Starting phenix.real_space_refine on Fri Jul 3 21:00:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f74_28894/07_2026/8f74_28894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f74_28894/07_2026/8f74_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8f74_28894/07_2026/8f74_28894.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f74_28894/07_2026/8f74_28894.cif" model { file = "/net/cci-nas-00/data/ceres_data/8f74_28894/07_2026/8f74_28894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f74_28894/07_2026/8f74_28894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f74_28894/07_2026/8f74_28894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f74_28894/07_2026/8f74_28894.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 75 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: 80 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: 21 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: 55 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: 85 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: 72 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: 3.47, per 1000 atoms: 0.22 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: 1.34 Conformation dependent library (CDL) restraints added in 617.4 milliseconds 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: 0.33 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: 2.03 Time building geometry restraints manager: 1.76 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: 9389 34.77 - 69.54: 299 69.54 - 104.31: 17 104.31 - 139.08: 1 139.08 - 173.86: 4 Dihedral angle restraints: 9710 sinusoidal: 4058 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=" N PEE A 901 " pdb=" C4 PEE A 901 " pdb=" C5 PEE A 901 " pdb=" O4P PEE A 901 " ideal model delta sinusoidal sigma weight residual -56.97 99.02 -155.99 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 9707 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: 6.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.020 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 16.783 173.856 5999 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 are 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/Z covalent geometry : bond 0.00493 / 0.25 (16429) covalent geometry : angle 0.72251 / 0.39 (22166) SS BOND : bond 0.00287 / 0.18 ( 17) SS BOND : angle 1.09901 / 0.68 ( 34) hydrogen bonds : bond 0.12465 / 8.38 ( 1096) hydrogen bonds : angle 5.59884 / 4.07 ( 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 : 0.592 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: 0.1102 time to fit residues: 43.6252 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 : 0.416 ------------------------------------------------------------------------------- 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... 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 = 0.4269 r_free = 0.4269 target = 0.180670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.135451 restraints weight = 21224.316| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.71 r_work: 0.3527 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16446 Z= 0.170 Angle : 0.496 10.838 22200 Z= 0.269 Chirality : 0.039 0.148 2399 Planarity : 0.004 0.038 2678 Dihedral : 8.914 155.367 2228 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.58 % Allowed : 16.94 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 1845 helix: 1.73 (0.14), residues: 1324 sheet: -0.22 (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 E 103 TYR 0.018 0.001 TYR C 382 PHE 0.023 0.002 PHE E 324 TRP 0.027 0.001 TRP F 23 HIS 0.011 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (16429) covalent geometry : angle 0.49522 / 0.27 (22166) SS BOND : bond 0.00272 / 0.17 ( 17) SS BOND : angle 0.99436 / 0.62 ( 34) hydrogen bonds : bond 0.03863 / 2.59 ( 1096) hydrogen bonds : angle 4.19864 / 3.03 ( 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 275 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7917 (tp30) cc_final: 0.7496 (tp30) REVERT: C 37 MET cc_start: 0.8287 (mtt) cc_final: 0.7018 (tmm) REVERT: C 308 TYR cc_start: 0.8727 (m-80) cc_final: 0.8435 (m-80) REVERT: E 99 TYR cc_start: 0.8271 (m-80) cc_final: 0.8025 (m-80) REVERT: E 250 PHE cc_start: 0.6536 (t80) cc_final: 0.6212 (t80) REVERT: F 279 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7846 (p90) outliers start: 45 outliers final: 24 residues processed: 260 average time/residue: 0.1033 time to fit residues: 41.9786 Evaluate side-chains 231 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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: 7.9990 chunk 116 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 5 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4262 r_free = 0.4262 target = 0.179581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.134875 restraints weight = 21461.465| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.44 r_work: 0.3549 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16446 Z= 0.152 Angle : 0.472 9.409 22200 Z= 0.255 Chirality : 0.038 0.182 2399 Planarity : 0.003 0.040 2678 Dihedral : 7.404 155.160 2228 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.75 % Allowed : 16.89 % 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 are not related in a simple way. whole: 1.62 (0.19), residues: 1845 helix: 1.90 (0.14), residues: 1318 sheet: -0.25 (0.50), residues: 107 loop : -1.22 (0.29), residues: 420 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 0.022 0.001 PHE E 324 TRP 0.024 0.001 TRP F 23 HIS 0.015 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (16429) covalent geometry : angle 0.47087 / 0.25 (22166) SS BOND : bond 0.00392 / 0.27 ( 17) SS BOND : angle 0.96635 / 0.60 ( 34) hydrogen bonds : bond 0.03635 / 2.44 ( 1096) hydrogen bonds : angle 4.05254 / 2.93 ( 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 278 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8093 (tp30) cc_final: 0.7595 (tp30) REVERT: B 309 ARG cc_start: 0.8585 (tpp80) cc_final: 0.8190 (ttm-80) REVERT: C 37 MET cc_start: 0.8358 (mtt) cc_final: 0.6992 (tmm) REVERT: C 308 TYR cc_start: 0.8854 (m-80) cc_final: 0.8384 (m-80) REVERT: E 337 MET cc_start: 0.7576 (mtp) cc_final: 0.7340 (mtp) REVERT: E 399 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6537 (mt-10) REVERT: F 279 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7854 (p90) outliers start: 48 outliers final: 31 residues processed: 263 average time/residue: 0.1170 time to fit residues: 47.7350 Evaluate side-chains 240 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 292 ASP 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 95 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 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 366 VAL Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS D 288 ASN 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 = 0.4267 r_free = 0.4267 target = 0.180022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133886 restraints weight = 21305.104| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.43 r_work: 0.3521 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1662 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= 0.134 Angle : 0.460 9.030 22200 Z= 0.249 Chirality : 0.038 0.198 2399 Planarity : 0.003 0.040 2678 Dihedral : 6.799 152.702 2228 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.38 % Allowed : 16.94 % Favored : 79.68 % 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 are not related in a simple way. whole: 1.74 (0.19), residues: 1845 helix: 1.98 (0.14), residues: 1317 sheet: -0.08 (0.50), residues: 107 loop : -1.18 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 347 TYR 0.013 0.001 TYR B 338 PHE 0.018 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/Z covalent geometry : bond 0.00306 / 0.13 (16429) covalent geometry : angle 0.45867 / 0.25 (22166) SS BOND : bond 0.00293 / 0.19 ( 17) SS BOND : angle 0.94862 / 0.59 ( 34) hydrogen bonds : bond 0.03466 / 2.32 ( 1096) hydrogen bonds : angle 3.97150 / 2.87 ( 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 286 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 154 GLU cc_start: 0.8060 (tp30) cc_final: 0.7548 (tp30) REVERT: B 309 ARG cc_start: 0.8550 (tpp80) cc_final: 0.8179 (ttm-80) REVERT: C 37 MET cc_start: 0.8331 (mtt) cc_final: 0.6995 (tmm) REVERT: C 308 TYR cc_start: 0.8841 (m-80) cc_final: 0.8395 (m-80) REVERT: E 99 TYR cc_start: 0.8439 (m-80) cc_final: 0.8099 (m-80) REVERT: F 279 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7907 (p90) outliers start: 59 outliers final: 37 residues processed: 273 average time/residue: 0.1077 time to fit residues: 45.9213 Evaluate side-chains 254 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 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 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 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 120 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL 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: 0.9990 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4262 r_free = 0.4262 target = 0.179430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133612 restraints weight = 21256.035| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.62 r_work: 0.3536 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1840 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= 0.138 Angle : 0.469 11.875 22200 Z= 0.252 Chirality : 0.038 0.208 2399 Planarity : 0.003 0.039 2678 Dihedral : 6.521 150.790 2228 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.98 % Allowed : 18.32 % Favored : 78.71 % 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 are not related in a simple way. whole: 1.80 (0.19), residues: 1845 helix: 2.01 (0.14), residues: 1319 sheet: -0.02 (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 0.019 0.001 PHE A 250 TRP 0.030 0.001 TRP F 23 HIS 0.008 0.001 HIS E 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16429) covalent geometry : angle 0.46769 / 0.25 (22166) SS BOND : bond 0.00256 / 0.17 ( 17) SS BOND : angle 0.96752 / 0.61 ( 34) hydrogen bonds : bond 0.03431 / 2.30 ( 1096) hydrogen bonds : angle 3.95864 / 2.87 ( 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 289 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8051 (tp30) cc_final: 0.7544 (tp30) REVERT: B 245 GLU cc_start: 0.8163 (tp30) cc_final: 0.7652 (tp30) REVERT: B 286 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8451 (t) REVERT: B 309 ARG cc_start: 0.8566 (tpp80) cc_final: 0.8254 (ttm-80) REVERT: C 37 MET cc_start: 0.8396 (mtt) cc_final: 0.7063 (tmm) REVERT: C 262 ARG cc_start: 0.6618 (mtm180) cc_final: 0.6345 (mtp-110) REVERT: C 308 TYR cc_start: 0.8856 (m-80) cc_final: 0.8361 (m-80) REVERT: D 275 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7962 (t80) REVERT: E 99 TYR cc_start: 0.8425 (m-80) cc_final: 0.8172 (m-80) REVERT: E 381 GLN cc_start: 0.7900 (mm110) cc_final: 0.7523 (mm-40) REVERT: F 279 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7925 (p90) outliers start: 52 outliers final: 38 residues processed: 279 average time/residue: 0.1155 time to fit residues: 49.3358 Evaluate side-chains 261 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 281 TYR 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 275 PHE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 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 366 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 0.0370 chunk 180 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 105 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 287 HIS E 155 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.184565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135590 restraints weight = 21354.349| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.39 r_work: 0.3701 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16446 Z= 0.105 Angle : 0.451 11.377 22200 Z= 0.242 Chirality : 0.037 0.206 2399 Planarity : 0.003 0.039 2678 Dihedral : 6.247 145.145 2228 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.09 % Allowed : 18.95 % Favored : 77.96 % 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 are not related in a simple way. whole: 1.94 (0.19), residues: 1845 helix: 2.10 (0.14), residues: 1324 sheet: 0.22 (0.51), residues: 106 loop : -1.13 (0.29), residues: 415 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 0.017 0.001 PHE E 250 TRP 0.032 0.001 TRP F 23 HIS 0.006 0.001 HIS E 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (16429) covalent geometry : angle 0.44967 / 0.24 (22166) SS BOND : bond 0.00227 / 0.15 ( 17) SS BOND : angle 0.90131 / 0.56 ( 34) hydrogen bonds : bond 0.03243 / 2.18 ( 1096) hydrogen bonds : angle 3.84686 / 2.78 ( 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 295 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8051 (tp30) cc_final: 0.7501 (tp30) REVERT: B 245 GLU cc_start: 0.8257 (tp30) cc_final: 0.7665 (tp30) REVERT: B 286 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8363 (t) REVERT: B 309 ARG cc_start: 0.8585 (tpp80) cc_final: 0.8126 (ttm-80) REVERT: C 37 MET cc_start: 0.8394 (mtt) cc_final: 0.6861 (tmm) REVERT: C 308 TYR cc_start: 0.8905 (m-80) cc_final: 0.8409 (m-80) REVERT: D 155 HIS cc_start: 0.7082 (t-170) cc_final: 0.6723 (t-170) REVERT: D 275 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7846 (t80) REVERT: E 99 TYR cc_start: 0.8374 (m-80) cc_final: 0.8133 (m-80) REVERT: E 115 GLU cc_start: 0.8369 (tp30) cc_final: 0.8158 (mm-30) REVERT: E 399 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6478 (mt-10) REVERT: F 46 GLN cc_start: 0.8316 (tp40) cc_final: 0.8089 (mm-40) REVERT: F 279 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7775 (p90) REVERT: F 309 ASN cc_start: 0.8660 (p0) cc_final: 0.8417 (p0) outliers start: 54 outliers final: 30 residues processed: 282 average time/residue: 0.1075 time to fit residues: 47.2642 Evaluate side-chains 258 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 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 275 PHE Chi-restraints excluded: chain C residue 395 SER 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 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 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 140 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 149 optimal weight: 0.1980 chunk 131 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 97 optimal weight: 0.0170 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 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 = 0.4389 r_free = 0.4389 target = 0.184954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.135780 restraints weight = 21289.251| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.42 r_work: 0.3702 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16446 Z= 0.107 Angle : 0.452 9.295 22200 Z= 0.243 Chirality : 0.038 0.190 2399 Planarity : 0.003 0.038 2678 Dihedral : 6.101 141.214 2228 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.03 % Allowed : 18.95 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.19), residues: 1845 helix: 2.19 (0.14), residues: 1325 sheet: 0.34 (0.51), residues: 106 loop : -1.07 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 389 TYR 0.014 0.001 TYR A 332 PHE 0.019 0.001 PHE A 250 TRP 0.034 0.001 TRP F 23 HIS 0.013 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (16429) covalent geometry : angle 0.45104 / 0.24 (22166) SS BOND : bond 0.00246 / 0.17 ( 17) SS BOND : angle 0.88711 / 0.56 ( 34) hydrogen bonds : bond 0.03163 / 2.13 ( 1096) hydrogen bonds : angle 3.78827 / 2.74 ( 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 294 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7853 (tp30) cc_final: 0.7298 (tp30) REVERT: B 18 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8046 (ttp-110) REVERT: B 245 GLU cc_start: 0.8120 (tp30) cc_final: 0.7508 (tp30) REVERT: B 286 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8287 (t) REVERT: B 309 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7913 (ttm-80) REVERT: C 37 MET cc_start: 0.8223 (mtt) cc_final: 0.6801 (tmm) REVERT: C 308 TYR cc_start: 0.8820 (m-80) cc_final: 0.8326 (m-80) REVERT: D 249 LYS cc_start: 0.8590 (ptmt) cc_final: 0.8318 (ptmm) REVERT: D 275 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7758 (t80) REVERT: E 99 TYR cc_start: 0.8254 (m-80) cc_final: 0.7977 (m-80) REVERT: E 115 GLU cc_start: 0.8128 (tp30) cc_final: 0.7886 (mm-30) REVERT: E 156 PHE cc_start: 0.7815 (t80) cc_final: 0.7571 (t80) REVERT: E 250 PHE cc_start: 0.6628 (t80) cc_final: 0.6424 (t80) REVERT: E 350 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7310 (pttp) REVERT: E 399 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6494 (mt-10) REVERT: F 279 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7566 (p90) REVERT: F 309 ASN cc_start: 0.8498 (p0) cc_final: 0.8233 (p0) outliers start: 53 outliers final: 33 residues processed: 285 average time/residue: 0.1149 time to fit residues: 50.7371 Evaluate side-chains 264 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 104 HIS Chi-restraints excluded: chain B residue 254 VAL 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 275 PHE Chi-restraints excluded: chain C residue 281 TYR 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 402 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 153 LEU 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 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 140 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.180514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130535 restraints weight = 21483.635| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.41 r_work: 0.3637 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16446 Z= 0.208 Angle : 0.536 10.020 22200 Z= 0.288 Chirality : 0.041 0.223 2399 Planarity : 0.003 0.033 2678 Dihedral : 6.610 148.369 2228 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.98 % Allowed : 19.35 % Favored : 77.68 % 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 are not related in a simple way. whole: 1.74 (0.19), residues: 1845 helix: 1.95 (0.14), residues: 1320 sheet: 0.15 (0.51), residues: 107 loop : -1.20 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 389 TYR 0.016 0.002 TYR E 281 PHE 0.019 0.002 PHE A 250 TRP 0.038 0.001 TRP F 23 HIS 0.008 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (16429) covalent geometry : angle 0.53420 / 0.29 (22166) SS BOND : bond 0.00387 / 0.24 ( 17) SS BOND : angle 1.15371 / 0.72 ( 34) hydrogen bonds : bond 0.03681 / 2.47 ( 1096) hydrogen bonds : angle 4.04991 / 2.93 ( 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: 52 poor density : 234 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8070 (tp30) cc_final: 0.7515 (tp30) REVERT: B 309 ARG cc_start: 0.8604 (tpp80) cc_final: 0.8174 (ttm-80) REVERT: C 37 MET cc_start: 0.8487 (mtt) cc_final: 0.7059 (tmm) REVERT: C 262 ARG cc_start: 0.6604 (mtm180) cc_final: 0.6290 (mtp-110) REVERT: D 275 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8043 (t80) REVERT: E 99 TYR cc_start: 0.8431 (m-80) cc_final: 0.8076 (m-80) REVERT: E 115 GLU cc_start: 0.8455 (tp30) cc_final: 0.8248 (mm-30) REVERT: E 281 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.8291 (p90) REVERT: E 350 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7496 (pttp) REVERT: F 145 TRP cc_start: 0.5886 (OUTLIER) cc_final: 0.4570 (t60) REVERT: F 279 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8017 (p90) outliers start: 52 outliers final: 35 residues processed: 278 average time/residue: 0.1108 time to fit residues: 47.7555 Evaluate side-chains 260 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 279 ILE Chi-restraints excluded: chain B residue 293 VAL 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 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 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 280 CYS Chi-restraints excluded: chain E residue 281 TYR 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 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 118 optimal weight: 0.0670 chunk 144 optimal weight: 0.5980 chunk 167 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 171 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 66 ASN C 105 GLN D 105 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS E 155 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.177279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.130908 restraints weight = 20811.309| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.24 r_work: 0.3616 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16446 Z= 0.115 Angle : 0.489 9.412 22200 Z= 0.262 Chirality : 0.038 0.169 2399 Planarity : 0.003 0.033 2678 Dihedral : 6.111 141.030 2228 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.23 % Allowed : 20.32 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 1845 helix: 2.09 (0.14), residues: 1324 sheet: 0.31 (0.51), residues: 106 loop : -1.12 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 389 TYR 0.013 0.001 TYR F 279 PHE 0.024 0.001 PHE A 250 TRP 0.042 0.002 TRP F 23 HIS 0.010 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (16429) covalent geometry : angle 0.48826 / 0.26 (22166) SS BOND : bond 0.00233 / 0.16 ( 17) SS BOND : angle 0.96858 / 0.61 ( 34) hydrogen bonds : bond 0.03273 / 2.21 ( 1096) hydrogen bonds : angle 3.88868 / 2.82 ( 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 275 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7947 (tp30) cc_final: 0.7374 (tp30) REVERT: B 286 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8387 (t) REVERT: B 309 ARG cc_start: 0.8580 (tpp80) cc_final: 0.8180 (ttm-80) REVERT: C 37 MET cc_start: 0.8434 (mtt) cc_final: 0.6979 (tmm) REVERT: C 286 VAL cc_start: 0.8076 (p) cc_final: 0.7875 (p) REVERT: C 308 TYR cc_start: 0.8915 (m-80) cc_final: 0.8400 (m-80) REVERT: D 249 LYS cc_start: 0.8591 (ptmt) cc_final: 0.8275 (ptmm) REVERT: D 275 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7831 (t80) REVERT: D 399 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6374 (mt-10) REVERT: E 99 TYR cc_start: 0.8374 (m-80) cc_final: 0.8172 (m-80) REVERT: E 350 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7468 (pttp) REVERT: F 58 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7470 (ttm110) REVERT: F 279 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7830 (p90) REVERT: F 309 ASN cc_start: 0.8754 (p0) cc_final: 0.8501 (p0) outliers start: 39 outliers final: 29 residues processed: 267 average time/residue: 0.1016 time to fit residues: 42.4234 Evaluate side-chains 256 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 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 C residue 19 ILE Chi-restraints excluded: chain C residue 38 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 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 378 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain F residue 20 LEU 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 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 105 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.178790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129380 restraints weight = 21165.741| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.42 r_work: 0.3596 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16446 Z= 0.125 Angle : 0.493 9.050 22200 Z= 0.265 Chirality : 0.039 0.236 2399 Planarity : 0.003 0.033 2678 Dihedral : 6.057 139.085 2228 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.06 % Allowed : 20.66 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.19), residues: 1845 helix: 2.11 (0.14), residues: 1324 sheet: 0.30 (0.51), residues: 107 loop : -1.13 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 389 TYR 0.013 0.001 TYR E 351 PHE 0.042 0.001 PHE E 250 TRP 0.043 0.001 TRP F 23 HIS 0.016 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (16429) covalent geometry : angle 0.49177 / 0.26 (22166) SS BOND : bond 0.00237 / 0.15 ( 17) SS BOND : angle 0.98024 / 0.62 ( 34) hydrogen bonds : bond 0.03303 / 2.23 ( 1096) hydrogen bonds : angle 3.88622 / 2.82 ( 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: 36 poor density : 234 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7808 (tp30) cc_final: 0.7239 (tp30) REVERT: A 279 ILE cc_start: 0.9191 (tp) cc_final: 0.8989 (tp) REVERT: B 245 GLU cc_start: 0.8060 (tp30) cc_final: 0.7496 (tp30) REVERT: B 286 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8343 (t) REVERT: B 309 ARG cc_start: 0.8287 (tpp80) cc_final: 0.7930 (ttm-80) REVERT: C 37 MET cc_start: 0.8237 (mtt) cc_final: 0.6832 (tmm) REVERT: C 286 VAL cc_start: 0.8102 (p) cc_final: 0.7886 (p) REVERT: C 308 TYR cc_start: 0.8816 (m-80) cc_final: 0.8299 (m-80) REVERT: D 249 LYS cc_start: 0.8605 (ptmt) cc_final: 0.8292 (ptmm) REVERT: D 275 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7733 (t80) REVERT: D 399 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6350 (mt-10) REVERT: E 99 TYR cc_start: 0.8292 (m-80) cc_final: 0.8030 (m-80) REVERT: E 350 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7615 (pttp) REVERT: F 30 TYR cc_start: 0.8113 (m-80) cc_final: 0.7891 (m-80) REVERT: F 58 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7502 (ttm110) REVERT: F 279 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7669 (p90) REVERT: F 309 ASN cc_start: 0.8595 (p0) cc_final: 0.8310 (p0) outliers start: 36 outliers final: 29 residues processed: 263 average time/residue: 0.1121 time to fit residues: 45.8513 Evaluate side-chains 258 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 C residue 19 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 38 ILE 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 378 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain F residue 20 LEU 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 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 68 optimal weight: 0.9990 chunk 141 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4305 r_free = 0.4305 target = 0.178337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.128891 restraints weight = 21117.945| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.40 r_work: 0.3590 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2289 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= 0.135 Angle : 0.495 8.751 22200 Z= 0.266 Chirality : 0.039 0.176 2399 Planarity : 0.003 0.033 2678 Dihedral : 6.051 138.441 2228 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.29 % Allowed : 20.66 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 1845 helix: 2.08 (0.14), residues: 1325 sheet: 0.33 (0.51), residues: 107 loop : -1.12 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 389 TYR 0.013 0.001 TYR E 351 PHE 0.036 0.001 PHE E 250 TRP 0.041 0.001 TRP F 23 HIS 0.014 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16429) covalent geometry : angle 0.49388 / 0.27 (22166) SS BOND : bond 0.00235 / 0.15 ( 17) SS BOND : angle 1.00400 / 0.64 ( 34) hydrogen bonds : bond 0.03320 / 2.24 ( 1096) hydrogen bonds : angle 3.89934 / 2.82 ( 3234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4322.51 seconds wall clock time: 74 minutes 47.61 seconds (4487.61 seconds total)