Starting phenix.real_space_refine on Sun Aug 24 03:33:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8drk_27677/08_2025/8drk_27677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8drk_27677/08_2025/8drk_27677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8drk_27677/08_2025/8drk_27677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8drk_27677/08_2025/8drk_27677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8drk_27677/08_2025/8drk_27677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8drk_27677/08_2025/8drk_27677.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.085 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 9 5.49 5 S 106 5.16 5 C 10903 2.51 5 N 2556 2.21 5 O 2869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16443 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "C" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "D" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2646 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.08, per 1000 atoms: 0.25 Number of scatterers: 16443 At special positions: 0 Unit cell: (99.56, 105.848, 136.24, 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 9 15.00 O 2869 8.00 N 2556 7.00 C 10903 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=2.02 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 561.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3692 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 9 sheets defined 75.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 4.018A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.668A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.912A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.840A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 285 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 315 through 345 Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.527A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.109A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.783A 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 16 through 21 removed outlier: 3.595A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.640A 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 141 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.789A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 3.606A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 258 through 285 Processing helix chain 'B' and resid 286 through 289 Processing helix chain 'B' and resid 314 through 343 removed outlier: 3.906A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) 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 392 removed outlier: 4.208A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.010A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 141 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.705A pdb=" N LYS C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 3.690A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 175 removed outlier: 4.270A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 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 343 Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 369 through 383 removed outlier: 3.537A pdb=" N ALA C 373 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.068A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 410 Processing helix chain 'D' and resid 16 through 21 removed outlier: 4.254A 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 146 removed outlier: 3.565A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.005A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 3.905A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 removed outlier: 3.653A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 258 through 286 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 314 through 346 removed outlier: 3.942A 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: 4.006A 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 407 Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 141 Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.766A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 removed outlier: 3.761A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) 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 343 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 392 removed outlier: 4.005A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 410 Processing helix chain 'F' and resid 16 through 21 removed outlier: 4.344A pdb=" N VAL F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 48 removed outlier: 3.960A pdb=" N MET F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 3.707A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 168 removed outlier: 3.882A pdb=" N SER F 153 " --> pdb=" O PRO F 149 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.335A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 253 removed outlier: 3.627A pdb=" N GLU F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 284 removed outlier: 3.514A pdb=" N ALA F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 312 through 343 Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 368 through 381 Processing helix chain 'F' and resid 382 through 393 removed outlier: 3.718A pdb=" N LYS F 386 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 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: 3.720A pdb=" N VAL A 60 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.577A 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 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'D' and resid 350 through 351 removed outlier: 3.721A pdb=" N VAL D 368 " --> pdb=" O TYR D 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.556A pdb=" N LEU E 55 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 52 through 56 1085 hydrogen bonds defined for protein. 3201 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2761 1.33 - 1.45: 4646 1.45 - 1.57: 9280 1.57 - 1.69: 10 1.69 - 1.81: 161 Bond restraints: 16858 Sorted by residual: bond pdb=" C10 PEE A 902 " pdb=" O4 PEE A 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" C10 PEE E 902 " pdb=" O4 PEE E 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE D 902 " pdb=" O4 PEE D 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C10 PEE E 903 " pdb=" O4 PEE E 903 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 16853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 22345 2.77 - 5.54: 247 5.54 - 8.31: 59 8.31 - 11.08: 11 11.08 - 13.85: 15 Bond angle restraints: 22677 Sorted by residual: angle pdb=" O1P PEE F 904 " pdb=" P PEE F 904 " pdb=" O2P PEE F 904 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.26 -13.83 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE D 904 " pdb=" P PEE D 904 " pdb=" O2P PEE D 904 " 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 C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.20 -13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.18 -13.75 3.00e+00 1.11e-01 2.10e+01 ... (remaining 22672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 9715 35.96 - 71.93: 316 71.93 - 107.89: 24 107.89 - 143.85: 14 143.85 - 179.82: 16 Dihedral angle restraints: 10085 sinusoidal: 4381 harmonic: 5704 Sorted by residual: dihedral pdb=" CB CYS B 113 " pdb=" SG CYS B 113 " pdb=" SG CYS B 295 " pdb=" CB CYS B 295 " ideal model delta sinusoidal sigma weight residual 93.00 50.48 42.52 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" N PEE A 901 " pdb=" C4 PEE A 901 " pdb=" C5 PEE A 901 " pdb=" O4P PEE A 901 " ideal model delta sinusoidal sigma weight residual -56.97 122.85 -179.82 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N PEE B 901 " pdb=" C4 PEE B 901 " pdb=" C5 PEE B 901 " pdb=" O4P PEE B 901 " ideal model delta sinusoidal sigma weight residual -56.97 119.91 -176.88 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2293 0.084 - 0.167: 132 0.167 - 0.251: 1 0.251 - 0.335: 0 0.335 - 0.418: 10 Chirality restraints: 2436 Sorted by residual: chirality pdb=" C2 PEE B 904 " pdb=" C1 PEE B 904 " pdb=" C3 PEE B 904 " pdb=" O2 PEE B 904 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C3 PEE C 901 " pdb=" O2 PEE C 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 2433 not shown) Planarity restraints: 2714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 321 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C LEU D 321 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU D 321 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA D 322 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 244 " -0.013 2.00e-02 2.50e+03 1.82e-02 5.81e+00 pdb=" CG PHE A 244 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 244 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 244 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 244 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 244 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 244 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 324 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C PHE D 324 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE D 324 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR D 325 " -0.013 2.00e-02 2.50e+03 ... (remaining 2711 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1636 2.75 - 3.29: 16335 3.29 - 3.82: 28838 3.82 - 4.36: 33048 4.36 - 4.90: 57706 Nonbonded interactions: 137563 Sorted by model distance: nonbonded pdb=" O SER E 395 " pdb=" OG SER E 398 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" O MET F 300 " model vdw 2.213 3.040 nonbonded pdb=" O SER A 166 " pdb=" OG1 THR A 169 " model vdw 2.232 3.040 nonbonded pdb=" O SER D 166 " pdb=" OG1 THR D 169 " model vdw 2.233 3.040 nonbonded pdb=" O SER B 166 " pdb=" OG1 THR B 169 " model vdw 2.233 3.040 ... (remaining 137558 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 407 or (resid 901 through 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 407 or (resid 901 through 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 407 or (resid 901 through 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 'D' and (resid 15 through 407 or (resid 902 through 904 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 'E' and (resid 15 through 407 or (resid 901 through 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 )))) } 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: 4.980 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.480 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.006 0.152 16875 Z= 0.318 Angle : 0.839 13.848 22711 Z= 0.403 Chirality : 0.048 0.418 2436 Planarity : 0.005 0.056 2714 Dihedral : 19.554 179.817 6342 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.28 % Allowed : 16.62 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.19), residues: 1865 helix: 1.11 (0.14), residues: 1276 sheet: 0.24 (0.52), residues: 104 loop : -0.72 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 389 TYR 0.018 0.001 TYR B 281 PHE 0.037 0.002 PHE A 244 TRP 0.033 0.002 TRP D 168 HIS 0.009 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00641 (16858) covalent geometry : angle 0.83884 (22677) SS BOND : bond 0.00289 ( 17) SS BOND : angle 0.75448 ( 34) hydrogen bonds : bond 0.12346 ( 1085) hydrogen bonds : angle 6.01626 ( 3201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 338 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.7947 (tp30) cc_final: 0.7364 (tp30) REVERT: A 258 ASP cc_start: 0.8320 (p0) cc_final: 0.7905 (p0) REVERT: B 245 GLU cc_start: 0.7589 (tp30) cc_final: 0.7209 (tp30) REVERT: B 248 LYS cc_start: 0.8311 (mppt) cc_final: 0.8006 (mmtp) REVERT: C 29 ASP cc_start: 0.7859 (t0) cc_final: 0.7526 (t0) REVERT: D 244 PHE cc_start: 0.5627 (m-80) cc_final: 0.5157 (t80) REVERT: D 250 PHE cc_start: 0.7249 (t80) cc_final: 0.7045 (t80) REVERT: E 375 MET cc_start: 0.7691 (mtm) cc_final: 0.7326 (mtp) REVERT: E 393 PHE cc_start: 0.5975 (m-80) cc_final: 0.5181 (m-80) REVERT: F 148 PHE cc_start: 0.6999 (t80) cc_final: 0.6633 (t80) REVERT: F 154 LYS cc_start: 0.7786 (mttt) cc_final: 0.6945 (mmpt) REVERT: F 170 TRP cc_start: 0.6076 (t-100) cc_final: 0.5298 (t-100) REVERT: F 367 LYS cc_start: 0.7639 (ptmt) cc_final: 0.7158 (mttp) REVERT: F 386 LYS cc_start: 0.8400 (mtpp) cc_final: 0.8119 (mmtt) outliers start: 5 outliers final: 0 residues processed: 342 average time/residue: 0.5544 time to fit residues: 211.6797 Evaluate side-chains 220 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 116 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS E 409 ASN F 251 HIS F 305 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.172584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.125148 restraints weight = 19309.739| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.21 r_work: 0.3487 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16875 Z= 0.177 Angle : 0.521 9.075 22711 Z= 0.275 Chirality : 0.039 0.193 2436 Planarity : 0.004 0.049 2714 Dihedral : 16.733 179.005 2542 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.57 % Allowed : 19.46 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.19), residues: 1865 helix: 1.82 (0.14), residues: 1311 sheet: 0.56 (0.52), residues: 108 loop : -0.91 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 389 TYR 0.018 0.001 TYR C 281 PHE 0.023 0.002 PHE F 144 TRP 0.016 0.001 TRP E 168 HIS 0.006 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00409 (16858) covalent geometry : angle 0.51993 (22677) SS BOND : bond 0.00423 ( 17) SS BOND : angle 0.91587 ( 34) hydrogen bonds : bond 0.03990 ( 1085) hydrogen bonds : angle 4.20402 ( 3201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 254 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7735 (tp30) cc_final: 0.7327 (mp0) REVERT: A 258 ASP cc_start: 0.8255 (p0) cc_final: 0.7910 (p0) REVERT: B 245 GLU cc_start: 0.7960 (tp30) cc_final: 0.7419 (tp30) REVERT: B 246 LYS cc_start: 0.8017 (ttpp) cc_final: 0.7794 (mtpt) REVERT: B 372 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7825 (t80) REVERT: C 29 ASP cc_start: 0.8152 (t0) cc_final: 0.7714 (t0) REVERT: C 168 TRP cc_start: 0.7667 (t-100) cc_final: 0.7329 (t-100) REVERT: C 280 CYS cc_start: 0.8907 (m) cc_final: 0.8569 (m) REVERT: C 352 SER cc_start: 0.8075 (OUTLIER) cc_final: 0.7831 (p) REVERT: C 375 MET cc_start: 0.7841 (mtm) cc_final: 0.7569 (mtm) REVERT: D 59 TRP cc_start: 0.7450 (m-10) cc_final: 0.6988 (m100) REVERT: D 244 PHE cc_start: 0.5222 (m-80) cc_final: 0.4811 (t80) REVERT: D 353 PHE cc_start: 0.6586 (m-80) cc_final: 0.6239 (m-80) REVERT: D 396 GLU cc_start: 0.7214 (tp30) cc_final: 0.6034 (pt0) REVERT: E 18 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8025 (ttt-90) REVERT: E 144 PHE cc_start: 0.8631 (m-10) cc_final: 0.8326 (m-10) REVERT: E 164 PHE cc_start: 0.6878 (t80) cc_final: 0.6537 (t80) REVERT: E 243 LEU cc_start: 0.7614 (tt) cc_final: 0.7321 (mt) REVERT: E 306 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7602 (ttp-110) REVERT: E 309 ARG cc_start: 0.8429 (tpt170) cc_final: 0.8101 (ttt180) REVERT: E 371 ASP cc_start: 0.7599 (t0) cc_final: 0.7361 (t0) REVERT: F 58 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7896 (mtm110) REVERT: F 96 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7832 (mtp) REVERT: F 146 PHE cc_start: 0.7799 (m-10) cc_final: 0.7499 (m-80) REVERT: F 148 PHE cc_start: 0.6755 (t80) cc_final: 0.6523 (t80) REVERT: F 170 TRP cc_start: 0.6601 (t-100) cc_final: 0.5902 (t-100) REVERT: F 367 LYS cc_start: 0.7719 (ptmt) cc_final: 0.7324 (ptpp) REVERT: F 386 LYS cc_start: 0.8280 (mtpp) cc_final: 0.8004 (mptt) outliers start: 63 outliers final: 15 residues processed: 293 average time/residue: 0.4994 time to fit residues: 166.6915 Evaluate side-chains 243 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 90 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 408 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS F 309 ASN F 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.172195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.119908 restraints weight = 20019.023| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.43 r_work: 0.3433 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16875 Z= 0.242 Angle : 0.548 7.972 22711 Z= 0.291 Chirality : 0.041 0.148 2436 Planarity : 0.004 0.049 2714 Dihedral : 14.950 177.185 2542 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.31 % Allowed : 19.85 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.19), residues: 1865 helix: 1.83 (0.14), residues: 1306 sheet: 0.62 (0.53), residues: 108 loop : -1.08 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 389 TYR 0.016 0.002 TYR C 281 PHE 0.018 0.002 PHE B 353 TRP 0.014 0.002 TRP E 168 HIS 0.005 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00570 (16858) covalent geometry : angle 0.54708 (22677) SS BOND : bond 0.00486 ( 17) SS BOND : angle 1.05994 ( 34) hydrogen bonds : bond 0.04089 ( 1085) hydrogen bonds : angle 4.15156 ( 3201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 232 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7716 (tp30) cc_final: 0.7325 (mp0) REVERT: A 258 ASP cc_start: 0.8354 (p0) cc_final: 0.7800 (p0) REVERT: A 375 MET cc_start: 0.8496 (mtp) cc_final: 0.8269 (mtp) REVERT: B 162 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6795 (mptt) REVERT: B 245 GLU cc_start: 0.8017 (tp30) cc_final: 0.7472 (tp30) REVERT: B 246 LYS cc_start: 0.8014 (ttpp) cc_final: 0.7778 (mtpt) REVERT: B 365 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6529 (mm) REVERT: B 372 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7831 (t80) REVERT: C 29 ASP cc_start: 0.8154 (t0) cc_final: 0.7614 (t0) REVERT: C 158 SER cc_start: 0.8810 (t) cc_final: 0.8601 (p) REVERT: C 168 TRP cc_start: 0.7728 (t-100) cc_final: 0.7349 (t-100) REVERT: C 280 CYS cc_start: 0.9002 (m) cc_final: 0.8570 (m) REVERT: D 59 TRP cc_start: 0.7455 (m-10) cc_final: 0.7008 (m100) REVERT: D 117 ARG cc_start: 0.8454 (mmt-90) cc_final: 0.8236 (mmt-90) REVERT: D 244 PHE cc_start: 0.5167 (OUTLIER) cc_final: 0.4770 (t80) REVERT: D 353 PHE cc_start: 0.6861 (m-80) cc_final: 0.6601 (m-80) REVERT: D 386 TYR cc_start: 0.6930 (m-80) cc_final: 0.6701 (m-80) REVERT: D 396 GLU cc_start: 0.7307 (tp30) cc_final: 0.6139 (pt0) REVERT: E 144 PHE cc_start: 0.8623 (m-10) cc_final: 0.8355 (m-10) REVERT: E 160 LEU cc_start: 0.7080 (tp) cc_final: 0.6669 (tp) REVERT: E 164 PHE cc_start: 0.6980 (t80) cc_final: 0.6539 (t80) REVERT: E 255 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6803 (tp30) REVERT: E 275 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7691 (t80) REVERT: E 306 ARG cc_start: 0.8119 (mtm110) cc_final: 0.7828 (ttp-110) REVERT: E 309 ARG cc_start: 0.8419 (tpt170) cc_final: 0.8103 (ttt180) REVERT: F 18 ARG cc_start: 0.8426 (ttp-110) cc_final: 0.7971 (ttt-90) REVERT: F 58 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7900 (mtm110) REVERT: F 96 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7905 (mtp) REVERT: F 146 PHE cc_start: 0.7728 (m-10) cc_final: 0.7463 (m-80) REVERT: F 170 TRP cc_start: 0.6798 (t-100) cc_final: 0.6209 (t-100) REVERT: F 261 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6921 (tpp) REVERT: F 367 LYS cc_start: 0.8088 (ptmt) cc_final: 0.7386 (ptpp) REVERT: F 386 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7926 (mmtt) outliers start: 76 outliers final: 28 residues processed: 285 average time/residue: 0.4956 time to fit residues: 161.0948 Evaluate side-chains 250 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS E 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.174036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.126372 restraints weight = 19528.541| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.22 r_work: 0.3505 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16875 Z= 0.146 Angle : 0.475 8.886 22711 Z= 0.253 Chirality : 0.038 0.146 2436 Planarity : 0.003 0.045 2714 Dihedral : 13.308 167.737 2542 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.03 % Allowed : 20.99 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.19), residues: 1865 helix: 2.03 (0.14), residues: 1307 sheet: 0.76 (0.53), residues: 108 loop : -0.99 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 117 TYR 0.014 0.001 TYR C 281 PHE 0.020 0.001 PHE D 250 TRP 0.013 0.001 TRP E 168 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00334 (16858) covalent geometry : angle 0.47432 (22677) SS BOND : bond 0.00270 ( 17) SS BOND : angle 0.95058 ( 34) hydrogen bonds : bond 0.03553 ( 1085) hydrogen bonds : angle 3.93876 ( 3201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 228 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8776 (mp) cc_final: 0.8563 (mt) REVERT: A 154 GLU cc_start: 0.7513 (tp30) cc_final: 0.7155 (mp0) REVERT: A 245 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7947 (mm-30) REVERT: B 18 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7875 (ptt180) REVERT: B 232 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5878 (pt) REVERT: B 245 GLU cc_start: 0.7964 (tp30) cc_final: 0.7358 (tp30) REVERT: C 29 ASP cc_start: 0.8093 (t0) cc_final: 0.7467 (t0) REVERT: C 33 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8305 (mp) REVERT: C 168 TRP cc_start: 0.7658 (t-100) cc_final: 0.7259 (t-100) REVERT: C 243 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7755 (mm) REVERT: C 280 CYS cc_start: 0.8885 (m) cc_final: 0.8570 (m) REVERT: D 244 PHE cc_start: 0.5288 (OUTLIER) cc_final: 0.4999 (t80) REVERT: D 353 PHE cc_start: 0.6839 (m-80) cc_final: 0.6625 (m-80) REVERT: D 375 MET cc_start: 0.7922 (mtm) cc_final: 0.7553 (mpp) REVERT: D 396 GLU cc_start: 0.7011 (tp30) cc_final: 0.6128 (mt-10) REVERT: E 164 PHE cc_start: 0.7024 (t80) cc_final: 0.6750 (t80) REVERT: E 306 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7787 (ttp-110) REVERT: E 309 ARG cc_start: 0.8407 (tpt170) cc_final: 0.8107 (ttt180) REVERT: F 18 ARG cc_start: 0.8411 (ttp-110) cc_final: 0.7964 (ttt-90) REVERT: F 58 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7858 (mtm110) REVERT: F 96 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: F 146 PHE cc_start: 0.7696 (m-10) cc_final: 0.7459 (m-80) REVERT: F 170 TRP cc_start: 0.6817 (t-100) cc_final: 0.6364 (t-100) REVERT: F 264 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.5810 (mmt180) REVERT: F 367 LYS cc_start: 0.7980 (ptmt) cc_final: 0.7475 (ptpp) REVERT: F 381 ASP cc_start: 0.6596 (t0) cc_final: 0.6266 (t70) REVERT: F 386 LYS cc_start: 0.8355 (mtpp) cc_final: 0.8012 (mmtt) REVERT: F 388 PHE cc_start: 0.6339 (t80) cc_final: 0.5560 (t80) outliers start: 71 outliers final: 32 residues processed: 276 average time/residue: 0.4361 time to fit residues: 137.3599 Evaluate side-chains 252 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 168 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 102 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 167 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 134 optimal weight: 0.0020 chunk 117 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.180021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127487 restraints weight = 19802.163| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.45 r_work: 0.3548 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16875 Z= 0.112 Angle : 0.449 9.559 22711 Z= 0.239 Chirality : 0.037 0.146 2436 Planarity : 0.003 0.042 2714 Dihedral : 11.840 152.775 2542 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.25 % Allowed : 21.61 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.19), residues: 1865 helix: 2.27 (0.14), residues: 1306 sheet: 0.81 (0.53), residues: 110 loop : -0.92 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.013 0.001 TYR D 281 PHE 0.026 0.001 PHE D 250 TRP 0.016 0.001 TRP D 341 HIS 0.005 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00246 (16858) covalent geometry : angle 0.44781 (22677) SS BOND : bond 0.00204 ( 17) SS BOND : angle 0.91870 ( 34) hydrogen bonds : bond 0.03291 ( 1085) hydrogen bonds : angle 3.79442 ( 3201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 229 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7479 (tp30) cc_final: 0.7116 (mp0) REVERT: A 245 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 18 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7799 (ptt180) REVERT: B 162 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6807 (mmpt) REVERT: B 232 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5892 (pt) REVERT: B 245 GLU cc_start: 0.7886 (tp30) cc_final: 0.7274 (tp30) REVERT: B 320 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 365 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6443 (mm) REVERT: B 385 LEU cc_start: 0.8120 (tt) cc_final: 0.7873 (tm) REVERT: C 29 ASP cc_start: 0.7828 (t0) cc_final: 0.7176 (t0) REVERT: C 33 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8185 (mp) REVERT: C 160 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6782 (tp) REVERT: C 168 TRP cc_start: 0.7532 (t-100) cc_final: 0.7245 (t-100) REVERT: C 243 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7714 (mm) REVERT: C 280 CYS cc_start: 0.8742 (m) cc_final: 0.8428 (m) REVERT: D 244 PHE cc_start: 0.5348 (OUTLIER) cc_final: 0.5037 (t80) REVERT: D 294 ASP cc_start: 0.8455 (m-30) cc_final: 0.8173 (m-30) REVERT: D 309 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.8074 (ttm-80) REVERT: D 375 MET cc_start: 0.7687 (mtm) cc_final: 0.7450 (mtp) REVERT: D 396 GLU cc_start: 0.6953 (tp30) cc_final: 0.6079 (mt-10) REVERT: D 405 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5936 (pp) REVERT: E 164 PHE cc_start: 0.6896 (t80) cc_final: 0.6618 (t80) REVERT: E 306 ARG cc_start: 0.7891 (mtm110) cc_final: 0.7418 (ttp-110) REVERT: F 18 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.8029 (ttt-90) REVERT: F 58 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7902 (mtm110) REVERT: F 96 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7658 (mtp) REVERT: F 146 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: F 170 TRP cc_start: 0.6783 (t-100) cc_final: 0.6448 (t-100) REVERT: F 367 LYS cc_start: 0.7973 (ptmt) cc_final: 0.7486 (ptpp) REVERT: F 381 ASP cc_start: 0.6407 (t0) cc_final: 0.6121 (t70) REVERT: F 386 LYS cc_start: 0.8343 (mtpp) cc_final: 0.8053 (mmtt) REVERT: F 388 PHE cc_start: 0.5787 (t80) cc_final: 0.5410 (t80) outliers start: 75 outliers final: 33 residues processed: 279 average time/residue: 0.4252 time to fit residues: 135.9010 Evaluate side-chains 257 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 146 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS E 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.175277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123644 restraints weight = 19612.718| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.44 r_work: 0.3480 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16875 Z= 0.126 Angle : 0.460 9.545 22711 Z= 0.245 Chirality : 0.038 0.151 2436 Planarity : 0.003 0.041 2714 Dihedral : 10.903 133.909 2542 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.74 % Allowed : 22.46 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.19), residues: 1865 helix: 2.34 (0.14), residues: 1306 sheet: 1.08 (0.54), residues: 106 loop : -0.90 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 118 TYR 0.014 0.001 TYR C 284 PHE 0.029 0.001 PHE D 250 TRP 0.024 0.001 TRP E 143 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00283 (16858) covalent geometry : angle 0.45888 (22677) SS BOND : bond 0.00225 ( 17) SS BOND : angle 0.92745 ( 34) hydrogen bonds : bond 0.03291 ( 1085) hydrogen bonds : angle 3.75612 ( 3201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 224 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7482 (tp30) cc_final: 0.7103 (mp0) REVERT: A 245 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8014 (mm-30) REVERT: A 258 ASP cc_start: 0.8044 (p0) cc_final: 0.7727 (p0) REVERT: A 358 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: B 18 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7815 (ptt180) REVERT: B 162 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6862 (mmpt) REVERT: B 232 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6004 (pt) REVERT: B 245 GLU cc_start: 0.7848 (tp30) cc_final: 0.7220 (tp30) REVERT: B 320 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8410 (mp) REVERT: C 29 ASP cc_start: 0.7834 (t0) cc_final: 0.7175 (t0) REVERT: C 33 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8199 (mp) REVERT: C 168 TRP cc_start: 0.7548 (t-100) cc_final: 0.7284 (t-100) REVERT: C 243 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7737 (mm) REVERT: C 280 CYS cc_start: 0.8686 (m) cc_final: 0.8336 (m) REVERT: D 244 PHE cc_start: 0.5152 (OUTLIER) cc_final: 0.4826 (t80) REVERT: D 309 ARG cc_start: 0.8341 (tpp-160) cc_final: 0.8015 (ttm-80) REVERT: D 353 PHE cc_start: 0.5886 (m-80) cc_final: 0.5201 (OUTLIER) REVERT: D 354 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6334 (mp0) REVERT: D 396 GLU cc_start: 0.6847 (tp30) cc_final: 0.5933 (mt-10) REVERT: D 405 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5920 (pp) REVERT: E 164 PHE cc_start: 0.6932 (t80) cc_final: 0.6621 (t80) REVERT: E 275 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7015 (t80) REVERT: E 306 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7431 (ttp-110) REVERT: F 18 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.8089 (ttt-90) REVERT: F 58 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7852 (mtm110) REVERT: F 96 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7673 (mtp) REVERT: F 146 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: F 367 LYS cc_start: 0.7955 (ptmt) cc_final: 0.7679 (ptpp) REVERT: F 381 ASP cc_start: 0.6407 (t0) cc_final: 0.6144 (t70) REVERT: F 386 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8155 (mmtt) outliers start: 66 outliers final: 37 residues processed: 267 average time/residue: 0.3972 time to fit residues: 122.2818 Evaluate side-chains 266 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 180 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.177801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.125178 restraints weight = 19863.973| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.43 r_work: 0.3508 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16875 Z= 0.173 Angle : 0.503 9.786 22711 Z= 0.266 Chirality : 0.039 0.162 2436 Planarity : 0.003 0.040 2714 Dihedral : 10.859 140.058 2542 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.14 % Allowed : 22.01 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.19), residues: 1865 helix: 2.25 (0.14), residues: 1306 sheet: 0.66 (0.53), residues: 110 loop : -0.91 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 118 TYR 0.017 0.001 TYR E 264 PHE 0.032 0.001 PHE E 144 TRP 0.029 0.002 TRP E 143 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00403 (16858) covalent geometry : angle 0.50210 (22677) SS BOND : bond 0.00324 ( 17) SS BOND : angle 1.03753 ( 34) hydrogen bonds : bond 0.03498 ( 1085) hydrogen bonds : angle 3.84583 ( 3201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 216 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7464 (tp30) cc_final: 0.7132 (mp0) REVERT: A 245 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8075 (mm-30) REVERT: A 258 ASP cc_start: 0.8022 (p0) cc_final: 0.7743 (p0) REVERT: A 375 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8117 (ptp) REVERT: B 18 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7958 (ptt180) REVERT: B 162 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6859 (mmpt) REVERT: B 245 GLU cc_start: 0.7809 (tp30) cc_final: 0.7154 (tp30) REVERT: B 320 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8450 (mp) REVERT: C 29 ASP cc_start: 0.7828 (t0) cc_final: 0.7153 (t0) REVERT: C 33 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8162 (mp) REVERT: C 168 TRP cc_start: 0.7479 (t-100) cc_final: 0.7228 (t-100) REVERT: C 280 CYS cc_start: 0.8789 (m) cc_final: 0.8404 (m) REVERT: D 244 PHE cc_start: 0.5183 (OUTLIER) cc_final: 0.4894 (t80) REVERT: D 309 ARG cc_start: 0.8364 (tpp-160) cc_final: 0.8121 (ttm-80) REVERT: D 396 GLU cc_start: 0.6919 (tp30) cc_final: 0.5993 (mt-10) REVERT: D 405 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5948 (pp) REVERT: E 164 PHE cc_start: 0.6938 (t80) cc_final: 0.6615 (t80) REVERT: E 275 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7449 (t80) REVERT: E 306 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7479 (ttp-110) REVERT: F 18 ARG cc_start: 0.8594 (ttp-110) cc_final: 0.8235 (ttt-90) REVERT: F 58 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7875 (mtm110) REVERT: F 96 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7718 (mtp) REVERT: F 146 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: F 264 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.5670 (mmt180) REVERT: F 367 LYS cc_start: 0.8106 (ptmt) cc_final: 0.7629 (ptpp) REVERT: F 386 LYS cc_start: 0.8441 (mtpp) cc_final: 0.8149 (mmtt) REVERT: F 388 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.5280 (t80) outliers start: 73 outliers final: 43 residues processed: 268 average time/residue: 0.4322 time to fit residues: 132.2180 Evaluate side-chains 260 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 388 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 33 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.174487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122756 restraints weight = 19732.821| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.43 r_work: 0.3468 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16875 Z= 0.142 Angle : 0.491 10.079 22711 Z= 0.260 Chirality : 0.039 0.164 2436 Planarity : 0.003 0.040 2714 Dihedral : 10.433 138.165 2542 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.25 % Allowed : 22.80 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.19), residues: 1865 helix: 2.29 (0.14), residues: 1306 sheet: 0.91 (0.53), residues: 106 loop : -0.87 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 118 TYR 0.018 0.001 TYR E 264 PHE 0.048 0.001 PHE E 250 TRP 0.036 0.002 TRP E 143 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00325 (16858) covalent geometry : angle 0.49021 (22677) SS BOND : bond 0.00247 ( 17) SS BOND : angle 1.00076 ( 34) hydrogen bonds : bond 0.03329 ( 1085) hydrogen bonds : angle 3.82021 ( 3201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 217 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7433 (tp30) cc_final: 0.7128 (mp0) REVERT: A 245 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8062 (mm-30) REVERT: A 258 ASP cc_start: 0.8003 (p0) cc_final: 0.7730 (p0) REVERT: A 365 ILE cc_start: 0.7971 (mt) cc_final: 0.7757 (mt) REVERT: B 162 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6874 (mmpt) REVERT: B 232 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6152 (pt) REVERT: B 245 GLU cc_start: 0.7787 (tp30) cc_final: 0.7173 (tp30) REVERT: B 246 LYS cc_start: 0.8248 (ttpt) cc_final: 0.8005 (ttpt) REVERT: B 320 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8463 (mp) REVERT: C 29 ASP cc_start: 0.7818 (t0) cc_final: 0.7131 (t0) REVERT: C 33 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8194 (mp) REVERT: C 168 TRP cc_start: 0.7480 (t-100) cc_final: 0.7253 (t-100) REVERT: C 243 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7698 (mm) REVERT: C 280 CYS cc_start: 0.8667 (m) cc_final: 0.8332 (m) REVERT: D 244 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.4902 (t80) REVERT: D 309 ARG cc_start: 0.8358 (tpp-160) cc_final: 0.8113 (ttm-80) REVERT: D 396 GLU cc_start: 0.6935 (tp30) cc_final: 0.6021 (mt-10) REVERT: D 405 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5960 (pp) REVERT: E 164 PHE cc_start: 0.6947 (t80) cc_final: 0.6666 (t80) REVERT: E 255 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6740 (tp30) REVERT: E 275 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7269 (t80) REVERT: E 306 ARG cc_start: 0.7863 (mtm110) cc_final: 0.7461 (ttp-110) REVERT: F 18 ARG cc_start: 0.8581 (ttp-110) cc_final: 0.8243 (ttt-90) REVERT: F 58 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7874 (mtm110) REVERT: F 96 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7656 (mtp) REVERT: F 146 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: F 386 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8127 (mmtt) REVERT: F 388 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.5260 (t80) outliers start: 75 outliers final: 43 residues processed: 271 average time/residue: 0.4615 time to fit residues: 143.7551 Evaluate side-chains 264 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 388 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 7 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 160 optimal weight: 0.5980 chunk 159 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS C 49 GLN C 253 HIS D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.174406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122746 restraints weight = 19730.642| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.44 r_work: 0.3463 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16875 Z= 0.142 Angle : 0.494 10.015 22711 Z= 0.263 Chirality : 0.038 0.162 2436 Planarity : 0.003 0.039 2714 Dihedral : 10.263 138.495 2542 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.63 % Allowed : 23.48 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.19), residues: 1865 helix: 2.26 (0.14), residues: 1307 sheet: 0.91 (0.53), residues: 106 loop : -0.84 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 118 TYR 0.018 0.001 TYR E 281 PHE 0.034 0.001 PHE D 250 TRP 0.043 0.002 TRP F 170 HIS 0.010 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00326 (16858) covalent geometry : angle 0.49307 (22677) SS BOND : bond 0.00250 ( 17) SS BOND : angle 1.01193 ( 34) hydrogen bonds : bond 0.03345 ( 1085) hydrogen bonds : angle 3.81543 ( 3201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 207 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7401 (tp30) cc_final: 0.7067 (mp0) REVERT: A 245 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8067 (mm-30) REVERT: A 258 ASP cc_start: 0.7880 (p0) cc_final: 0.7600 (p0) REVERT: A 358 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8209 (mm-30) REVERT: B 162 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6898 (mmpt) REVERT: B 245 GLU cc_start: 0.7785 (tp30) cc_final: 0.7111 (tp30) REVERT: B 246 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7955 (ttpt) REVERT: B 320 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8432 (mp) REVERT: C 29 ASP cc_start: 0.7804 (t0) cc_final: 0.7105 (t0) REVERT: C 33 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8121 (mp) REVERT: C 168 TRP cc_start: 0.7456 (t-100) cc_final: 0.7252 (t-100) REVERT: C 280 CYS cc_start: 0.8710 (m) cc_final: 0.8359 (m) REVERT: D 244 PHE cc_start: 0.5162 (OUTLIER) cc_final: 0.4875 (t80) REVERT: D 284 TYR cc_start: 0.8284 (t80) cc_final: 0.7957 (t80) REVERT: D 309 ARG cc_start: 0.8379 (tpp-160) cc_final: 0.8134 (ttm-80) REVERT: D 396 GLU cc_start: 0.6945 (tp30) cc_final: 0.6007 (mt-10) REVERT: D 405 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5977 (pp) REVERT: E 164 PHE cc_start: 0.6903 (t80) cc_final: 0.6612 (t80) REVERT: E 275 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7354 (t80) REVERT: E 306 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7459 (ttp-110) REVERT: F 18 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8242 (ttt-90) REVERT: F 58 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7871 (mtm110) REVERT: F 96 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7623 (mtp) REVERT: F 146 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: F 264 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.5640 (mmt180) REVERT: F 381 ASP cc_start: 0.6554 (t70) cc_final: 0.6297 (t0) REVERT: F 386 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8136 (mmtt) outliers start: 64 outliers final: 43 residues processed: 254 average time/residue: 0.4542 time to fit residues: 132.4732 Evaluate side-chains 260 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 13 optimal weight: 0.5980 chunk 170 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 124 optimal weight: 0.0000 chunk 181 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 253 HIS D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.173647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124468 restraints weight = 19644.410| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.34 r_work: 0.3495 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16875 Z= 0.123 Angle : 0.487 10.156 22711 Z= 0.259 Chirality : 0.038 0.170 2436 Planarity : 0.003 0.040 2714 Dihedral : 9.960 136.124 2542 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.23 % Allowed : 23.94 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.19), residues: 1865 helix: 2.33 (0.14), residues: 1308 sheet: 0.98 (0.53), residues: 106 loop : -0.79 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 118 TYR 0.018 0.001 TYR C 284 PHE 0.035 0.001 PHE D 250 TRP 0.059 0.002 TRP F 170 HIS 0.011 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00275 (16858) covalent geometry : angle 0.48576 (22677) SS BOND : bond 0.00222 ( 17) SS BOND : angle 0.99748 ( 34) hydrogen bonds : bond 0.03202 ( 1085) hydrogen bonds : angle 3.76694 ( 3201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7541 (tp30) cc_final: 0.7098 (mp0) REVERT: A 245 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8185 (mm-30) REVERT: A 258 ASP cc_start: 0.8112 (p0) cc_final: 0.7832 (p0) REVERT: A 358 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8207 (mm-30) REVERT: A 365 ILE cc_start: 0.7962 (mt) cc_final: 0.7754 (mt) REVERT: B 162 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6893 (mmpt) REVERT: B 171 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7541 (ptm-80) REVERT: B 245 GLU cc_start: 0.7872 (tp30) cc_final: 0.7167 (tp30) REVERT: B 246 LYS cc_start: 0.8224 (ttpt) cc_final: 0.8000 (ttpt) REVERT: B 320 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8537 (mp) REVERT: C 29 ASP cc_start: 0.8069 (t0) cc_final: 0.7393 (t0) REVERT: C 33 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8274 (mp) REVERT: C 243 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7735 (mm) REVERT: C 280 CYS cc_start: 0.8760 (m) cc_final: 0.8461 (m) REVERT: D 244 PHE cc_start: 0.5189 (OUTLIER) cc_final: 0.4901 (t80) REVERT: D 309 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8445 (ttm-80) REVERT: D 396 GLU cc_start: 0.6897 (tp30) cc_final: 0.5979 (mt-10) REVERT: D 405 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.6001 (pp) REVERT: E 164 PHE cc_start: 0.6800 (t80) cc_final: 0.6491 (t80) REVERT: E 248 LYS cc_start: 0.7539 (tttt) cc_final: 0.6882 (pttt) REVERT: E 266 ARG cc_start: 0.7708 (mpt-90) cc_final: 0.7451 (mpp80) REVERT: E 275 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7202 (t80) REVERT: E 306 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7743 (ttp-110) REVERT: F 18 ARG cc_start: 0.8570 (ttp-110) cc_final: 0.8242 (ttt-90) REVERT: F 58 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7896 (mtm110) REVERT: F 96 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7731 (mtp) REVERT: F 146 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: F 386 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8207 (mmtt) outliers start: 57 outliers final: 33 residues processed: 258 average time/residue: 0.4844 time to fit residues: 143.6468 Evaluate side-chains 253 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 45 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN C 49 GLN C 253 HIS D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.175141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123597 restraints weight = 19654.505| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.44 r_work: 0.3477 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16875 Z= 0.138 Angle : 0.503 10.230 22711 Z= 0.267 Chirality : 0.039 0.184 2436 Planarity : 0.003 0.040 2714 Dihedral : 9.940 135.165 2542 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.06 % Allowed : 24.05 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.19), residues: 1865 helix: 2.31 (0.14), residues: 1308 sheet: 0.97 (0.53), residues: 106 loop : -0.79 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 118 TYR 0.018 0.001 TYR E 281 PHE 0.035 0.001 PHE D 250 TRP 0.064 0.002 TRP F 170 HIS 0.011 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00314 (16858) covalent geometry : angle 0.50204 (22677) SS BOND : bond 0.00232 ( 17) SS BOND : angle 0.98923 ( 34) hydrogen bonds : bond 0.03297 ( 1085) hydrogen bonds : angle 3.78471 ( 3201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5318.29 seconds wall clock time: 91 minutes 46.46 seconds (5506.46 seconds total)