Starting phenix.real_space_refine on Tue Dec 31 17:19:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f74_28894/12_2024/8f74_28894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f74_28894/12_2024/8f74_28894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f74_28894/12_2024/8f74_28894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f74_28894/12_2024/8f74_28894.map" model { file = "/net/cci-nas-00/data/ceres_data/8f74_28894/12_2024/8f74_28894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f74_28894/12_2024/8f74_28894.cif" } resolution = 3.1 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= 0.003 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 106 5.16 5 C 10580 2.51 5 N 2524 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16008 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2672 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2668 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "C" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2560 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 2 Chain: "D" Number of atoms: 2637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2637 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 2 Chain: "E" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2652 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2569 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 7, 'TRANS': 301} Chain breaks: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 11.41, per 1000 atoms: 0.71 Number of scatterers: 16008 At special positions: 0 Unit cell: (97.464, 108.992, 134.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 4 15.00 O 2794 8.00 N 2524 7.00 C 10580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " 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=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 2.0 seconds 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 12 sheets defined 77.3% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.098A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 50 removed outlier: 3.681A pdb=" N ASP A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.563A pdb=" N LYS A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.141A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 4.019A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 256 removed outlier: 4.172A pdb=" N GLU A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 285 removed outlier: 3.972A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 289 removed outlier: 3.779A pdb=" N ILE A 289 " --> pdb=" O VAL A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 315 through 346 removed outlier: 3.986A pdb=" N ARG A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.304A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.567A pdb=" N ARG B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.789A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 4.604A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 Processing helix chain 'B' and resid 166 through 175 removed outlier: 4.331A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 258 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 343 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 383 through 391 removed outlier: 4.209A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 22 through 50 removed outlier: 3.603A pdb=" N MET C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP C 50 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 4.657A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 167 through 175 removed outlier: 4.151A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 255 Processing helix chain 'C' and resid 258 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 315 through 344 Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 370 through 383 Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.059A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 402 removed outlier: 3.675A pdb=" N GLU C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 4.282A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 142 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 146 through 165 Processing helix chain 'D' and resid 166 through 175 Processing helix chain 'D' and resid 233 through 256 removed outlier: 4.094A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 removed outlier: 3.664A pdb=" N ARG D 262 " --> pdb=" O ASP D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 315 through 346 removed outlier: 4.258A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 370 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 3.890A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.670A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.817A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.521A pdb=" N ARG E 117 " --> pdb=" O CYS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 4.643A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.163A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 258 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 315 through 345 removed outlier: 3.553A pdb=" N LEU E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 370 through 383 Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.051A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 395 through 409 Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.525A pdb=" N ARG F 118 " --> pdb=" O MET F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 4.027A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 removed outlier: 3.582A pdb=" N PHE F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 168 Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.338A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 253 Processing helix chain 'F' and resid 257 through 284 Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'F' and resid 312 through 344 removed outlier: 3.907A pdb=" N ARG F 344 " --> pdb=" O TRP F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 368 through 381 Processing helix chain 'F' and resid 381 through 389 removed outlier: 4.016A pdb=" N SER F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 392 No H-bonds generated for 'chain 'F' and resid 390 through 392' Processing helix chain 'F' and resid 393 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.828A pdb=" N VAL A 60 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL F 94 " --> pdb=" O VAL A 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.557A pdb=" N ILE B 53 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 350 through 351 removed outlier: 3.503A pdb=" N VAL D 368 " --> pdb=" O TYR D 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.749A pdb=" N ILE E 53 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 350 through 351 removed outlier: 3.602A pdb=" N TYR E 351 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 368 " --> pdb=" O TYR E 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AB3, first strand: chain 'F' and resid 348 through 349 removed outlier: 3.668A pdb=" N VAL F 366 " --> pdb=" O TYR F 349 " (cutoff:3.500A) 1096 hydrogen bonds defined for protein. 3234 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: 4.94 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2602 1.32 - 1.45: 4684 1.45 - 1.57: 8982 1.57 - 1.69: 6 1.69 - 1.81: 155 Bond restraints: 16429 Sorted by residual: bond pdb=" C10 PEE D 901 " pdb=" O4 PEE D 901 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C10 PEE B 903 " pdb=" O4 PEE B 903 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " ideal model delta sigma weight residual 1.653 1.779 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" O4P PEE C 901 " pdb=" P PEE C 901 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " ideal model delta sigma weight residual 1.653 1.775 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 16424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 21927 2.76 - 5.52: 194 5.52 - 8.28: 34 8.28 - 11.04: 6 11.04 - 13.81: 5 Bond angle restraints: 22166 Sorted by residual: angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.24 -13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.22 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE B 901 " pdb=" P PEE B 901 " pdb=" O2P PEE B 901 " ideal model delta sigma weight residual 119.43 133.13 -13.70 3.00e+00 1.11e-01 2.09e+01 angle pdb=" C11 PEE B 903 " pdb=" C10 PEE B 903 " pdb=" O2 PEE B 903 " ideal model delta sigma weight residual 111.70 124.70 -13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" C11 PEE D 901 " pdb=" C10 PEE D 901 " pdb=" O2 PEE D 901 " ideal model delta sigma weight residual 111.70 124.60 -12.90 3.00e+00 1.11e-01 1.85e+01 ... (remaining 22161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 9403 34.77 - 69.54: 305 69.54 - 104.31: 23 104.31 - 139.08: 2 139.08 - 173.86: 5 Dihedral angle restraints: 9738 sinusoidal: 4086 harmonic: 5652 Sorted by residual: dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 295 " pdb=" CB CYS C 295 " ideal model delta sinusoidal sigma weight residual 93.00 43.52 49.48 1 1.00e+01 1.00e-02 3.36e+01 dihedral pdb=" N PEE C 901 " pdb=" C4 PEE C 901 " pdb=" C5 PEE C 901 " pdb=" O4P PEE C 901 " ideal model delta sinusoidal sigma weight residual 303.03 129.17 173.86 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C2 PEE C 901 " pdb=" O3P PEE C 901 " ideal model delta sinusoidal sigma weight residual -59.96 111.18 -171.14 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 9735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2000 0.056 - 0.112: 374 0.112 - 0.168: 20 0.168 - 0.224: 2 0.224 - 0.280: 3 Chirality restraints: 2399 Sorted by residual: chirality pdb=" CB VAL E 283 " pdb=" CA VAL E 283 " pdb=" CG1 VAL E 283 " pdb=" CG2 VAL E 283 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C2 PEE F 901 " pdb=" C1 PEE F 901 " pdb=" C3 PEE F 901 " pdb=" O2 PEE F 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.61 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR B 44 " pdb=" CA THR B 44 " pdb=" OG1 THR B 44 " pdb=" CG2 THR B 44 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2396 not shown) Planarity restraints: 2678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 23 " -0.021 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP F 23 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP F 23 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 23 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 23 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 23 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " -0.017 2.00e-02 2.50e+03 1.67e-02 6.94e+00 pdb=" CG TRP C 168 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 155 " -0.020 2.00e-02 2.50e+03 2.05e-02 6.33e+00 pdb=" CG HIS D 155 " 0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS D 155 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS D 155 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS D 155 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS D 155 " -0.003 2.00e-02 2.50e+03 ... (remaining 2675 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1358 2.74 - 3.28: 16023 3.28 - 3.82: 28443 3.82 - 4.36: 32182 4.36 - 4.90: 56308 Nonbonded interactions: 134314 Sorted by model distance: nonbonded pdb=" NE2 GLN A 46 " pdb=" O LYS A 123 " model vdw 2.206 3.120 nonbonded pdb=" OH TYR B 351 " pdb=" OD2 ASP B 380 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR E 303 " pdb=" OH TYR E 308 " model vdw 2.269 3.040 nonbonded pdb=" O PRO D 167 " pdb=" OG1 THR D 170 " model vdw 2.272 3.040 nonbonded pdb=" O ILE E 278 " pdb=" OG1 THR E 282 " model vdw 2.273 3.040 ... (remaining 134309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 68 or resid 93 through 175 or resid 235 through \ 402 or (resid 903 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 68 or resid 93 through 175 or resid 235 through \ 402 or (resid 903 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name O2 or name O4 )))) selection = (chain 'C' and (resid 15 through 402 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name O2 or name O4 ) \ ))) selection = (chain 'D' and (resid 15 through 175 or resid 235 through 402 or resid 902)) selection = (chain 'E' and (resid 15 through 175 or resid 235 through 402 or resid 903)) } 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 37.690 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 0.150 16429 Z= 0.300 Angle : 0.723 13.805 22166 Z= 0.389 Chirality : 0.041 0.280 2399 Planarity : 0.005 0.046 2678 Dihedral : 17.290 173.856 6027 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.06 % Allowed : 18.43 % Favored : 81.51 % 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: 0.91 (0.19), residues: 1845 helix: 1.23 (0.13), residues: 1289 sheet: -0.28 (0.51), residues: 107 loop : -0.85 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP F 23 HIS 0.021 0.001 HIS D 155 PHE 0.034 0.002 PHE C 142 TYR 0.030 0.002 TYR E 281 ARG 0.009 0.001 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 1.792 Fit side-chains revert: symmetry clash REVERT: A 388 LYS cc_start: 0.8103 (tttt) cc_final: 0.7687 (tmtt) REVERT: C 337 MET cc_start: 0.6264 (tmm) cc_final: 0.6021 (tmm) REVERT: D 249 LYS cc_start: 0.8530 (ptmt) cc_final: 0.8269 (ptmm) REVERT: D 399 GLU cc_start: 0.6297 (mt-10) cc_final: 0.5806 (tp30) REVERT: E 30 TYR cc_start: 0.7565 (m-10) cc_final: 0.7358 (m-10) REVERT: E 99 TYR cc_start: 0.8508 (m-80) cc_final: 0.8268 (m-80) REVERT: F 144 PHE cc_start: 0.5912 (t80) cc_final: 0.5565 (t80) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.2787 time to fit residues: 107.6962 Evaluate side-chains 216 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 chunk 74 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS B 239 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16429 Z= 0.297 Angle : 0.520 10.897 22166 Z= 0.281 Chirality : 0.040 0.152 2399 Planarity : 0.004 0.037 2678 Dihedral : 9.136 154.969 2256 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.86 % Allowed : 16.77 % Favored : 80.37 % 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 (0.19), residues: 1845 helix: 1.69 (0.14), residues: 1320 sheet: -0.26 (0.50), residues: 106 loop : -1.22 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 23 HIS 0.012 0.001 HIS A 253 PHE 0.024 0.002 PHE E 324 TYR 0.018 0.002 TYR C 382 ARG 0.005 0.000 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7771 (tp30) cc_final: 0.7361 (tp30) REVERT: C 37 MET cc_start: 0.8350 (mtt) cc_final: 0.7268 (tmm) REVERT: C 308 TYR cc_start: 0.9102 (m-80) cc_final: 0.8714 (m-80) REVERT: C 337 MET cc_start: 0.6308 (tmm) cc_final: 0.6023 (tmm) REVERT: E 99 TYR cc_start: 0.8462 (m-80) cc_final: 0.8238 (m-80) REVERT: E 250 PHE cc_start: 0.6597 (t80) cc_final: 0.6215 (t80) REVERT: F 279 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8051 (p90) outliers start: 50 outliers final: 31 residues processed: 262 average time/residue: 0.2662 time to fit residues: 106.7586 Evaluate side-chains 238 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 139 optimal weight: 0.0270 chunk 113 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 49 GLN E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16429 Z= 0.262 Angle : 0.492 9.800 22166 Z= 0.266 Chirality : 0.039 0.189 2399 Planarity : 0.003 0.041 2678 Dihedral : 8.036 154.558 2256 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.09 % Allowed : 16.89 % Favored : 80.02 % 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: 1.50 (0.19), residues: 1845 helix: 1.80 (0.14), residues: 1317 sheet: -0.28 (0.50), residues: 107 loop : -1.26 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 23 HIS 0.017 0.001 HIS A 253 PHE 0.022 0.001 PHE E 324 TYR 0.015 0.001 TYR E 281 ARG 0.004 0.000 ARG F 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7761 (tp30) cc_final: 0.7281 (tp30) REVERT: C 37 MET cc_start: 0.8373 (mtt) cc_final: 0.7206 (tmm) REVERT: C 262 ARG cc_start: 0.6396 (mtm180) cc_final: 0.5966 (mtp-110) REVERT: C 308 TYR cc_start: 0.9111 (m-80) cc_final: 0.8524 (m-80) REVERT: C 337 MET cc_start: 0.6131 (tmm) cc_final: 0.5829 (tmm) REVERT: E 399 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6417 (mt-10) REVERT: F 279 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8066 (p90) outliers start: 54 outliers final: 34 residues processed: 263 average time/residue: 0.2669 time to fit residues: 107.3100 Evaluate side-chains 240 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN D 288 ASN E 155 HIS E 287 HIS E 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16429 Z= 0.212 Angle : 0.468 9.154 22166 Z= 0.253 Chirality : 0.038 0.207 2399 Planarity : 0.003 0.039 2678 Dihedral : 7.409 151.583 2256 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.66 % Allowed : 16.89 % Favored : 79.45 % 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: 1.63 (0.19), residues: 1845 helix: 1.90 (0.14), residues: 1317 sheet: -0.09 (0.51), residues: 107 loop : -1.23 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 23 HIS 0.005 0.001 HIS E 253 PHE 0.018 0.001 PHE E 324 TYR 0.014 0.001 TYR B 338 ARG 0.004 0.000 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 235 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8240 (mp) REVERT: A 154 GLU cc_start: 0.7729 (tp30) cc_final: 0.7227 (tp30) REVERT: C 33 ILE cc_start: 0.8524 (tp) cc_final: 0.8309 (tp) REVERT: C 37 MET cc_start: 0.8353 (mtt) cc_final: 0.7227 (tmm) REVERT: C 262 ARG cc_start: 0.6413 (mtm180) cc_final: 0.6114 (mtp-110) REVERT: C 308 TYR cc_start: 0.9124 (m-80) cc_final: 0.8478 (m-80) REVERT: C 337 MET cc_start: 0.6024 (tmm) cc_final: 0.5701 (tmm) REVERT: E 99 TYR cc_start: 0.8461 (m-80) cc_final: 0.8156 (m-80) REVERT: F 279 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.8034 (p90) outliers start: 64 outliers final: 36 residues processed: 284 average time/residue: 0.2712 time to fit residues: 117.5294 Evaluate side-chains 252 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 49 GLN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16429 Z= 0.277 Angle : 0.509 12.418 22166 Z= 0.274 Chirality : 0.040 0.219 2399 Planarity : 0.003 0.037 2678 Dihedral : 7.393 152.615 2256 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.78 % Allowed : 17.80 % Favored : 78.42 % 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: 1.59 (0.19), residues: 1845 helix: 1.87 (0.14), residues: 1316 sheet: -0.06 (0.51), residues: 107 loop : -1.27 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 23 HIS 0.011 0.001 HIS A 253 PHE 0.019 0.001 PHE A 250 TYR 0.017 0.001 TYR E 351 ARG 0.003 0.000 ARG F 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 232 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 154 GLU cc_start: 0.7742 (tp30) cc_final: 0.7246 (tp30) REVERT: B 168 TRP cc_start: 0.8200 (t-100) cc_final: 0.7954 (t-100) REVERT: C 33 ILE cc_start: 0.8524 (tp) cc_final: 0.8311 (tp) REVERT: C 37 MET cc_start: 0.8355 (mtt) cc_final: 0.7230 (tmm) REVERT: C 262 ARG cc_start: 0.6452 (mtm180) cc_final: 0.6146 (mtp-110) REVERT: C 337 MET cc_start: 0.6081 (tmm) cc_final: 0.5747 (tmm) REVERT: D 275 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8049 (t80) REVERT: E 99 TYR cc_start: 0.8426 (m-80) cc_final: 0.8161 (m-80) REVERT: F 279 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8071 (p90) outliers start: 66 outliers final: 50 residues processed: 284 average time/residue: 0.2627 time to fit residues: 114.9854 Evaluate side-chains 265 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 212 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16429 Z= 0.237 Angle : 0.495 12.543 22166 Z= 0.266 Chirality : 0.039 0.228 2399 Planarity : 0.003 0.036 2678 Dihedral : 7.224 150.998 2256 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.55 % Allowed : 18.89 % Favored : 77.56 % 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: 1.66 (0.19), residues: 1845 helix: 1.91 (0.14), residues: 1318 sheet: 0.04 (0.51), residues: 107 loop : -1.22 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 23 HIS 0.011 0.001 HIS A 253 PHE 0.016 0.001 PHE A 250 TYR 0.016 0.001 TYR F 323 ARG 0.004 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 231 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7722 (tp30) cc_final: 0.7200 (tp30) REVERT: B 168 TRP cc_start: 0.8224 (t-100) cc_final: 0.7924 (t-100) REVERT: B 245 GLU cc_start: 0.7842 (tp30) cc_final: 0.7351 (tp30) REVERT: B 286 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8617 (t) REVERT: C 33 ILE cc_start: 0.8520 (tp) cc_final: 0.8317 (tp) REVERT: C 37 MET cc_start: 0.8361 (mtt) cc_final: 0.7251 (tmm) REVERT: C 262 ARG cc_start: 0.6448 (mtm180) cc_final: 0.6122 (mtp-110) REVERT: C 337 MET cc_start: 0.6132 (tmm) cc_final: 0.5806 (tmm) REVERT: D 155 HIS cc_start: 0.7205 (t-170) cc_final: 0.6946 (t-170) REVERT: D 275 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.8057 (t80) REVERT: E 99 TYR cc_start: 0.8414 (m-80) cc_final: 0.8143 (m-80) REVERT: F 279 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7998 (p90) outliers start: 62 outliers final: 47 residues processed: 278 average time/residue: 0.2644 time to fit residues: 112.8352 Evaluate side-chains 265 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN D 105 GLN D 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16429 Z= 0.202 Angle : 0.480 12.230 22166 Z= 0.258 Chirality : 0.039 0.161 2399 Planarity : 0.003 0.037 2678 Dihedral : 6.918 146.689 2256 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.78 % Allowed : 18.95 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 1845 helix: 2.01 (0.14), residues: 1315 sheet: 0.17 (0.52), residues: 107 loop : -1.09 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 23 HIS 0.005 0.001 HIS E 253 PHE 0.020 0.001 PHE A 250 TYR 0.013 0.001 TYR D 382 ARG 0.005 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 232 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7693 (tp30) cc_final: 0.7157 (tp30) REVERT: A 388 LYS cc_start: 0.8273 (tttt) cc_final: 0.8057 (tttt) REVERT: B 168 TRP cc_start: 0.8205 (t-100) cc_final: 0.7830 (t-100) REVERT: B 245 GLU cc_start: 0.7888 (tp30) cc_final: 0.7401 (tp30) REVERT: B 286 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8659 (t) REVERT: C 33 ILE cc_start: 0.8508 (tp) cc_final: 0.8299 (tp) REVERT: C 37 MET cc_start: 0.8305 (mtt) cc_final: 0.7144 (tmm) REVERT: D 275 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8060 (t80) REVERT: E 350 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7360 (pttp) REVERT: E 381 GLN cc_start: 0.7988 (mm110) cc_final: 0.7621 (mm-40) REVERT: E 399 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6493 (mt-10) REVERT: F 279 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7987 (p90) outliers start: 66 outliers final: 46 residues processed: 282 average time/residue: 0.2545 time to fit residues: 111.1138 Evaluate side-chains 264 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 53 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 105 GLN E 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16429 Z= 0.195 Angle : 0.487 12.093 22166 Z= 0.261 Chirality : 0.039 0.228 2399 Planarity : 0.003 0.034 2678 Dihedral : 6.756 143.417 2256 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.55 % Allowed : 19.12 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 1845 helix: 2.03 (0.14), residues: 1318 sheet: 0.14 (0.51), residues: 107 loop : -1.11 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 23 HIS 0.013 0.001 HIS A 253 PHE 0.028 0.001 PHE F 391 TYR 0.022 0.001 TYR C 382 ARG 0.005 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7680 (tp30) cc_final: 0.7143 (tp30) REVERT: A 388 LYS cc_start: 0.8286 (tttt) cc_final: 0.8051 (tttt) REVERT: B 168 TRP cc_start: 0.8191 (t-100) cc_final: 0.7780 (t-100) REVERT: B 245 GLU cc_start: 0.7876 (tp30) cc_final: 0.7384 (tp30) REVERT: B 286 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8583 (t) REVERT: C 37 MET cc_start: 0.8308 (mtt) cc_final: 0.7160 (tmm) REVERT: C 262 ARG cc_start: 0.6454 (mtm180) cc_final: 0.6133 (mtp-110) REVERT: D 275 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.8002 (t80) REVERT: E 350 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7342 (pttp) REVERT: E 399 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6367 (mt-10) REVERT: F 279 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7924 (p90) REVERT: F 323 TYR cc_start: 0.8385 (t80) cc_final: 0.8113 (t80) outliers start: 62 outliers final: 49 residues processed: 277 average time/residue: 0.2558 time to fit residues: 109.7999 Evaluate side-chains 266 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.0980 chunk 156 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 105 GLN E 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16429 Z= 0.181 Angle : 0.487 10.191 22166 Z= 0.261 Chirality : 0.039 0.173 2399 Planarity : 0.003 0.032 2678 Dihedral : 6.502 139.633 2256 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.43 % Allowed : 19.46 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 1845 helix: 2.06 (0.14), residues: 1318 sheet: 0.15 (0.51), residues: 107 loop : -1.10 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP F 23 HIS 0.017 0.001 HIS A 253 PHE 0.028 0.001 PHE E 156 TYR 0.014 0.001 TYR D 382 ARG 0.005 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 221 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7601 (tp30) cc_final: 0.7222 (tp30) REVERT: A 388 LYS cc_start: 0.8288 (tttt) cc_final: 0.8050 (tttt) REVERT: B 168 TRP cc_start: 0.8182 (t-100) cc_final: 0.7760 (t-100) REVERT: B 245 GLU cc_start: 0.7869 (tp30) cc_final: 0.7374 (tp30) REVERT: B 286 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8627 (t) REVERT: C 37 MET cc_start: 0.8290 (mtt) cc_final: 0.7132 (tmm) REVERT: C 262 ARG cc_start: 0.6472 (mtm180) cc_final: 0.6142 (mtp-110) REVERT: C 308 TYR cc_start: 0.9112 (m-80) cc_final: 0.8424 (m-80) REVERT: D 249 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8382 (ptmm) REVERT: D 275 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7995 (t80) REVERT: E 350 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7458 (pttp) REVERT: E 399 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6536 (mt-10) REVERT: F 279 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7880 (p90) REVERT: F 309 ASN cc_start: 0.8871 (p0) cc_final: 0.8651 (p0) REVERT: F 323 TYR cc_start: 0.8424 (t80) cc_final: 0.8150 (t80) outliers start: 60 outliers final: 43 residues processed: 267 average time/residue: 0.2516 time to fit residues: 106.5587 Evaluate side-chains 261 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 49 GLN D 105 GLN D 287 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16429 Z= 0.220 Angle : 0.509 10.337 22166 Z= 0.272 Chirality : 0.040 0.263 2399 Planarity : 0.003 0.031 2678 Dihedral : 6.514 138.278 2256 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.92 % Allowed : 19.81 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 1845 helix: 2.03 (0.14), residues: 1317 sheet: 0.17 (0.51), residues: 107 loop : -1.10 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP F 23 HIS 0.018 0.001 HIS A 253 PHE 0.023 0.001 PHE A 250 TYR 0.014 0.001 TYR D 382 ARG 0.004 0.000 ARG B 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7611 (tp30) cc_final: 0.7232 (tp30) REVERT: A 388 LYS cc_start: 0.8329 (tttt) cc_final: 0.8100 (tttt) REVERT: B 168 TRP cc_start: 0.8182 (t-100) cc_final: 0.7754 (t-100) REVERT: B 245 GLU cc_start: 0.7889 (tp30) cc_final: 0.7391 (tp30) REVERT: B 286 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8569 (t) REVERT: C 37 MET cc_start: 0.8300 (mtt) cc_final: 0.7118 (tmm) REVERT: C 262 ARG cc_start: 0.6496 (mtm180) cc_final: 0.6169 (mtp-110) REVERT: D 249 LYS cc_start: 0.8636 (ptmt) cc_final: 0.8367 (ptmm) REVERT: D 275 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.8004 (t80) REVERT: E 350 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7538 (pttp) REVERT: F 279 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7932 (p90) outliers start: 51 outliers final: 44 residues processed: 261 average time/residue: 0.2521 time to fit residues: 102.3292 Evaluate side-chains 260 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 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 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 105 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS E 155 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.177671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127811 restraints weight = 21114.932| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.40 r_work: 0.3581 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16429 Z= 0.207 Angle : 0.501 9.939 22166 Z= 0.270 Chirality : 0.039 0.176 2399 Planarity : 0.003 0.030 2678 Dihedral : 6.439 136.629 2256 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.98 % Allowed : 19.92 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 1845 helix: 2.06 (0.14), residues: 1317 sheet: 0.18 (0.51), residues: 107 loop : -1.08 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP F 23 HIS 0.019 0.001 HIS A 253 PHE 0.033 0.001 PHE E 250 TYR 0.014 0.001 TYR D 382 ARG 0.004 0.000 ARG B 309 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3692.42 seconds wall clock time: 68 minutes 31.79 seconds (4111.79 seconds total)