 0.7931 (t) cc_final: 0.7720 (p) REVERT: B 381 CYS cc_start: 0.5315 (m) cc_final: 0.4636 (t) REVERT: B 393 THR cc_start: 0.7452 (p) cc_final: 0.7211 (m) REVERT: B 407 GLU cc_start: 0.7963 (tt0) cc_final: 0.7440 (tt0) REVERT: B 413 SER cc_start: 0.8828 (m) cc_final: 0.8596 (p) REVERT: B 480 ASP cc_start: 0.7384 (m-30) cc_final: 0.7096 (m-30) REVERT: B 518 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6331 (mt-10) REVERT: B 525 ASP cc_start: 0.6895 (t0) cc_final: 0.6598 (t0) REVERT: C 29 MET cc_start: 0.7562 (mmm) cc_final: 0.7150 (mmm) REVERT: C 116 ARG cc_start: 0.7610 (mtp180) cc_final: 0.7339 (mtp85) REVERT: C 120 LYS cc_start: 0.7674 (ttmt) cc_final: 0.7430 (ttmm) REVERT: C 166 GLU cc_start: 0.7954 (tt0) cc_final: 0.7729 (tt0) REVERT: C 235 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 238 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7257 (ttp) REVERT: C 303 LYS cc_start: 0.8340 (ptpp) cc_final: 0.7977 (ptmm) REVERT: C 311 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6532 (mm-30) REVERT: C 321 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6553 (mtt) REVERT: C 388 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7090 (ttpp) REVERT: C 407 GLU cc_start: 0.7981 (tt0) cc_final: 0.7744 (tt0) REVERT: C 437 GLU cc_start: 0.7636 (tp30) cc_final: 0.7173 (tp30) REVERT: C 480 ASP cc_start: 0.7427 (m-30) cc_final: 0.7072 (m-30) REVERT: C 494 ARG cc_start: 0.7025 (ttp-110) cc_final: 0.6795 (ttp-110) REVERT: C 527 PHE cc_start: 0.7200 (t80) cc_final: 0.6972 (t80) outliers start: 49 outliers final: 28 residues processed: 387 average time/residue: 1.4997 time to fit residues: 624.4329 Evaluate side-chains 400 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 364 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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 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 462 SER Chi-restraints excluded: chain A residue 490 GLU 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 99 GLU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 513 LEU 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 124 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 388 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 490 GLU 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: 0.5980 chunk 140 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 374 GLN A 400 ASN A 495 ASN B 374 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN B 495 ASN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13341 Z= 0.220 Angle : 0.632 10.407 18069 Z= 0.308 Chirality : 0.046 0.239 1989 Planarity : 0.004 0.046 2319 Dihedral : 6.101 57.998 2172 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.49 % Allowed : 15.46 % Favored : 81.05 % 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: 1.34 (0.21), residues: 1569 helix: 1.51 (0.20), residues: 711 sheet: 1.23 (0.30), residues: 264 loop : 0.07 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 419 HIS 0.006 0.001 HIS C 376 PHE 0.016 0.001 PHE C 45 TYR 0.012 0.001 TYR A 414 ARG 0.011 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 423 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 374 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7436 (mmtt) cc_final: 0.7046 (mmtp) REVERT: A 26 LYS cc_start: 0.8244 (mttt) cc_final: 0.7561 (mtmm) REVERT: A 66 GLU cc_start: 0.8284 (pt0) cc_final: 0.8065 (pt0) REVERT: A 95 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7359 (mtt-85) REVERT: A 156 GLU cc_start: 0.7638 (tt0) cc_final: 0.7280 (tt0) REVERT: A 235 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 242 LEU cc_start: 0.8513 (mt) cc_final: 0.8104 (mt) REVERT: A 269 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: A 311 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6511 (mm-30) REVERT: A 381 CYS cc_start: 0.5522 (m) cc_final: 0.4942 (t) REVERT: A 391 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7878 (mmtm) REVERT: A 396 MET cc_start: 0.7589 (mmm) cc_final: 0.7325 (mmp) REVERT: A 409 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8435 (p) REVERT: A 413 SER cc_start: 0.8811 (m) cc_final: 0.8477 (p) REVERT: A 465 GLU cc_start: 0.7967 (mp0) cc_final: 0.7674 (mp0) REVERT: A 488 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7796 (mt-10) REVERT: A 490 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: B 29 MET cc_start: 0.7002 (mmm) cc_final: 0.6634 (mmm) REVERT: B 44 MET cc_start: 0.7194 (mmm) cc_final: 0.6595 (mmm) REVERT: B 49 MET cc_start: 0.7665 (tpp) cc_final: 0.7452 (mmp) REVERT: B 86 ASP cc_start: 0.7967 (t0) cc_final: 0.7680 (t0) REVERT: B 135 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7183 (mt-10) REVERT: B 141 GLN cc_start: 0.7743 (mm110) cc_final: 0.7456 (mm-40) REVERT: B 145 SER cc_start: 0.8340 (p) cc_final: 0.8103 (m) REVERT: B 156 GLU cc_start: 0.7668 (tt0) cc_final: 0.7348 (tt0) REVERT: B 166 GLU cc_start: 0.8047 (tt0) cc_final: 0.7640 (tt0) REVERT: B 177 HIS cc_start: 0.7370 (m-70) cc_final: 0.7112 (m-70) REVERT: B 178 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7742 (ttm170) REVERT: B 213 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7330 (pt0) REVERT: B 252 SER cc_start: 0.8149 (p) cc_final: 0.7928 (t) REVERT: B 253 GLU cc_start: 0.8048 (tt0) cc_final: 0.7704 (tt0) REVERT: B 303 LYS cc_start: 0.8377 (ptpp) cc_final: 0.8111 (ptpp) REVERT: B 311 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6461 (mm-30) REVERT: B 316 MET cc_start: 0.7603 (mtm) cc_final: 0.7190 (mtp) REVERT: B 329 GLU cc_start: 0.7431 (tt0) cc_final: 0.6903 (mp0) REVERT: B 362 PHE cc_start: 0.8154 (m-80) cc_final: 0.7858 (m-80) REVERT: B 381 CYS cc_start: 0.5513 (m) cc_final: 0.4559 (t) REVERT: B 393 THR cc_start: 0.7451 (p) cc_final: 0.7214 (m) REVERT: B 407 GLU cc_start: 0.7975 (tt0) cc_final: 0.7455 (tt0) REVERT: B 480 ASP cc_start: 0.7386 (m-30) cc_final: 0.7064 (m-30) REVERT: B 518 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6169 (mt-10) REVERT: B 521 GLU cc_start: 0.7237 (tt0) cc_final: 0.7001 (tm-30) REVERT: B 525 ASP cc_start: 0.6895 (t0) cc_final: 0.6578 (t0) REVERT: C 28 SER cc_start: 0.6928 (m) cc_final: 0.6627 (t) REVERT: C 29 MET cc_start: 0.7544 (mmm) cc_final: 0.7213 (mmm) REVERT: C 99 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: C 116 ARG cc_start: 0.7604 (mtp180) cc_final: 0.7322 (mtp85) REVERT: C 120 LYS cc_start: 0.7717 (ttmt) cc_final: 0.7463 (ttmm) REVERT: C 124 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7919 (mptp) REVERT: C 166 GLU cc_start: 0.7953 (tt0) cc_final: 0.7739 (tt0) REVERT: C 178 ARG cc_start: 0.8077 (ttp-170) cc_final: 0.7811 (ttp-170) REVERT: C 235 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7548 (mt-10) REVERT: C 238 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7251 (ttp) REVERT: C 303 LYS cc_start: 0.8349 (ptpp) cc_final: 0.7992 (ptmm) REVERT: C 311 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6542 (mm-30) REVERT: C 321 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6561 (mtt) REVERT: C 407 GLU cc_start: 0.7990 (tt0) cc_final: 0.7753 (tt0) REVERT: C 480 ASP cc_start: 0.7438 (m-30) cc_final: 0.7072 (m-30) REVERT: C 527 PHE cc_start: 0.7195 (t80) cc_final: 0.6966 (t80) outliers start: 49 outliers final: 27 residues processed: 386 average time/residue: 1.5008 time to fit residues: 622.8697 Evaluate side-chains 398 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 362 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 293 ILE Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU 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 99 GLU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 513 LEU 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 124 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 321 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 405 CYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 490 GLU 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: 2.9990 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN 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 482 ASN B 495 ASN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 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: 0.7543 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13341 Z= 0.285 Angle : 0.661 11.816 18069 Z= 0.323 Chirality : 0.047 0.242 1989 Planarity : 0.004 0.045 2319 Dihedral : 6.163 58.200 2172 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.42 % Allowed : 17.24 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1569 helix: 1.45 (0.20), residues: 711 sheet: 1.21 (0.30), residues: 264 loop : 0.02 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 219 HIS 0.005 0.001 HIS A 376 PHE 0.014 0.001 PHE B 188 TYR 0.014 0.001 TYR A 414 ARG 0.011 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 407 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 373 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8263 (mttt) cc_final: 0.7577 (mtmm) REVERT: A 66 GLU cc_start: 0.8285 (pt0) cc_final: 0.8066 (pt0) REVERT: A 95 ARG cc_start: 0.7818 (mtt180) cc_final: 0.7356 (mtt-85) REVERT: A 96 MET cc_start: 0.7878 (mtm) cc_final: 0.7659 (mtm) REVERT: A 156 GLU cc_start: 0.7633 (tt0) cc_final: 0.7278 (tt0) REVERT: A 235 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7477 (mt-10) REVERT: A 242 LEU cc_start: 0.8541 (mt) cc_final: 0.8125 (mt) REVERT: A 269 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: A 311 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6486 (mm-30) REVERT: A 381 CYS cc_start: 0.5673 (m) cc_final: 0.5012 (t) REVERT: A 391 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7877 (mmtm) REVERT: A 396 MET cc_start: 0.7592 (mmm) cc_final: 0.7321 (mmp) REVERT: A 409 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8425 (p) REVERT: A 413 SER cc_start: 0.8785 (m) cc_final: 0.8444 (p) REVERT: A 465 GLU cc_start: 0.7953 (mp0) cc_final: 0.7676 (mp0) REVERT: A 488 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7857 (mt-10) REVERT: A 490 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: B 29 MET cc_start: 0.7014 (mmm) cc_final: 0.6642 (mmm) REVERT: B 44 MET cc_start: 0.7214 (mmm) cc_final: 0.6557 (mmm) REVERT: B 49 MET cc_start: 0.7577 (tpp) cc_final: 0.7331 (mmp) REVERT: B 86 ASP cc_start: 0.7986 (t0) cc_final: 0.7721 (t0) REVERT: B 135 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7204 (mt-10) REVERT: B 141 GLN cc_start: 0.7746 (mm110) cc_final: 0.7466 (mm-40) REVERT: B 145 SER cc_start: 0.8331 (p) cc_final: 0.8102 (m) REVERT: B 156 GLU cc_start: 0.7684 (tt0) cc_final: 0.7363 (tt0) REVERT: B 166 GLU cc_start: 0.8043 (tt0) cc_final: 0.7639 (tt0) REVERT: B 177 HIS cc_start: 0.7386 (m-70) cc_final: 0.7130 (m-70) REVERT: B 178 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7721 (ttm170) REVERT: B 213 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7362 (pt0) REVERT: B 252 SER cc_start: 0.8225 (p) cc_final: 0.7971 (t) REVERT: B 253 GLU cc_start: 0.8122 (tt0) cc_final: 0.7797 (tt0) REVERT: B 303 LYS cc_start: 0.8361 (ptpp) cc_final: 0.8108 (ptpp) REVERT: B 311 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6454 (mm-30) REVERT: B 316 MET cc_start: 0.7613 (mtm) cc_final: 0.7219 (mtp) REVERT: B 329 GLU cc_start: 0.7478 (tt0) cc_final: 0.6925 (mp0) REVERT: B 362 PHE cc_start: 0.8146 (m-80) cc_final: 0.7883 (m-80) REVERT: B 393 THR cc_start: 0.7458 (p) cc_final: 0.7222 (m) REVERT: B 407 GLU cc_start: 0.7979 (tt0) cc_final: 0.7467 (tt0) REVERT: B 480 ASP cc_start: 0.7270 (m-30) cc_final: 0.6966 (m-30) REVERT: B 518 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6343 (mt-10) REVERT: B 525 ASP cc_start: 0.6890 (t0) cc_final: 0.6583 (t0) REVERT: C 28 SER cc_start: 0.6959 (m) cc_final: 0.6630 (t) REVERT: C 29 MET cc_start: 0.7554 (mmm) cc_final: 0.7224 (mmm) REVERT: C 49 MET cc_start: 0.7574 (tpp) cc_final: 0.7065 (mpp) REVERT: C 116 ARG cc_start: 0.7630 (mtp180) cc_final: 0.7328 (mtp85) REVERT: C 120 LYS cc_start: 0.7682 (ttmt) cc_final: 0.7434 (ttmm) REVERT: C 166 GLU cc_start: 0.7924 (tt0) cc_final: 0.7712 (tt0) REVERT: C 216 GLU cc_start: 0.7754 (mp0) cc_final: 0.7455 (mp0) REVERT: C 235 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7560 (mt-10) REVERT: C 238 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7274 (ttp) REVERT: C 311 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6504 (mm-30) REVERT: C 329 GLU cc_start: 0.7628 (tt0) cc_final: 0.7190 (mp0) REVERT: C 381 CYS cc_start: 0.5440 (m) cc_final: 0.4824 (t) REVERT: C 480 ASP cc_start: 0.7447 (m-30) cc_final: 0.7097 (m-30) REVERT: C 488 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7939 (mt-10) REVERT: C 527 PHE cc_start: 0.7189 (t80) cc_final: 0.6959 (t80) outliers start: 34 outliers final: 22 residues processed: 380 average time/residue: 1.5894 time to fit residues: 648.7990 Evaluate side-chains 397 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 369 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 293 ILE Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 213 GLU 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 513 LEU 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 387 SER Chi-restraints excluded: chain C residue 405 CYS Chi-restraints excluded: chain C residue 490 GLU 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: 0.5980 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 108 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 374 GLN A 400 ASN A 495 ASN B 319 GLN B 374 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN B 495 ASN ** C 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.133257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.122221 restraints weight = 17309.073| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.62 r_work: 0.3630 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13341 Z= 0.176 Angle : 0.622 10.109 18069 Z= 0.299 Chirality : 0.045 0.239 1989 Planarity : 0.004 0.040 2319 Dihedral : 6.057 57.828 2172 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.14 % Allowed : 17.88 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1569 helix: 1.53 (0.20), residues: 711 sheet: 1.12 (0.30), residues: 267 loop : -0.03 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 419 HIS 0.004 0.001 HIS C 376 PHE 0.013 0.001 PHE C 45 TYR 0.012 0.001 TYR B 118 ARG 0.010 0.000 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8334.58 seconds wall clock time: 148 minutes 3.28 seconds (8883.28 seconds total)