Starting phenix.real_space_refine on Sun Aug 24 02:11:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f74_28894/08_2025/8f74_28894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f74_28894/08_2025/8f74_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_28894/08_2025/8f74_28894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f74_28894/08_2025/8f74_28894.map" model { file = "/net/cci-nas-00/data/ceres_data/8f74_28894/08_2025/8f74_28894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f74_28894/08_2025/8f74_28894.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.36, per 1000 atoms: 0.27 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: 1.46 Conformation dependent library (CDL) restraints added in 806.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.53 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: 2.92 Time building geometry restraints manager: 1.91 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: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.730 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.050 ------------------------------------------------------------------------------- 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 16446 Z= 0.250 Angle : 0.723 13.805 22200 Z= 0.390 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 : 5.85 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG C 389 TYR 0.030 0.002 TYR E 281 PHE 0.034 0.002 PHE C 142 TRP 0.060 0.002 TRP F 23 HIS 0.021 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00493 (16429) covalent geometry : angle 0.72251 (22166) SS BOND : bond 0.00287 ( 17) SS BOND : angle 1.09901 ( 34) hydrogen bonds : bond 0.12465 ( 1096) hydrogen bonds : angle 5.59884 ( 3234) *********************** 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 : 0.727 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: 0.1341 time to fit residues: 52.4125 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 : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 E 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.180535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135182 restraints weight = 21218.233| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.66 r_work: 0.3537 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16446 Z= 0.171 Angle : 0.499 10.806 22200 Z= 0.270 Chirality : 0.039 0.150 2399 Planarity : 0.004 0.038 2678 Dihedral : 8.943 153.557 2256 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.58 % Allowed : 17.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.19), residues: 1845 helix: 1.74 (0.14), residues: 1324 sheet: -0.23 (0.50), residues: 106 loop : -1.22 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 389 TYR 0.018 0.001 TYR C 382 PHE 0.025 0.002 PHE E 324 TRP 0.028 0.001 TRP F 23 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00394 (16429) covalent geometry : angle 0.49739 (22166) SS BOND : bond 0.00282 ( 17) SS BOND : angle 1.00516 ( 34) hydrogen bonds : bond 0.03838 ( 1096) hydrogen bonds : angle 4.18277 ( 3234) *********************** 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 274 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8109 (tp30) cc_final: 0.7680 (tp30) REVERT: C 37 MET cc_start: 0.8442 (mtt) cc_final: 0.7059 (tmm) REVERT: C 308 TYR cc_start: 0.8821 (m-80) cc_final: 0.8520 (m-80) REVERT: E 99 TYR cc_start: 0.8418 (m-80) cc_final: 0.8172 (m-80) REVERT: E 250 PHE cc_start: 0.6429 (t80) cc_final: 0.6088 (t80) REVERT: F 279 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7887 (p90) outliers start: 45 outliers final: 24 residues processed: 259 average time/residue: 0.1242 time to fit residues: 49.7030 Evaluate side-chains 230 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 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 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 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 279 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 136 optimal weight: 9.9990 chunk 166 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 5 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN D 287 HIS E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.180940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133895 restraints weight = 21497.123| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.70 r_work: 0.3547 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16446 Z= 0.133 Angle : 0.458 9.615 22200 Z= 0.248 Chirality : 0.038 0.181 2399 Planarity : 0.003 0.040 2678 Dihedral : 7.706 149.858 2256 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.63 % Allowed : 17.06 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.19), residues: 1845 helix: 1.91 (0.14), residues: 1324 sheet: -0.19 (0.50), residues: 107 loop : -1.23 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 347 TYR 0.014 0.001 TYR B 338 PHE 0.021 0.001 PHE E 324 TRP 0.023 0.001 TRP F 23 HIS 0.017 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00301 (16429) covalent geometry : angle 0.45731 (22166) SS BOND : bond 0.00336 ( 17) SS BOND : angle 0.92459 ( 34) hydrogen bonds : bond 0.03545 ( 1096) hydrogen bonds : angle 4.00855 ( 3234) *********************** 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 279 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7893 (tp30) cc_final: 0.7416 (tp30) REVERT: C 37 MET cc_start: 0.8211 (mtt) cc_final: 0.7000 (tmm) REVERT: C 308 TYR cc_start: 0.8726 (m-80) cc_final: 0.8342 (m-80) REVERT: E 399 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6549 (mt-10) REVERT: F 279 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7857 (p90) REVERT: F 323 TYR cc_start: 0.8303 (t80) cc_final: 0.7950 (t80) outliers start: 46 outliers final: 28 residues processed: 265 average time/residue: 0.1211 time to fit residues: 49.8561 Evaluate side-chains 239 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 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 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 263 VAL Chi-restraints excluded: chain F residue 279 TYR 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 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** D 287 HIS E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.179012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132879 restraints weight = 21345.595| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.51 r_work: 0.3534 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16446 Z= 0.154 Angle : 0.473 9.004 22200 Z= 0.256 Chirality : 0.039 0.199 2399 Planarity : 0.003 0.039 2678 Dihedral : 7.254 149.192 2256 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.32 % Allowed : 17.06 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.19), residues: 1845 helix: 1.94 (0.14), residues: 1320 sheet: -0.10 (0.50), residues: 107 loop : -1.18 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 347 TYR 0.014 0.001 TYR E 281 PHE 0.019 0.001 PHE E 324 TRP 0.027 0.001 TRP F 23 HIS 0.005 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00357 (16429) covalent geometry : angle 0.47149 (22166) SS BOND : bond 0.00290 ( 17) SS BOND : angle 0.96844 ( 34) hydrogen bonds : bond 0.03553 ( 1096) hydrogen bonds : angle 3.99641 ( 3234) *********************** 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 285 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 227 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 154 GLU cc_start: 0.8049 (tp30) cc_final: 0.7562 (tp30) REVERT: B 309 ARG cc_start: 0.8549 (tpp80) cc_final: 0.8217 (ttm-80) REVERT: C 37 MET cc_start: 0.8341 (mtt) cc_final: 0.7056 (tmm) REVERT: E 99 TYR cc_start: 0.8439 (m-80) cc_final: 0.8107 (m-80) REVERT: F 279 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7913 (p90) outliers start: 58 outliers final: 37 residues processed: 271 average time/residue: 0.1230 time to fit residues: 51.3335 Evaluate side-chains 249 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU 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 249 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 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 169 THR 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 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 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 377 ILE Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 61 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.179178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134144 restraints weight = 21299.226| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.43 r_work: 0.3529 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16446 Z= 0.140 Angle : 0.471 11.665 22200 Z= 0.253 Chirality : 0.038 0.212 2399 Planarity : 0.003 0.039 2678 Dihedral : 6.916 146.451 2256 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.98 % Allowed : 18.49 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.19), residues: 1845 helix: 2.00 (0.14), residues: 1319 sheet: -0.04 (0.51), residues: 107 loop : -1.17 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 347 TYR 0.016 0.001 TYR E 351 PHE 0.018 0.001 PHE A 250 TRP 0.030 0.001 TRP F 23 HIS 0.007 0.001 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00322 (16429) covalent geometry : angle 0.46998 (22166) SS BOND : bond 0.00260 ( 17) SS BOND : angle 0.98171 ( 34) hydrogen bonds : bond 0.03449 ( 1096) hydrogen bonds : angle 3.96901 ( 3234) *********************** 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 284 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8071 (tp30) cc_final: 0.7567 (tp30) REVERT: B 286 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8444 (t) REVERT: B 309 ARG cc_start: 0.8571 (tpp80) cc_final: 0.8222 (ttm-80) REVERT: C 37 MET cc_start: 0.8396 (mtt) cc_final: 0.7064 (tmm) REVERT: C 262 ARG cc_start: 0.6608 (mtm180) cc_final: 0.6342 (mtp-110) REVERT: C 308 TYR cc_start: 0.8861 (m-80) cc_final: 0.8359 (m-80) REVERT: D 275 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7963 (t80) REVERT: E 99 TYR cc_start: 0.8455 (m-80) cc_final: 0.8178 (m-80) REVERT: E 381 GLN cc_start: 0.7909 (mm110) cc_final: 0.7528 (mm-40) REVERT: F 279 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7948 (p90) outliers start: 52 outliers final: 35 residues processed: 270 average time/residue: 0.1299 time to fit residues: 53.4498 Evaluate side-chains 255 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 254 VAL Chi-restraints excluded: chain A residue 283 VAL 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 286 VAL 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 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 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 378 LEU Chi-restraints excluded: chain E residue 130 LEU 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 F residue 19 VAL Chi-restraints excluded: chain F residue 20 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 395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 0.0060 chunk 180 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS E 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.178368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.129068 restraints weight = 21297.441| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.42 r_work: 0.3591 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16446 Z= 0.119 Angle : 0.460 11.547 22200 Z= 0.247 Chirality : 0.038 0.212 2399 Planarity : 0.003 0.039 2678 Dihedral : 6.607 142.039 2256 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.32 % Allowed : 19.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.19), residues: 1845 helix: 2.05 (0.14), residues: 1323 sheet: 0.15 (0.51), residues: 107 loop : -1.17 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 347 TYR 0.013 0.001 TYR E 351 PHE 0.018 0.001 PHE E 250 TRP 0.033 0.001 TRP F 23 HIS 0.007 0.001 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00267 (16429) covalent geometry : angle 0.45878 (22166) SS BOND : bond 0.00245 ( 17) SS BOND : angle 0.93968 ( 34) hydrogen bonds : bond 0.03316 ( 1096) hydrogen bonds : angle 3.88323 ( 3234) *********************** 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 304 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 246 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7886 (tp30) cc_final: 0.7333 (tp30) REVERT: B 245 GLU cc_start: 0.8090 (tp30) cc_final: 0.7485 (tp30) REVERT: B 286 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8349 (t) REVERT: B 309 ARG cc_start: 0.8302 (tpp80) cc_final: 0.7898 (ttm-80) REVERT: C 37 MET cc_start: 0.8307 (mtt) cc_final: 0.6932 (tmm) REVERT: C 308 TYR cc_start: 0.8844 (m-80) cc_final: 0.8316 (m-80) REVERT: D 155 HIS cc_start: 0.7074 (t-170) cc_final: 0.6716 (t-170) REVERT: D 275 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7737 (t80) REVERT: F 279 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7692 (p90) REVERT: F 309 ASN cc_start: 0.8601 (p0) cc_final: 0.8319 (p0) outliers start: 58 outliers final: 31 residues processed: 290 average time/residue: 0.1220 time to fit residues: 54.8341 Evaluate side-chains 254 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR 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 360 SER Chi-restraints excluded: chain D residue 378 LEU 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 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 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR 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 149 optimal weight: 8.9990 chunk 131 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 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 155 HIS E 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.183642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134426 restraints weight = 21303.556| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.38 r_work: 0.3686 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16446 Z= 0.121 Angle : 0.466 9.706 22200 Z= 0.249 Chirality : 0.038 0.161 2399 Planarity : 0.003 0.038 2678 Dihedral : 6.457 138.791 2256 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.32 % Allowed : 18.83 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.19), residues: 1845 helix: 2.10 (0.14), residues: 1324 sheet: 0.26 (0.51), residues: 107 loop : -1.15 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 389 TYR 0.013 0.001 TYR E 351 PHE 0.019 0.001 PHE A 250 TRP 0.035 0.001 TRP F 23 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00274 (16429) covalent geometry : angle 0.46513 (22166) SS BOND : bond 0.00226 ( 17) SS BOND : angle 0.93120 ( 34) hydrogen bonds : bond 0.03265 ( 1096) hydrogen bonds : angle 3.85285 ( 3234) *********************** 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 292 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 234 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8046 (tp30) cc_final: 0.7494 (tp30) REVERT: B 245 GLU cc_start: 0.8281 (tp30) cc_final: 0.7684 (tp30) REVERT: B 286 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8421 (t) REVERT: B 309 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8130 (ttm-80) REVERT: C 37 MET cc_start: 0.8367 (mtt) cc_final: 0.6869 (tmm) REVERT: C 308 TYR cc_start: 0.8924 (m-80) cc_final: 0.8419 (m-80) REVERT: D 249 LYS cc_start: 0.8616 (ptmt) cc_final: 0.8339 (ptmm) REVERT: D 275 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7876 (t80) REVERT: E 350 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7362 (pttp) REVERT: E 399 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6623 (mt-10) REVERT: F 279 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7712 (p90) REVERT: F 309 ASN cc_start: 0.8688 (p0) cc_final: 0.8432 (p0) outliers start: 58 outliers final: 37 residues processed: 280 average time/residue: 0.1250 time to fit residues: 54.2341 Evaluate side-chains 261 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 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 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 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR 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 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 379 ILE 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 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 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 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 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS D 288 ASN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.176112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125896 restraints weight = 21408.202| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.44 r_work: 0.3540 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16446 Z= 0.185 Angle : 0.522 10.347 22200 Z= 0.281 Chirality : 0.040 0.225 2399 Planarity : 0.003 0.033 2678 Dihedral : 6.736 140.883 2256 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.38 % Allowed : 18.89 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.19), residues: 1845 helix: 1.99 (0.14), residues: 1320 sheet: 0.16 (0.51), residues: 107 loop : -1.18 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 389 TYR 0.023 0.001 TYR C 382 PHE 0.025 0.001 PHE F 391 TRP 0.038 0.001 TRP F 23 HIS 0.009 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00434 (16429) covalent geometry : angle 0.52098 (22166) SS BOND : bond 0.00310 ( 17) SS BOND : angle 1.05602 ( 34) hydrogen bonds : bond 0.03585 ( 1096) hydrogen bonds : angle 4.01652 ( 3234) *********************** 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 286 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8261 (mp) REVERT: A 154 GLU cc_start: 0.8024 (tp30) cc_final: 0.7451 (tp30) REVERT: B 245 GLU cc_start: 0.8309 (tp30) cc_final: 0.7692 (tp30) REVERT: B 309 ARG cc_start: 0.8630 (tpp80) cc_final: 0.8208 (ttm-80) REVERT: C 37 MET cc_start: 0.8496 (mtt) cc_final: 0.7089 (tmm) REVERT: C 262 ARG cc_start: 0.6559 (mtm180) cc_final: 0.6256 (mtp-110) REVERT: D 250 PHE cc_start: 0.6690 (t80) cc_final: 0.6426 (t80) REVERT: D 275 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7988 (t80) REVERT: D 399 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6391 (mt-10) REVERT: E 99 TYR cc_start: 0.8458 (m-80) cc_final: 0.8098 (m-80) REVERT: E 350 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7435 (pttp) REVERT: F 145 TRP cc_start: 0.5902 (OUTLIER) cc_final: 0.4626 (t60) REVERT: F 279 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7896 (p90) outliers start: 59 outliers final: 41 residues processed: 274 average time/residue: 0.1224 time to fit residues: 51.9908 Evaluate side-chains 259 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 253 HIS 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 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 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 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 326 ILE 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 145 TRP 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 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 118 optimal weight: 9.9990 chunk 144 optimal weight: 0.6980 chunk 167 optimal weight: 30.0000 chunk 81 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS E 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.177692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127957 restraints weight = 21201.230| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.41 r_work: 0.3580 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16446 Z= 0.132 Angle : 0.502 10.303 22200 Z= 0.268 Chirality : 0.039 0.174 2399 Planarity : 0.003 0.032 2678 Dihedral : 6.425 137.609 2256 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.98 % Allowed : 19.23 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.19), residues: 1845 helix: 2.03 (0.14), residues: 1324 sheet: 0.21 (0.51), residues: 107 loop : -1.14 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 389 TYR 0.012 0.001 TYR F 279 PHE 0.023 0.001 PHE E 250 TRP 0.042 0.001 TRP F 23 HIS 0.007 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00302 (16429) covalent geometry : angle 0.50031 (22166) SS BOND : bond 0.00264 ( 17) SS BOND : angle 1.03510 ( 34) hydrogen bonds : bond 0.03375 ( 1096) hydrogen bonds : angle 3.94041 ( 3234) *********************** 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 276 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7813 (tp30) cc_final: 0.7251 (tp30) REVERT: B 245 GLU cc_start: 0.8170 (tp30) cc_final: 0.7550 (tp30) REVERT: B 286 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8391 (t) REVERT: B 309 ARG cc_start: 0.8301 (tpp80) cc_final: 0.7902 (ttm-80) REVERT: C 37 MET cc_start: 0.8316 (mtt) cc_final: 0.6957 (tmm) REVERT: C 262 ARG cc_start: 0.6474 (mtm180) cc_final: 0.6166 (mtp-110) REVERT: D 249 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8340 (ptmm) REVERT: D 275 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7791 (t80) REVERT: D 399 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6351 (mt-10) REVERT: E 99 TYR cc_start: 0.8235 (m-80) cc_final: 0.7961 (m-80) REVERT: E 350 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7405 (pttp) REVERT: F 30 TYR cc_start: 0.8092 (m-80) cc_final: 0.7888 (m-80) REVERT: F 145 TRP cc_start: 0.5766 (OUTLIER) cc_final: 0.4515 (t60) REVERT: F 279 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7748 (p90) REVERT: F 309 ASN cc_start: 0.8659 (p0) cc_final: 0.8379 (p0) outliers start: 52 outliers final: 36 residues processed: 266 average time/residue: 0.1231 time to fit residues: 51.0007 Evaluate side-chains 257 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 253 HIS 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 168 TRP 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 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 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 360 SER Chi-restraints excluded: chain D residue 378 LEU 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 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 145 TRP 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 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: 0.8980 chunk 115 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 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 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.178215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.128577 restraints weight = 21189.209| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.43 r_work: 0.3574 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16446 Z= 0.126 Angle : 0.500 9.783 22200 Z= 0.267 Chirality : 0.039 0.226 2399 Planarity : 0.003 0.032 2678 Dihedral : 6.254 133.989 2256 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.58 % Allowed : 19.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.19), residues: 1845 helix: 2.07 (0.14), residues: 1323 sheet: 0.27 (0.51), residues: 107 loop : -1.14 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 389 TYR 0.012 0.001 TYR E 351 PHE 0.020 0.001 PHE E 250 TRP 0.043 0.001 TRP F 23 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00285 (16429) covalent geometry : angle 0.49833 (22166) SS BOND : bond 0.00250 ( 17) SS BOND : angle 1.01002 ( 34) hydrogen bonds : bond 0.03333 ( 1096) hydrogen bonds : angle 3.92305 ( 3234) ********************** 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 270 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7806 (tp30) cc_final: 0.7234 (tp30) REVERT: B 245 GLU cc_start: 0.8173 (tp30) cc_final: 0.7553 (tp30) REVERT: B 286 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8341 (t) REVERT: B 298 ASP cc_start: 0.7810 (t0) cc_final: 0.7347 (p0) REVERT: B 309 ARG cc_start: 0.8299 (tpp80) cc_final: 0.7877 (ttm-80) REVERT: C 37 MET cc_start: 0.8304 (mtt) cc_final: 0.6847 (tmm) REVERT: C 262 ARG cc_start: 0.6482 (mtm180) cc_final: 0.6168 (mtp-110) REVERT: C 308 TYR cc_start: 0.8825 (m-80) cc_final: 0.8217 (m-80) REVERT: D 249 LYS cc_start: 0.8625 (ptmt) cc_final: 0.8383 (ptmm) REVERT: D 275 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7709 (t80) REVERT: D 399 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6343 (mt-10) REVERT: E 99 TYR cc_start: 0.8296 (m-80) cc_final: 0.8039 (m-80) REVERT: E 350 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7521 (pttp) REVERT: F 58 ARG cc_start: 0.8136 (mmm-85) cc_final: 0.7489 (ttm110) REVERT: F 145 TRP cc_start: 0.5748 (OUTLIER) cc_final: 0.4521 (t60) REVERT: F 279 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7674 (p90) REVERT: F 309 ASN cc_start: 0.8598 (p0) cc_final: 0.8322 (p0) outliers start: 45 outliers final: 33 residues processed: 260 average time/residue: 0.1179 time to fit residues: 47.9361 Evaluate side-chains 257 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 253 HIS 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 168 TRP 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 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 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 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE 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 145 TRP 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 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 68 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS E 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.178025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.128245 restraints weight = 21150.745| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.42 r_work: 0.3569 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16446 Z= 0.137 Angle : 0.504 9.680 22200 Z= 0.268 Chirality : 0.039 0.197 2399 Planarity : 0.003 0.031 2678 Dihedral : 6.205 131.819 2256 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.63 % Allowed : 20.15 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.19), residues: 1845 helix: 2.07 (0.14), residues: 1323 sheet: 0.28 (0.51), residues: 107 loop : -1.17 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 389 TYR 0.026 0.001 TYR E 382 PHE 0.023 0.001 PHE A 250 TRP 0.044 0.001 TRP F 23 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00314 (16429) covalent geometry : angle 0.50228 (22166) SS BOND : bond 0.00251 ( 17) SS BOND : angle 1.04371 ( 34) hydrogen bonds : bond 0.03355 ( 1096) hydrogen bonds : angle 3.92937 ( 3234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4828.99 seconds wall clock time: 83 minutes 43.42 seconds (5023.42 seconds total)