Starting phenix.real_space_refine on Sat Jun 14 15:00:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f74_28894/06_2025/8f74_28894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f74_28894/06_2025/8f74_28894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f74_28894/06_2025/8f74_28894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f74_28894/06_2025/8f74_28894.map" model { file = "/net/cci-nas-00/data/ceres_data/8f74_28894/06_2025/8f74_28894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f74_28894/06_2025/8f74_28894.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 106 5.16 5 C 10580 2.51 5 N 2524 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16008 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2672 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2668 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "C" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2560 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 2 Chain: "D" Number of atoms: 2637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2637 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 2 Chain: "E" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2652 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2569 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 7, 'TRANS': 301} Chain breaks: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 12.32, per 1000 atoms: 0.77 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: 4.15 Conformation dependent library (CDL) restraints added in 2.1 seconds 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 12 sheets defined 77.3% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.098A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 50 removed outlier: 3.681A pdb=" N ASP A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.563A pdb=" N LYS A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.141A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 4.019A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 256 removed outlier: 4.172A pdb=" N GLU A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 285 removed outlier: 3.972A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 289 removed outlier: 3.779A pdb=" N ILE A 289 " --> pdb=" O VAL A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 315 through 346 removed outlier: 3.986A pdb=" N ARG A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.304A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.567A pdb=" N ARG B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.789A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 4.604A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 Processing helix chain 'B' and resid 166 through 175 removed outlier: 4.331A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 258 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 343 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 383 through 391 removed outlier: 4.209A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 22 through 50 removed outlier: 3.603A pdb=" N MET C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP C 50 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 4.657A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 167 through 175 removed outlier: 4.151A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 255 Processing helix chain 'C' and resid 258 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 315 through 344 Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 370 through 383 Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.059A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 402 removed outlier: 3.675A pdb=" N GLU C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 4.282A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 142 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 146 through 165 Processing helix chain 'D' and resid 166 through 175 Processing helix chain 'D' and resid 233 through 256 removed outlier: 4.094A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 removed outlier: 3.664A pdb=" N ARG D 262 " --> pdb=" O ASP D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 315 through 346 removed outlier: 4.258A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 370 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 3.890A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.670A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.817A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.521A pdb=" N ARG E 117 " --> pdb=" O CYS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 4.643A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.163A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 258 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 315 through 345 removed outlier: 3.553A pdb=" N LEU E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 370 through 383 Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.051A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 395 through 409 Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.525A pdb=" N ARG F 118 " --> pdb=" O MET F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 4.027A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 removed outlier: 3.582A pdb=" N PHE F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 168 Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.338A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 253 Processing helix chain 'F' and resid 257 through 284 Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'F' and resid 312 through 344 removed outlier: 3.907A pdb=" N ARG F 344 " --> pdb=" O TRP F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 368 through 381 Processing helix chain 'F' and resid 381 through 389 removed outlier: 4.016A pdb=" N SER F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 392 No H-bonds generated for 'chain 'F' and resid 390 through 392' Processing helix chain 'F' and resid 393 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.828A pdb=" N VAL A 60 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL F 94 " --> pdb=" O VAL A 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.557A pdb=" N ILE B 53 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 350 through 351 removed outlier: 3.503A pdb=" N VAL D 368 " --> pdb=" O TYR D 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.749A pdb=" N ILE E 53 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 350 through 351 removed outlier: 3.602A pdb=" N TYR E 351 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 368 " --> pdb=" O TYR E 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AB3, first strand: chain 'F' and resid 348 through 349 removed outlier: 3.668A pdb=" N VAL F 366 " --> pdb=" O TYR F 349 " (cutoff:3.500A) 1096 hydrogen bonds defined for protein. 3234 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2602 1.32 - 1.45: 4684 1.45 - 1.57: 8982 1.57 - 1.69: 6 1.69 - 1.81: 155 Bond restraints: 16429 Sorted by residual: bond pdb=" C10 PEE D 901 " pdb=" O4 PEE D 901 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C10 PEE B 903 " pdb=" O4 PEE B 903 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " ideal model delta sigma weight residual 1.653 1.779 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" O4P PEE C 901 " pdb=" P PEE C 901 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " ideal model delta sigma weight residual 1.653 1.775 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 16424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 21927 2.76 - 5.52: 194 5.52 - 8.28: 34 8.28 - 11.04: 6 11.04 - 13.81: 5 Bond angle restraints: 22166 Sorted by residual: angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.24 -13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.22 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE B 901 " pdb=" P PEE B 901 " pdb=" O2P PEE B 901 " ideal model delta sigma weight residual 119.43 133.13 -13.70 3.00e+00 1.11e-01 2.09e+01 angle pdb=" C11 PEE B 903 " pdb=" C10 PEE B 903 " pdb=" O2 PEE B 903 " ideal model delta sigma weight residual 111.70 124.70 -13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" C11 PEE D 901 " pdb=" C10 PEE D 901 " pdb=" O2 PEE D 901 " ideal model delta sigma weight residual 111.70 124.60 -12.90 3.00e+00 1.11e-01 1.85e+01 ... (remaining 22161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 9403 34.77 - 69.54: 305 69.54 - 104.31: 23 104.31 - 139.08: 2 139.08 - 173.86: 5 Dihedral angle restraints: 9738 sinusoidal: 4086 harmonic: 5652 Sorted by residual: dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 295 " pdb=" CB CYS C 295 " ideal model delta sinusoidal sigma weight residual 93.00 43.52 49.48 1 1.00e+01 1.00e-02 3.36e+01 dihedral pdb=" N PEE C 901 " pdb=" C4 PEE C 901 " pdb=" C5 PEE C 901 " pdb=" O4P PEE C 901 " ideal model delta sinusoidal sigma weight residual 303.03 129.17 173.86 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C2 PEE C 901 " pdb=" O3P PEE C 901 " ideal model delta sinusoidal sigma weight residual -59.96 111.18 -171.14 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 9735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2000 0.056 - 0.112: 374 0.112 - 0.168: 20 0.168 - 0.224: 2 0.224 - 0.280: 3 Chirality restraints: 2399 Sorted by residual: chirality pdb=" CB VAL E 283 " pdb=" CA VAL E 283 " pdb=" CG1 VAL E 283 " pdb=" CG2 VAL E 283 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C2 PEE F 901 " pdb=" C1 PEE F 901 " pdb=" C3 PEE F 901 " pdb=" O2 PEE F 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.61 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR B 44 " pdb=" CA THR B 44 " pdb=" OG1 THR B 44 " pdb=" CG2 THR B 44 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2396 not shown) Planarity restraints: 2678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 23 " -0.021 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP F 23 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP F 23 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 23 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 23 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 23 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " -0.017 2.00e-02 2.50e+03 1.67e-02 6.94e+00 pdb=" CG TRP C 168 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 155 " -0.020 2.00e-02 2.50e+03 2.05e-02 6.33e+00 pdb=" CG HIS D 155 " 0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS D 155 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS D 155 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS D 155 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS D 155 " -0.003 2.00e-02 2.50e+03 ... (remaining 2675 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1358 2.74 - 3.28: 16023 3.28 - 3.82: 28443 3.82 - 4.36: 32182 4.36 - 4.90: 56308 Nonbonded interactions: 134314 Sorted by model distance: nonbonded pdb=" NE2 GLN A 46 " pdb=" O LYS A 123 " model vdw 2.206 3.120 nonbonded pdb=" OH TYR B 351 " pdb=" OD2 ASP B 380 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR E 303 " pdb=" OH TYR E 308 " model vdw 2.269 3.040 nonbonded pdb=" O PRO D 167 " pdb=" OG1 THR D 170 " model vdw 2.272 3.040 nonbonded pdb=" O ILE E 278 " pdb=" OG1 THR E 282 " model vdw 2.273 3.040 ... (remaining 134309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 68 or resid 93 through 175 or resid 235 through \ 402 or (resid 903 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 68 or resid 93 through 175 or resid 235 through \ 402 or (resid 903 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name O2 or name O4 )))) selection = (chain 'C' and (resid 15 through 402 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name O2 or name O4 ) \ ))) selection = (chain 'D' and (resid 15 through 175 or resid 235 through 402 or resid 902)) selection = (chain 'E' and (resid 15 through 175 or resid 235 through 402 or resid 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.620 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 16446 Z= 0.250 Angle : 0.723 13.805 22200 Z= 0.390 Chirality : 0.041 0.280 2399 Planarity : 0.005 0.046 2678 Dihedral : 17.290 173.856 6027 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.06 % Allowed : 18.43 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1845 helix: 1.23 (0.13), residues: 1289 sheet: -0.28 (0.51), residues: 107 loop : -0.85 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP F 23 HIS 0.021 0.001 HIS D 155 PHE 0.034 0.002 PHE C 142 TYR 0.030 0.002 TYR E 281 ARG 0.009 0.001 ARG C 389 Details of bonding type rmsd hydrogen bonds : bond 0.12465 ( 1096) hydrogen bonds : angle 5.59884 ( 3234) SS BOND : bond 0.00287 ( 17) SS BOND : angle 1.09901 ( 34) covalent geometry : bond 0.00493 (16429) covalent geometry : angle 0.72251 (22166) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 1.759 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: 0.2719 time to fit residues: 106.0511 Evaluate side-chains 216 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 chunk 74 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS B 239 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.179023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133825 restraints weight = 21267.153| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.74 r_work: 0.3506 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16446 Z= 0.200 Angle : 0.521 10.897 22200 Z= 0.282 Chirality : 0.040 0.152 2399 Planarity : 0.004 0.037 2678 Dihedral : 9.136 154.969 2256 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.86 % Allowed : 16.77 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.19), residues: 1845 helix: 1.69 (0.14), residues: 1320 sheet: -0.26 (0.50), residues: 106 loop : -1.22 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 23 HIS 0.012 0.001 HIS A 253 PHE 0.024 0.002 PHE E 324 TYR 0.018 0.002 TYR C 382 ARG 0.005 0.000 ARG C 389 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 1096) hydrogen bonds : angle 4.25944 ( 3234) SS BOND : bond 0.00312 ( 17) SS BOND : angle 1.05474 ( 34) covalent geometry : bond 0.00466 (16429) covalent geometry : angle 0.51966 (22166) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7915 (tp30) cc_final: 0.7507 (tp30) REVERT: C 37 MET cc_start: 0.8333 (mtt) cc_final: 0.7186 (tmm) REVERT: C 308 TYR cc_start: 0.8759 (m-80) cc_final: 0.8459 (m-80) REVERT: C 337 MET cc_start: 0.6259 (tmm) cc_final: 0.5971 (tmm) REVERT: E 99 TYR cc_start: 0.8311 (m-80) cc_final: 0.8060 (m-80) REVERT: E 250 PHE cc_start: 0.6435 (t80) cc_final: 0.6048 (t80) REVERT: F 279 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7974 (p90) outliers start: 50 outliers final: 31 residues processed: 262 average time/residue: 0.2575 time to fit residues: 104.9008 Evaluate side-chains 238 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 21 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 49 GLN E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.179735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133769 restraints weight = 21038.842| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.60 r_work: 0.3505 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1487 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 : 0.467 9.662 22200 Z= 0.252 Chirality : 0.038 0.189 2399 Planarity : 0.003 0.040 2678 Dihedral : 7.883 151.628 2256 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.75 % Allowed : 17.12 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.19), residues: 1845 helix: 1.87 (0.14), residues: 1319 sheet: -0.23 (0.50), residues: 107 loop : -1.21 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 168 HIS 0.016 0.001 HIS A 253 PHE 0.022 0.001 PHE E 324 TYR 0.014 0.001 TYR B 338 ARG 0.004 0.000 ARG F 347 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 1096) hydrogen bonds : angle 4.04786 ( 3234) SS BOND : bond 0.00280 ( 17) SS BOND : angle 0.96161 ( 34) covalent geometry : bond 0.00315 (16429) covalent geometry : angle 0.46559 (22166) *********************** 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 277 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8112 (tp30) cc_final: 0.7623 (tp30) REVERT: B 309 ARG cc_start: 0.8601 (tpp80) cc_final: 0.8218 (ttm-80) REVERT: C 37 MET cc_start: 0.8395 (mtt) cc_final: 0.7032 (tmm) REVERT: C 308 TYR cc_start: 0.8821 (m-80) cc_final: 0.8435 (m-80) REVERT: C 337 MET cc_start: 0.6118 (tmm) cc_final: 0.5814 (tmm) REVERT: E 337 MET cc_start: 0.7565 (mtp) cc_final: 0.7347 (mtp) REVERT: E 399 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6530 (mt-10) REVERT: F 279 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7935 (p90) outliers start: 48 outliers final: 27 residues processed: 260 average time/residue: 0.3001 time to fit residues: 120.7077 Evaluate side-chains 238 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 391 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 95 optimal weight: 0.3980 chunk 161 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 119 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN E 155 HIS 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 = 0.4268 r_free = 0.4268 target = 0.179990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134608 restraints weight = 21118.231| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.63 r_work: 0.3545 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1689 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= 0.126 Angle : 0.452 9.027 22200 Z= 0.245 Chirality : 0.038 0.197 2399 Planarity : 0.003 0.042 2678 Dihedral : 7.169 148.105 2256 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.15 % Allowed : 17.63 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.19), residues: 1845 helix: 1.95 (0.14), residues: 1323 sheet: -0.07 (0.50), residues: 107 loop : -1.18 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 23 HIS 0.005 0.001 HIS E 253 PHE 0.018 0.001 PHE E 324 TYR 0.013 0.001 TYR B 338 ARG 0.003 0.000 ARG E 389 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 1096) hydrogen bonds : angle 3.94242 ( 3234) SS BOND : bond 0.00257 ( 17) SS BOND : angle 0.92274 ( 34) covalent geometry : bond 0.00284 (16429) covalent geometry : angle 0.45122 (22166) *********************** 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 288 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 233 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8305 (mp) REVERT: A 154 GLU cc_start: 0.8051 (tp30) cc_final: 0.7553 (tp30) REVERT: B 309 ARG cc_start: 0.8577 (tpp80) cc_final: 0.8226 (ttm-80) REVERT: C 37 MET cc_start: 0.8359 (mtt) cc_final: 0.7052 (tmm) REVERT: C 256 GLU cc_start: 0.6764 (mp0) cc_final: 0.6368 (mp0) REVERT: C 308 TYR cc_start: 0.8833 (m-80) cc_final: 0.8403 (m-80) REVERT: C 337 MET cc_start: 0.6149 (tmm) cc_final: 0.5815 (tmm) REVERT: F 279 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7909 (p90) outliers start: 55 outliers final: 29 residues processed: 276 average time/residue: 0.2479 time to fit residues: 105.6000 Evaluate side-chains 243 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 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 377 HIS Chi-restraints excluded: chain F residue 19 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 93 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 105 GLN E 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.178586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.129130 restraints weight = 21446.123| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.45 r_work: 0.3596 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1834 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= 0.121 Angle : 0.458 11.836 22200 Z= 0.248 Chirality : 0.038 0.199 2399 Planarity : 0.003 0.042 2678 Dihedral : 6.842 144.322 2256 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.26 % Allowed : 18.15 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 1845 helix: 2.03 (0.14), residues: 1323 sheet: 0.04 (0.51), residues: 107 loop : -1.15 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 23 HIS 0.011 0.001 HIS A 253 PHE 0.019 0.001 PHE A 250 TYR 0.015 0.001 TYR E 351 ARG 0.003 0.000 ARG F 347 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 1096) hydrogen bonds : angle 3.89674 ( 3234) SS BOND : bond 0.00249 ( 17) SS BOND : angle 0.92776 ( 34) covalent geometry : bond 0.00272 (16429) covalent geometry : angle 0.45731 (22166) *********************** 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 295 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 154 GLU cc_start: 0.7870 (tp30) cc_final: 0.7331 (tp30) REVERT: B 245 GLU cc_start: 0.8109 (tp30) cc_final: 0.7512 (tp30) REVERT: B 309 ARG cc_start: 0.8310 (tpp80) cc_final: 0.7875 (ttm-80) REVERT: B 375 MET cc_start: 0.8515 (mtm) cc_final: 0.8291 (mtm) REVERT: C 37 MET cc_start: 0.8299 (mtt) cc_final: 0.6840 (tmm) REVERT: C 145 LYS cc_start: 0.6832 (mmmt) cc_final: 0.5955 (mtpt) REVERT: C 262 ARG cc_start: 0.6364 (mtm180) cc_final: 0.6072 (mtp-110) REVERT: C 308 TYR cc_start: 0.8848 (m-80) cc_final: 0.8307 (m-80) REVERT: C 337 MET cc_start: 0.5984 (tmm) cc_final: 0.5611 (tmm) REVERT: D 275 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7738 (t80) REVERT: E 99 TYR cc_start: 0.8404 (m-80) cc_final: 0.8139 (m-80) REVERT: F 46 GLN cc_start: 0.8182 (tp40) cc_final: 0.7889 (mm-40) REVERT: F 279 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7708 (p90) REVERT: F 309 ASN cc_start: 0.8637 (p0) cc_final: 0.8356 (p0) REVERT: F 323 TYR cc_start: 0.8312 (t80) cc_final: 0.7793 (t80) outliers start: 57 outliers final: 38 residues processed: 277 average time/residue: 0.2699 time to fit residues: 113.7999 Evaluate side-chains 259 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 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 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 343 MET 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 279 ILE 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 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE 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 168 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 139 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.178408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.128936 restraints weight = 21301.966| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.45 r_work: 0.3589 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16446 Z= 0.127 Angle : 0.460 9.811 22200 Z= 0.247 Chirality : 0.038 0.196 2399 Planarity : 0.003 0.040 2678 Dihedral : 6.705 142.188 2256 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.26 % Allowed : 18.66 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 1845 helix: 2.06 (0.14), residues: 1323 sheet: 0.08 (0.51), residues: 107 loop : -1.13 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 23 HIS 0.013 0.001 HIS A 253 PHE 0.018 0.001 PHE E 250 TYR 0.013 0.001 TYR E 351 ARG 0.004 0.000 ARG E 389 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 1096) hydrogen bonds : angle 3.86571 ( 3234) SS BOND : bond 0.00238 ( 17) SS BOND : angle 0.93598 ( 34) covalent geometry : bond 0.00288 (16429) covalent geometry : angle 0.45839 (22166) *********************** 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 292 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7884 (tp30) cc_final: 0.7331 (tp30) REVERT: B 245 GLU cc_start: 0.8169 (tp30) cc_final: 0.7560 (tp30) REVERT: B 286 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8264 (t) REVERT: B 309 ARG cc_start: 0.8299 (tpp80) cc_final: 0.7867 (ttm-80) REVERT: C 37 MET cc_start: 0.8283 (mtt) cc_final: 0.6841 (tmm) REVERT: C 262 ARG cc_start: 0.6407 (mtm180) cc_final: 0.6112 (mtp-110) REVERT: C 308 TYR cc_start: 0.8836 (m-80) cc_final: 0.8290 (m-80) REVERT: C 337 MET cc_start: 0.6027 (tmm) cc_final: 0.5641 (tmm) REVERT: D 275 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7726 (t80) REVERT: E 99 TYR cc_start: 0.8443 (m-80) cc_final: 0.8171 (m-80) REVERT: E 115 GLU cc_start: 0.8225 (tp30) cc_final: 0.7982 (mm-30) REVERT: E 350 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7422 (pttp) REVERT: E 399 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6489 (mt-10) REVERT: F 279 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7717 (p90) REVERT: F 309 ASN cc_start: 0.8652 (p0) cc_final: 0.8362 (p0) REVERT: F 343 TYR cc_start: 0.6050 (t80) cc_final: 0.5849 (t80) outliers start: 57 outliers final: 38 residues processed: 276 average time/residue: 0.2571 time to fit residues: 109.2210 Evaluate side-chains 266 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 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 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 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 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 73 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 182 optimal weight: 0.4980 chunk 131 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.182393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.133191 restraints weight = 21426.642| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.42 r_work: 0.3674 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16446 Z= 0.136 Angle : 0.468 9.119 22200 Z= 0.252 Chirality : 0.038 0.164 2399 Planarity : 0.003 0.037 2678 Dihedral : 6.630 140.144 2256 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.21 % Allowed : 19.06 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 1845 helix: 2.07 (0.14), residues: 1323 sheet: 0.05 (0.51), residues: 107 loop : -1.14 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 23 HIS 0.012 0.001 HIS A 253 PHE 0.021 0.001 PHE A 250 TYR 0.014 0.001 TYR E 351 ARG 0.005 0.000 ARG E 389 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 1096) hydrogen bonds : angle 3.87995 ( 3234) SS BOND : bond 0.00241 ( 17) SS BOND : angle 0.99036 ( 34) covalent geometry : bond 0.00314 (16429) covalent geometry : angle 0.46693 (22166) *********************** 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: 56 poor density : 238 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8037 (tp30) cc_final: 0.7482 (tp30) REVERT: A 241 LYS cc_start: 0.7911 (tppt) cc_final: 0.7710 (tppt) REVERT: B 245 GLU cc_start: 0.8259 (tp30) cc_final: 0.7646 (tp30) REVERT: B 286 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8347 (t) REVERT: B 309 ARG cc_start: 0.8579 (tpp80) cc_final: 0.8128 (ttm-80) REVERT: B 375 MET cc_start: 0.8692 (mtm) cc_final: 0.8476 (mtm) REVERT: C 37 MET cc_start: 0.8388 (mtt) cc_final: 0.6977 (tmm) REVERT: C 308 TYR cc_start: 0.8910 (m-80) cc_final: 0.8390 (m-80) REVERT: D 249 LYS cc_start: 0.8617 (ptmt) cc_final: 0.8344 (ptmm) REVERT: D 250 PHE cc_start: 0.6580 (t80) cc_final: 0.6323 (t80) REVERT: D 275 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7893 (t80) REVERT: E 99 TYR cc_start: 0.8443 (m-80) cc_final: 0.8207 (m-80) REVERT: E 350 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7464 (pttp) REVERT: E 381 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7613 (mm-40) REVERT: E 399 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6490 (mt-10) REVERT: F 279 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7810 (p90) outliers start: 56 outliers final: 41 residues processed: 281 average time/residue: 0.2499 time to fit residues: 107.4742 Evaluate side-chains 270 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 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 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 379 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR 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 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 47 optimal weight: 0.0670 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 105 GLN D 287 HIS D 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.177191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127508 restraints weight = 21225.476| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.40 r_work: 0.3571 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16446 Z= 0.152 Angle : 0.489 8.852 22200 Z= 0.264 Chirality : 0.039 0.225 2399 Planarity : 0.003 0.034 2678 Dihedral : 6.679 139.245 2256 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.32 % Allowed : 19.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 1845 helix: 2.02 (0.14), residues: 1323 sheet: 0.05 (0.52), residues: 107 loop : -1.17 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 23 HIS 0.013 0.001 HIS A 253 PHE 0.026 0.001 PHE F 391 TYR 0.023 0.001 TYR C 382 ARG 0.005 0.000 ARG E 389 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 1096) hydrogen bonds : angle 3.91993 ( 3234) SS BOND : bond 0.00298 ( 17) SS BOND : angle 1.00403 ( 34) covalent geometry : bond 0.00355 (16429) covalent geometry : angle 0.48797 (22166) *********************** 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 291 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8037 (tp30) cc_final: 0.7467 (tp30) REVERT: B 245 GLU cc_start: 0.8262 (tp30) cc_final: 0.7643 (tp30) REVERT: B 286 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8352 (t) REVERT: B 309 ARG cc_start: 0.8606 (tpp80) cc_final: 0.8181 (ttm-80) REVERT: C 37 MET cc_start: 0.8463 (mtt) cc_final: 0.7019 (tmm) REVERT: C 308 TYR cc_start: 0.8939 (m-80) cc_final: 0.8387 (m-80) REVERT: D 155 HIS cc_start: 0.7213 (t-170) cc_final: 0.6893 (t-170) REVERT: D 249 LYS cc_start: 0.8621 (ptmt) cc_final: 0.8304 (ptmm) REVERT: D 275 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7913 (t80) REVERT: E 99 TYR cc_start: 0.8455 (m-80) cc_final: 0.8192 (m-80) REVERT: E 350 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7496 (pttp) REVERT: E 381 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7521 (mm-40) REVERT: F 145 TRP cc_start: 0.5859 (OUTLIER) cc_final: 0.4599 (t60) REVERT: F 279 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7895 (p90) REVERT: F 343 TYR cc_start: 0.6287 (t80) cc_final: 0.5162 (t80) outliers start: 58 outliers final: 43 residues processed: 282 average time/residue: 0.2509 time to fit residues: 109.8756 Evaluate side-chains 268 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 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 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 119 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 133 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 105 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.177384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127432 restraints weight = 21279.570| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.43 r_work: 0.3558 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16446 Z= 0.151 Angle : 0.500 9.043 22200 Z= 0.269 Chirality : 0.039 0.169 2399 Planarity : 0.003 0.032 2678 Dihedral : 6.595 137.570 2256 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.15 % Allowed : 19.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 1845 helix: 2.02 (0.14), residues: 1322 sheet: 0.05 (0.52), residues: 107 loop : -1.20 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP F 23 HIS 0.015 0.001 HIS A 253 PHE 0.024 0.001 PHE A 250 TYR 0.022 0.001 TYR C 382 ARG 0.005 0.000 ARG E 389 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 1096) hydrogen bonds : angle 3.93149 ( 3234) SS BOND : bond 0.00268 ( 17) SS BOND : angle 1.02590 ( 34) covalent geometry : bond 0.00352 (16429) covalent geometry : angle 0.49889 (22166) *********************** 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 283 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7825 (tp30) cc_final: 0.7256 (tp30) REVERT: B 245 GLU cc_start: 0.8165 (tp30) cc_final: 0.7536 (tp30) REVERT: B 286 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8281 (t) REVERT: B 309 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7934 (ttm-80) REVERT: C 37 MET cc_start: 0.8326 (mtt) cc_final: 0.6971 (tmm) REVERT: D 155 HIS cc_start: 0.7103 (t-170) cc_final: 0.6774 (t-170) REVERT: D 249 LYS cc_start: 0.8613 (ptmt) cc_final: 0.8296 (ptmm) REVERT: D 275 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7783 (t80) REVERT: E 99 TYR cc_start: 0.8364 (m-80) cc_final: 0.8099 (m-80) REVERT: E 350 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7532 (pttp) REVERT: E 381 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7410 (mm-40) REVERT: F 30 TYR cc_start: 0.8105 (m-80) cc_final: 0.7897 (m-80) REVERT: F 145 TRP cc_start: 0.5788 (OUTLIER) cc_final: 0.4524 (t60) REVERT: F 279 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7786 (p90) REVERT: F 323 TYR cc_start: 0.8196 (t80) cc_final: 0.7958 (t80) outliers start: 55 outliers final: 44 residues processed: 271 average time/residue: 0.2526 time to fit residues: 107.3283 Evaluate side-chains 269 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 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 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 116 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 105 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS E 155 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.177355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127726 restraints weight = 21303.254| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.40 r_work: 0.3572 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16446 Z= 0.146 Angle : 0.502 8.839 22200 Z= 0.269 Chirality : 0.039 0.257 2399 Planarity : 0.003 0.031 2678 Dihedral : 6.510 135.384 2256 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.09 % Allowed : 19.52 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 1845 helix: 2.03 (0.14), residues: 1322 sheet: 0.06 (0.52), residues: 107 loop : -1.17 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP F 23 HIS 0.016 0.001 HIS A 253 PHE 0.023 0.001 PHE A 250 TYR 0.015 0.001 TYR F 323 ARG 0.004 0.000 ARG E 389 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 1096) hydrogen bonds : angle 3.92431 ( 3234) SS BOND : bond 0.00258 ( 17) SS BOND : angle 1.02541 ( 34) covalent geometry : bond 0.00337 (16429) covalent geometry : angle 0.50029 (22166) ********************** 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 277 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 223 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7812 (tp30) cc_final: 0.7246 (tp30) REVERT: B 245 GLU cc_start: 0.8168 (tp30) cc_final: 0.7538 (tp30) REVERT: B 286 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8287 (t) REVERT: B 298 ASP cc_start: 0.7842 (t0) cc_final: 0.7372 (p0) REVERT: B 309 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7946 (ttm-80) REVERT: C 37 MET cc_start: 0.8333 (mtt) cc_final: 0.6980 (tmm) REVERT: D 155 HIS cc_start: 0.7108 (t-170) cc_final: 0.6757 (t-170) REVERT: D 249 LYS cc_start: 0.8599 (ptmt) cc_final: 0.8289 (ptmm) REVERT: D 275 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7852 (t80) REVERT: E 99 TYR cc_start: 0.8342 (m-80) cc_final: 0.8092 (m-80) REVERT: E 350 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7523 (pttp) REVERT: E 381 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7462 (mm-40) REVERT: F 30 TYR cc_start: 0.8075 (m-80) cc_final: 0.7844 (m-80) REVERT: F 145 TRP cc_start: 0.5775 (OUTLIER) cc_final: 0.4526 (t60) REVERT: F 279 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7788 (p90) REVERT: F 323 TYR cc_start: 0.8261 (t80) cc_final: 0.8030 (t80) outliers start: 54 outliers final: 45 residues processed: 267 average time/residue: 0.2391 time to fit residues: 99.9268 Evaluate side-chains 268 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 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 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 133 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 167 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 105 GLN D 105 GLN D 287 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.178500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129032 restraints weight = 21218.319| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.39 r_work: 0.3589 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2267 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= 0.126 Angle : 0.497 10.734 22200 Z= 0.266 Chirality : 0.038 0.173 2399 Planarity : 0.003 0.031 2678 Dihedral : 6.290 131.458 2256 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.03 % Allowed : 19.46 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 1845 helix: 2.07 (0.14), residues: 1322 sheet: 0.09 (0.52), residues: 107 loop : -1.14 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP F 23 HIS 0.020 0.001 HIS A 253 PHE 0.022 0.001 PHE A 250 TYR 0.013 0.001 TYR E 351 ARG 0.004 0.000 ARG E 389 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 1096) hydrogen bonds : angle 3.90023 ( 3234) SS BOND : bond 0.00227 ( 17) SS BOND : angle 0.95564 ( 34) covalent geometry : bond 0.00286 (16429) covalent geometry : angle 0.49594 (22166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9276.90 seconds wall clock time: 160 minutes 5.08 seconds (9605.08 seconds total)