Starting phenix.real_space_refine on Fri Jul 3 22:39:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8drk_27677/07_2026/8drk_27677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8drk_27677/07_2026/8drk_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_27677/07_2026/8drk_27677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8drk_27677/07_2026/8drk_27677.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8drk_27677/07_2026/8drk_27677.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8drk_27677/07_2026/8drk_27677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8drk_27677/07_2026/8drk_27677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8drk_27677/07_2026/8drk_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-dev-6108/lib/python3.11/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: 65 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: 69 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: 65 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: 67 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: 67 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: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.89, per 1000 atoms: 0.24 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: 1.25 Conformation dependent library (CDL) restraints added in 599.6 milliseconds 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: 0.41 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: 2.70 Time building geometry restraints manager: 1.73 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: 9665 35.96 - 71.93: 297 71.93 - 107.89: 11 107.89 - 143.85: 8 143.85 - 179.82: 14 Dihedral angle restraints: 9995 sinusoidal: 4291 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 9992 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: 6.540 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.300 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:8.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 18.327 179.817 6252 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 are 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/Z covalent geometry : bond 0.00641 / 0.32 (16858) covalent geometry : angle 0.83884 / 0.40 (22677) SS BOND : bond 0.00289 / 0.18 ( 17) SS BOND : angle 0.75448 / 0.46 ( 34) hydrogen bonds : bond 0.12346 / 7.99 ( 1085) hydrogen bonds : angle 6.01626 / 4.31 ( 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 : 0.498 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: 0.5413 time to fit residues: 207.7252 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 : 0.633 ------------------------------------------------------------------------------- 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... 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 = 0.4208 r_free = 0.4208 target = 0.172470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.124698 restraints weight = 19311.910| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.23 r_work: 0.3480 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1907 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= 0.179 Angle : 0.518 9.299 22711 Z= 0.275 Chirality : 0.039 0.190 2436 Planarity : 0.004 0.049 2714 Dihedral : 15.332 178.910 2452 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.69 % Allowed : 19.40 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.19), residues: 1865 helix: 1.84 (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 0.024 0.002 PHE F 144 TRP 0.016 0.002 TRP E 168 HIS 0.006 0.001 HIS F 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (16858) covalent geometry : angle 0.51746 / 0.27 (22677) SS BOND : bond 0.00747 / 0.56 ( 17) SS BOND : angle 0.85733 / 0.55 ( 34) hydrogen bonds : bond 0.03944 / 2.59 ( 1085) hydrogen bonds : angle 4.18767 / 2.98 ( 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: 65 poor density : 252 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7806 (tp30) cc_final: 0.7358 (mp0) REVERT: A 258 ASP cc_start: 0.8218 (p0) cc_final: 0.7886 (p0) REVERT: B 245 GLU cc_start: 0.7960 (tp30) cc_final: 0.7437 (tp30) REVERT: B 246 LYS cc_start: 0.8020 (ttpp) cc_final: 0.7803 (mtpt) REVERT: C 29 ASP cc_start: 0.8146 (t0) cc_final: 0.7707 (t0) REVERT: C 103 ARG cc_start: 0.8218 (ttt-90) cc_final: 0.7578 (tpp-160) REVERT: C 168 TRP cc_start: 0.7688 (t-100) cc_final: 0.7336 (t-100) REVERT: C 280 CYS cc_start: 0.8919 (m) cc_final: 0.8586 (m) REVERT: C 352 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.7840 (p) REVERT: C 375 MET cc_start: 0.7819 (mtm) cc_final: 0.7561 (mtm) REVERT: D 59 TRP cc_start: 0.7466 (m-10) cc_final: 0.6997 (m100) REVERT: D 244 PHE cc_start: 0.5215 (m-80) cc_final: 0.4813 (t80) REVERT: D 353 PHE cc_start: 0.6569 (m-80) cc_final: 0.6238 (m-80) REVERT: D 396 GLU cc_start: 0.7209 (tp30) cc_final: 0.6024 (pt0) REVERT: E 18 ARG cc_start: 0.8389 (ttp80) cc_final: 0.8027 (ttt-90) REVERT: E 144 PHE cc_start: 0.8624 (m-10) cc_final: 0.8362 (m-10) REVERT: E 164 PHE cc_start: 0.6889 (t80) cc_final: 0.6557 (t80) REVERT: E 243 LEU cc_start: 0.7617 (tt) cc_final: 0.7324 (mt) REVERT: E 306 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7617 (ttp-110) REVERT: E 309 ARG cc_start: 0.8427 (tpt170) cc_final: 0.8091 (ttt180) REVERT: E 371 ASP cc_start: 0.7597 (t0) cc_final: 0.7347 (t0) REVERT: F 58 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7896 (mtm110) REVERT: F 146 PHE cc_start: 0.7801 (m-10) cc_final: 0.7491 (m-80) REVERT: F 148 PHE cc_start: 0.6756 (t80) cc_final: 0.6520 (t80) REVERT: F 170 TRP cc_start: 0.6539 (t-100) cc_final: 0.5849 (t-100) REVERT: F 367 LYS cc_start: 0.7726 (ptmt) cc_final: 0.7330 (ptpp) REVERT: F 386 LYS cc_start: 0.8280 (mtpp) cc_final: 0.8008 (mptt) outliers start: 65 outliers final: 15 residues processed: 292 average time/residue: 0.4399 time to fit residues: 147.0095 Evaluate side-chains 240 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 47 VAL 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 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: 0.0970 chunk 113 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 116 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS F 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.176197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.123449 restraints weight = 19908.546| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.46 r_work: 0.3477 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16875 Z= 0.172 Angle : 0.489 8.110 22711 Z= 0.261 Chirality : 0.039 0.148 2436 Planarity : 0.003 0.047 2714 Dihedral : 13.329 179.140 2452 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.80 % Allowed : 20.14 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.19), residues: 1865 helix: 2.01 (0.14), residues: 1304 sheet: 0.70 (0.53), residues: 108 loop : -0.90 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 117 TYR 0.017 0.001 TYR C 281 PHE 0.015 0.001 PHE F 144 TRP 0.014 0.001 TRP E 168 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (16858) covalent geometry : angle 0.48793 / 0.26 (22677) SS BOND : bond 0.00367 / 0.25 ( 17) SS BOND : angle 0.95526 / 0.62 ( 34) hydrogen bonds : bond 0.03722 / 2.44 ( 1085) hydrogen bonds : angle 4.00409 / 2.84 ( 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 301 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 234 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8270 (tp30) cc_final: 0.7707 (tp30) REVERT: A 154 GLU cc_start: 0.7562 (tp30) cc_final: 0.7277 (mp0) REVERT: A 258 ASP cc_start: 0.8246 (p0) cc_final: 0.7894 (p0) REVERT: B 162 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6714 (mptt) REVERT: B 232 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6020 (pt) REVERT: B 245 GLU cc_start: 0.7915 (tp30) cc_final: 0.7369 (tp30) REVERT: B 246 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7760 (mtpt) REVERT: C 29 ASP cc_start: 0.7896 (t0) cc_final: 0.7335 (t0) REVERT: C 103 ARG cc_start: 0.7992 (ttt-90) cc_final: 0.7452 (tpp-160) REVERT: C 168 TRP cc_start: 0.7667 (t-100) cc_final: 0.7310 (t-100) REVERT: C 280 CYS cc_start: 0.8750 (m) cc_final: 0.8399 (m) REVERT: D 117 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7924 (tpp-160) REVERT: D 244 PHE cc_start: 0.5214 (m-80) cc_final: 0.4783 (t80) REVERT: D 309 ARG cc_start: 0.8400 (tpp-160) cc_final: 0.8159 (ttm-80) REVERT: D 396 GLU cc_start: 0.7282 (tp30) cc_final: 0.6153 (pt0) REVERT: E 18 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8046 (ttt-90) REVERT: E 144 PHE cc_start: 0.8548 (m-10) cc_final: 0.8324 (m-10) REVERT: E 164 PHE cc_start: 0.6949 (t80) cc_final: 0.6622 (t80) REVERT: E 306 ARG cc_start: 0.7871 (mtm110) cc_final: 0.7521 (ttp-110) REVERT: F 18 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.7982 (ttt-90) REVERT: F 58 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7868 (mtm110) REVERT: F 96 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7721 (mtp) REVERT: F 146 PHE cc_start: 0.7559 (m-10) cc_final: 0.7258 (m-80) REVERT: F 170 TRP cc_start: 0.6549 (t-100) cc_final: 0.5898 (t-100) REVERT: F 367 LYS cc_start: 0.7979 (ptmt) cc_final: 0.7349 (ptpp) REVERT: F 386 LYS cc_start: 0.8259 (mtpp) cc_final: 0.7931 (mmtt) outliers start: 67 outliers final: 22 residues processed: 279 average time/residue: 0.4590 time to fit residues: 147.1806 Evaluate side-chains 247 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 402 LEU 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 246 LYS Chi-restraints excluded: chain C residue 20 LEU 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 314 LEU Chi-restraints excluded: chain D residue 253 HIS 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 330 ILE Chi-restraints excluded: chain E residue 379 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 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: 1.9990 chunk 89 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 158 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 408 ASN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 309 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.176565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.128270 restraints weight = 19650.280| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.25 r_work: 0.3534 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16875 Z= 0.144 Angle : 0.468 8.844 22711 Z= 0.249 Chirality : 0.038 0.142 2436 Planarity : 0.003 0.044 2714 Dihedral : 11.388 172.909 2452 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.63 % Allowed : 20.93 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 1865 helix: 2.15 (0.14), residues: 1306 sheet: 0.85 (0.53), residues: 108 loop : -0.91 (0.28), residues: 451 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 0.014 0.001 PHE C 324 TRP 0.012 0.001 TRP E 168 HIS 0.005 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (16858) covalent geometry : angle 0.46673 / 0.25 (22677) SS BOND : bond 0.00257 / 0.17 ( 17) SS BOND : angle 0.95412 / 0.61 ( 34) hydrogen bonds : bond 0.03490 / 2.28 ( 1085) hydrogen bonds : angle 3.87998 / 2.75 ( 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: 64 poor density : 235 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7670 (tp30) cc_final: 0.7259 (mp0) REVERT: A 245 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7859 (mm-30) REVERT: A 258 ASP cc_start: 0.8348 (p0) cc_final: 0.7991 (p0) REVERT: B 245 GLU cc_start: 0.7995 (tp30) cc_final: 0.7351 (tp30) REVERT: B 365 ILE cc_start: 0.6628 (OUTLIER) cc_final: 0.6407 (mm) REVERT: C 29 ASP cc_start: 0.8075 (t0) cc_final: 0.7465 (t0) REVERT: C 33 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8285 (mp) REVERT: C 103 ARG cc_start: 0.8218 (ttt-90) cc_final: 0.7601 (tpp-160) REVERT: C 168 TRP cc_start: 0.7650 (t-100) cc_final: 0.7190 (t-100) REVERT: C 243 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7768 (mm) REVERT: C 280 CYS cc_start: 0.8951 (m) cc_final: 0.8642 (m) REVERT: D 117 ARG cc_start: 0.8278 (mmt-90) cc_final: 0.8063 (tpp-160) REVERT: D 244 PHE cc_start: 0.5207 (OUTLIER) cc_final: 0.4837 (t80) REVERT: D 309 ARG cc_start: 0.8665 (tpp-160) cc_final: 0.8366 (ttm-80) REVERT: D 353 PHE cc_start: 0.6145 (m-80) cc_final: 0.5913 (OUTLIER) REVERT: D 396 GLU cc_start: 0.7003 (tp30) cc_final: 0.6115 (mt-10) REVERT: E 18 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8110 (ttt-90) REVERT: E 164 PHE cc_start: 0.7046 (t80) cc_final: 0.6741 (t80) REVERT: E 275 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7212 (t80) REVERT: E 306 ARG cc_start: 0.8137 (mtm110) cc_final: 0.7777 (ttp-110) REVERT: F 18 ARG cc_start: 0.8436 (ttp-110) cc_final: 0.8041 (ttt-90) REVERT: F 58 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7892 (mtm110) REVERT: F 96 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7939 (mtp) REVERT: F 146 PHE cc_start: 0.7624 (m-10) cc_final: 0.7343 (m-80) REVERT: F 170 TRP cc_start: 0.6729 (t-100) cc_final: 0.6258 (t-100) REVERT: F 261 MET cc_start: 0.7408 (tpp) cc_final: 0.6907 (tpp) REVERT: F 357 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6738 (mp0) REVERT: F 367 LYS cc_start: 0.7939 (ptmt) cc_final: 0.7304 (mttp) REVERT: F 386 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7999 (mmtt) REVERT: F 388 PHE cc_start: 0.6240 (t80) cc_final: 0.5596 (t80) outliers start: 64 outliers final: 31 residues processed: 279 average time/residue: 0.4502 time to fit residues: 143.6797 Evaluate side-chains 259 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 327 SER 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 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 314 LEU Chi-restraints excluded: chain C residue 352 SER 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 47 VAL Chi-restraints excluded: chain E residue 134 LEU 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 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 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 168 optimal weight: 0.0470 chunk 166 optimal weight: 7.9990 chunk 16 optimal weight: 0.0870 chunk 102 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN C 105 GLN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.174301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124746 restraints weight = 19575.958| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.33 r_work: 0.3507 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16875 Z= 0.109 Angle : 0.442 9.306 22711 Z= 0.236 Chirality : 0.037 0.143 2436 Planarity : 0.003 0.042 2714 Dihedral : 9.890 156.545 2452 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.69 % Allowed : 21.27 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.19), residues: 1865 helix: 2.34 (0.14), residues: 1306 sheet: 1.03 (0.53), residues: 108 loop : -0.82 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 118 TYR 0.013 0.001 TYR C 284 PHE 0.023 0.001 PHE D 250 TRP 0.015 0.001 TRP E 143 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (16858) covalent geometry : angle 0.44070 / 0.24 (22677) SS BOND : bond 0.00203 / 0.14 ( 17) SS BOND : angle 0.90376 / 0.58 ( 34) hydrogen bonds : bond 0.03211 / 2.10 ( 1085) hydrogen bonds : angle 3.73313 / 2.64 ( 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 301 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7600 (tp30) cc_final: 0.7149 (mp0) REVERT: A 245 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7998 (mm-30) REVERT: A 258 ASP cc_start: 0.8259 (p0) cc_final: 0.7905 (p0) REVERT: B 18 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7852 (ptt180) REVERT: B 162 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6881 (mmpt) REVERT: B 245 GLU cc_start: 0.7981 (tp30) cc_final: 0.7254 (tp30) REVERT: B 246 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7870 (ttpt) REVERT: B 365 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6453 (mm) REVERT: B 385 LEU cc_start: 0.8195 (tt) cc_final: 0.7984 (tm) REVERT: C 29 ASP cc_start: 0.8058 (t0) cc_final: 0.7428 (t0) REVERT: C 33 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8339 (mp) REVERT: C 103 ARG cc_start: 0.8251 (ttt-90) cc_final: 0.7562 (tpp-160) REVERT: C 168 TRP cc_start: 0.7519 (t-100) cc_final: 0.7169 (t-100) REVERT: C 243 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7735 (mm) REVERT: C 280 CYS cc_start: 0.8810 (m) cc_final: 0.8504 (m) REVERT: D 244 PHE cc_start: 0.5261 (OUTLIER) cc_final: 0.4905 (t80) REVERT: D 309 ARG cc_start: 0.8634 (tpp-160) cc_final: 0.8368 (ttm-80) REVERT: D 353 PHE cc_start: 0.6025 (m-80) cc_final: 0.5806 (m-80) REVERT: D 375 MET cc_start: 0.7771 (mtm) cc_final: 0.7517 (mpp) REVERT: D 396 GLU cc_start: 0.6961 (tp30) cc_final: 0.6088 (mt-10) REVERT: D 405 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5996 (pp) REVERT: E 18 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8052 (ttt-90) REVERT: E 164 PHE cc_start: 0.6839 (t80) cc_final: 0.6560 (t80) REVERT: E 275 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7049 (t80) REVERT: E 306 ARG cc_start: 0.8107 (mtm110) cc_final: 0.7757 (ttp-110) REVERT: F 18 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8068 (ttt-90) REVERT: F 58 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7911 (mtm110) REVERT: F 96 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7848 (mtp) REVERT: F 146 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: F 170 TRP cc_start: 0.6769 (t-100) cc_final: 0.6333 (t-100) REVERT: F 349 TYR cc_start: 0.6375 (t80) cc_final: 0.6002 (t80) REVERT: F 357 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6657 (mp0) REVERT: F 367 LYS cc_start: 0.8039 (ptmt) cc_final: 0.7397 (mttp) REVERT: F 370 PHE cc_start: 0.7184 (t80) cc_final: 0.6949 (t80) REVERT: F 386 LYS cc_start: 0.8360 (mtpp) cc_final: 0.8044 (mmtt) REVERT: F 388 PHE cc_start: 0.6097 (t80) cc_final: 0.5708 (t80) outliers start: 65 outliers final: 29 residues processed: 278 average time/residue: 0.4732 time to fit residues: 150.6755 Evaluate side-chains 257 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 162 LYS 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 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 281 TYR Chi-restraints excluded: chain C residue 314 LEU 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 D residue 405 LEU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 146 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 140 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS C 105 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 = 0.4220 r_free = 0.4220 target = 0.174197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124932 restraints weight = 19586.316| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.32 r_work: 0.3492 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16875 Z= 0.117 Angle : 0.453 9.504 22711 Z= 0.240 Chirality : 0.037 0.152 2436 Planarity : 0.003 0.040 2714 Dihedral : 9.074 150.282 2452 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.97 % Allowed : 21.50 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.19), residues: 1865 helix: 2.40 (0.14), residues: 1307 sheet: 1.24 (0.54), residues: 106 loop : -0.79 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 118 TYR 0.014 0.001 TYR E 264 PHE 0.031 0.001 PHE D 250 TRP 0.027 0.001 TRP E 143 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16858) covalent geometry : angle 0.45188 / 0.24 (22677) SS BOND : bond 0.00205 / 0.14 ( 17) SS BOND : angle 0.88971 / 0.57 ( 34) hydrogen bonds : bond 0.03213 / 2.10 ( 1085) hydrogen bonds : angle 3.69211 / 2.62 ( 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 300 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 230 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7688 (tp30) cc_final: 0.7217 (mp0) REVERT: A 245 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8013 (mm-30) REVERT: A 258 ASP cc_start: 0.8243 (p0) cc_final: 0.7897 (p0) REVERT: A 275 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8249 (t80) REVERT: B 18 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7916 (ptt180) REVERT: B 162 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6866 (mmpt) REVERT: B 245 GLU cc_start: 0.7819 (tp30) cc_final: 0.7181 (tp30) REVERT: B 246 LYS cc_start: 0.8049 (ttpp) cc_final: 0.7794 (ttpt) REVERT: B 365 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6426 (mm) REVERT: C 29 ASP cc_start: 0.8044 (t0) cc_final: 0.7394 (t0) REVERT: C 33 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8320 (mp) REVERT: C 103 ARG cc_start: 0.8245 (ttt-90) cc_final: 0.7538 (tpp-160) REVERT: C 160 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6925 (tp) REVERT: C 168 TRP cc_start: 0.7525 (t-100) cc_final: 0.7222 (t-100) REVERT: C 243 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7699 (mm) REVERT: C 280 CYS cc_start: 0.8830 (m) cc_final: 0.8459 (m) REVERT: D 244 PHE cc_start: 0.5235 (OUTLIER) cc_final: 0.4927 (t80) REVERT: D 309 ARG cc_start: 0.8620 (tpp-160) cc_final: 0.8362 (ttm-80) REVERT: D 353 PHE cc_start: 0.6173 (m-80) cc_final: 0.5948 (m-80) REVERT: D 375 MET cc_start: 0.7717 (mtm) cc_final: 0.7464 (mtp) REVERT: D 396 GLU cc_start: 0.6945 (tp30) cc_final: 0.6018 (mt-10) REVERT: D 405 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5923 (pp) REVERT: E 18 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7999 (ttt-90) REVERT: E 164 PHE cc_start: 0.6862 (t80) cc_final: 0.6582 (t80) REVERT: E 275 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7056 (t80) REVERT: E 306 ARG cc_start: 0.8124 (mtm110) cc_final: 0.7807 (ttp-110) REVERT: F 18 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.8105 (ttt-90) REVERT: F 58 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7894 (mtm110) REVERT: F 96 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7812 (mtp) REVERT: F 146 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: F 170 TRP cc_start: 0.6893 (t-100) cc_final: 0.6648 (t-100) REVERT: F 367 LYS cc_start: 0.8052 (ptmt) cc_final: 0.7561 (ptpp) REVERT: F 370 PHE cc_start: 0.7156 (t80) cc_final: 0.6931 (t80) REVERT: F 386 LYS cc_start: 0.8352 (mtpp) cc_final: 0.8048 (mmtt) REVERT: F 388 PHE cc_start: 0.6017 (t80) cc_final: 0.5617 (t80) outliers start: 70 outliers final: 33 residues processed: 276 average time/residue: 0.4567 time to fit residues: 145.0001 Evaluate side-chains 264 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 395 SER 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 327 SER 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 140 SER 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 286 VAL 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 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 405 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 180 optimal weight: 0.9980 chunk 140 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4210 r_free = 0.4210 target = 0.173335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.126574 restraints weight = 19208.026| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.20 r_work: 0.3496 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3180 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= 0.113 Angle : 0.456 9.720 22711 Z= 0.242 Chirality : 0.037 0.157 2436 Planarity : 0.003 0.039 2714 Dihedral : 8.583 145.967 2452 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.86 % Allowed : 21.95 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.19), residues: 1865 helix: 2.44 (0.14), residues: 1307 sheet: 1.28 (0.54), residues: 106 loop : -0.74 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 118 TYR 0.015 0.001 TYR C 284 PHE 0.034 0.001 PHE D 250 TRP 0.031 0.001 TRP E 143 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (16858) covalent geometry : angle 0.45485 / 0.24 (22677) SS BOND : bond 0.00202 / 0.14 ( 17) SS BOND : angle 0.91017 / 0.59 ( 34) hydrogen bonds : bond 0.03165 / 2.07 ( 1085) hydrogen bonds : angle 3.66505 / 2.60 ( 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 292 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7675 (tp30) cc_final: 0.7237 (mp0) REVERT: A 245 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8092 (mm-30) REVERT: A 258 ASP cc_start: 0.8271 (p0) cc_final: 0.7896 (p0) REVERT: A 275 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8233 (t80) REVERT: B 162 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6889 (mmpt) REVERT: B 245 GLU cc_start: 0.7794 (tp30) cc_final: 0.7151 (tp30) REVERT: B 246 LYS cc_start: 0.8092 (ttpp) cc_final: 0.7872 (ttmt) REVERT: B 320 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8472 (mp) REVERT: B 359 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7550 (pt0) REVERT: C 29 ASP cc_start: 0.8031 (t0) cc_final: 0.7385 (t0) REVERT: C 33 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8333 (mp) REVERT: C 103 ARG cc_start: 0.8223 (ttt-90) cc_final: 0.7545 (tpp-160) REVERT: C 168 TRP cc_start: 0.7546 (t-100) cc_final: 0.7264 (t-100) REVERT: C 243 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7721 (mm) REVERT: C 280 CYS cc_start: 0.8796 (m) cc_final: 0.8434 (m) REVERT: D 244 PHE cc_start: 0.5125 (OUTLIER) cc_final: 0.4783 (t80) REVERT: D 353 PHE cc_start: 0.6235 (m-80) cc_final: 0.5522 (m-80) REVERT: D 354 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: D 396 GLU cc_start: 0.7110 (tp30) cc_final: 0.6226 (mt-10) REVERT: D 405 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5890 (pp) REVERT: E 18 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8009 (ttt-90) REVERT: E 164 PHE cc_start: 0.6846 (t80) cc_final: 0.6568 (t80) REVERT: E 275 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7050 (t80) REVERT: E 306 ARG cc_start: 0.8124 (mtm110) cc_final: 0.7679 (ttp-110) REVERT: F 18 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.8216 (ttt-90) REVERT: F 58 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7896 (mtm110) REVERT: F 96 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7808 (mtp) REVERT: F 146 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: F 170 TRP cc_start: 0.6901 (t-100) cc_final: 0.6638 (t-100) REVERT: F 367 LYS cc_start: 0.8070 (ptmt) cc_final: 0.7570 (ptpp) REVERT: F 370 PHE cc_start: 0.7164 (t80) cc_final: 0.6952 (t80) REVERT: F 381 ASP cc_start: 0.6536 (t0) cc_final: 0.6309 (t70) REVERT: F 386 LYS cc_start: 0.8311 (mtpp) cc_final: 0.8043 (mmtt) REVERT: F 388 PHE cc_start: 0.5997 (t80) cc_final: 0.5690 (t80) outliers start: 68 outliers final: 36 residues processed: 271 average time/residue: 0.4650 time to fit residues: 145.1706 Evaluate side-chains 264 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 395 SER 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 49 GLN 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 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 354 GLU Chi-restraints excluded: chain D residue 405 LEU 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 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 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 377 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 33 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.173404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.123859 restraints weight = 19688.896| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.34 r_work: 0.3496 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16875 Z= 0.137 Angle : 0.480 9.866 22711 Z= 0.254 Chirality : 0.038 0.158 2436 Planarity : 0.003 0.039 2714 Dihedral : 8.606 142.345 2452 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.40 % Allowed : 22.12 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.19), residues: 1865 helix: 2.40 (0.14), residues: 1307 sheet: 0.91 (0.53), residues: 110 loop : -0.72 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 118 TYR 0.015 0.001 TYR D 284 PHE 0.034 0.001 PHE D 250 TRP 0.030 0.002 TRP E 143 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (16858) covalent geometry : angle 0.47890 / 0.25 (22677) SS BOND : bond 0.00241 / 0.16 ( 17) SS BOND : angle 0.94764 / 0.61 ( 34) hydrogen bonds : bond 0.03290 / 2.15 ( 1085) hydrogen bonds : angle 3.72262 / 2.64 ( 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 277 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 217 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7591 (tp30) cc_final: 0.7166 (mp0) REVERT: A 245 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8136 (mm-30) REVERT: A 258 ASP cc_start: 0.8286 (p0) cc_final: 0.7933 (p0) REVERT: B 162 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7023 (mmpt) REVERT: B 245 GLU cc_start: 0.7804 (tp30) cc_final: 0.7157 (tp30) REVERT: B 246 LYS cc_start: 0.8054 (ttpp) cc_final: 0.7838 (ttmt) REVERT: B 320 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8536 (mp) REVERT: B 359 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7506 (pt0) REVERT: C 29 ASP cc_start: 0.8057 (t0) cc_final: 0.7379 (t0) REVERT: C 33 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8316 (mp) REVERT: C 103 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.7579 (tpp-160) REVERT: C 168 TRP cc_start: 0.7501 (t-100) cc_final: 0.7258 (t-100) REVERT: C 243 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7732 (mm) REVERT: C 280 CYS cc_start: 0.8859 (m) cc_final: 0.8478 (m) REVERT: D 244 PHE cc_start: 0.5073 (OUTLIER) cc_final: 0.4768 (t80) REVERT: D 396 GLU cc_start: 0.7099 (tp30) cc_final: 0.6181 (mt-10) REVERT: D 405 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5887 (pp) REVERT: E 18 ARG cc_start: 0.8355 (ttp80) cc_final: 0.7999 (ttt-90) REVERT: E 164 PHE cc_start: 0.6877 (t80) cc_final: 0.6570 (t80) REVERT: E 275 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7339 (t80) REVERT: E 306 ARG cc_start: 0.8167 (mtm110) cc_final: 0.7749 (ttp-110) REVERT: F 18 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8277 (ttt-90) REVERT: F 58 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7821 (mtm110) REVERT: F 96 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7854 (mtp) REVERT: F 146 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: F 170 TRP cc_start: 0.6934 (t-100) cc_final: 0.6702 (t-100) REVERT: F 367 LYS cc_start: 0.8069 (ptmt) cc_final: 0.7123 (pmtt) REVERT: F 370 PHE cc_start: 0.7236 (t80) cc_final: 0.6901 (t80) REVERT: F 381 ASP cc_start: 0.6620 (t0) cc_final: 0.6378 (t70) REVERT: F 386 LYS cc_start: 0.8427 (mtpp) cc_final: 0.8154 (mmtt) REVERT: F 388 PHE cc_start: 0.5889 (t80) cc_final: 0.5448 (t80) outliers start: 60 outliers final: 34 residues processed: 258 average time/residue: 0.4558 time to fit residues: 135.7719 Evaluate side-chains 254 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 395 SER 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 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 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 392 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 163 CYS 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 330 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 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 377 ILE 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: 0.6980 chunk 26 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 174 optimal weight: 0.0980 chunk 163 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 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 = 0.4216 r_free = 0.4216 target = 0.173737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.124415 restraints weight = 19642.135| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.33 r_work: 0.3500 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16875 Z= 0.133 Angle : 0.489 10.141 22711 Z= 0.258 Chirality : 0.038 0.164 2436 Planarity : 0.003 0.039 2714 Dihedral : 8.431 141.340 2452 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.40 % Allowed : 22.69 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.19), residues: 1865 helix: 2.39 (0.14), residues: 1307 sheet: 0.89 (0.53), residues: 110 loop : -0.70 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 118 TYR 0.017 0.001 TYR C 284 PHE 0.047 0.001 PHE E 250 TRP 0.027 0.001 TRP E 143 HIS 0.004 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (16858) covalent geometry : angle 0.48839 / 0.26 (22677) SS BOND : bond 0.00225 / 0.15 ( 17) SS BOND : angle 0.92028 / 0.59 ( 34) hydrogen bonds : bond 0.03239 / 2.11 ( 1085) hydrogen bonds : angle 3.74242 / 2.65 ( 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 275 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7587 (tp30) cc_final: 0.7159 (mp0) REVERT: A 245 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 258 ASP cc_start: 0.8292 (p0) cc_final: 0.7941 (p0) REVERT: A 275 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8265 (t80) REVERT: B 162 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7041 (mmpt) REVERT: B 232 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.6148 (mt) REVERT: B 245 GLU cc_start: 0.7795 (tp30) cc_final: 0.7062 (tp30) REVERT: B 320 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8535 (mp) REVERT: B 359 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7514 (pt0) REVERT: C 29 ASP cc_start: 0.8054 (t0) cc_final: 0.7388 (t0) REVERT: C 33 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8309 (mp) REVERT: C 103 ARG cc_start: 0.8273 (ttt-90) cc_final: 0.7571 (tpp-160) REVERT: C 243 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7716 (mm) REVERT: C 280 CYS cc_start: 0.8798 (m) cc_final: 0.8484 (m) REVERT: D 244 PHE cc_start: 0.5103 (OUTLIER) cc_final: 0.4789 (t80) REVERT: D 284 TYR cc_start: 0.8373 (t80) cc_final: 0.8021 (t80) REVERT: D 353 PHE cc_start: 0.6158 (m-80) cc_final: 0.5464 (m-80) REVERT: D 354 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: D 396 GLU cc_start: 0.7072 (tp30) cc_final: 0.6133 (mt-10) REVERT: D 405 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5875 (pp) REVERT: E 18 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8086 (ttt-90) REVERT: E 164 PHE cc_start: 0.6734 (t80) cc_final: 0.6466 (t80) REVERT: E 266 ARG cc_start: 0.7745 (mpt-90) cc_final: 0.7465 (mpp80) REVERT: E 275 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7334 (t80) REVERT: E 306 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7780 (ttp-110) REVERT: E 375 MET cc_start: 0.7938 (mtm) cc_final: 0.7626 (mtm) REVERT: F 18 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8282 (ttt-90) REVERT: F 58 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7879 (mtm110) REVERT: F 96 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7839 (mtp) REVERT: F 146 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: F 367 LYS cc_start: 0.7921 (ptmt) cc_final: 0.7562 (ptpp) REVERT: F 370 PHE cc_start: 0.7184 (t80) cc_final: 0.6901 (t80) REVERT: F 381 ASP cc_start: 0.6618 (t0) cc_final: 0.6380 (t70) REVERT: F 386 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8160 (mmtt) REVERT: F 388 PHE cc_start: 0.6018 (t80) cc_final: 0.5580 (t80) outliers start: 60 outliers final: 33 residues processed: 257 average time/residue: 0.4466 time to fit residues: 132.4946 Evaluate side-chains 253 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 395 SER 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 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 49 GLN 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 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 352 SER 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 354 GLU Chi-restraints excluded: chain D residue 392 VAL 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 330 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 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 13 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 124 optimal weight: 0.0670 chunk 181 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 305 ASN ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.123401 restraints weight = 19553.812| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.44 r_work: 0.3473 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16875 Z= 0.143 Angle : 0.502 10.096 22711 Z= 0.266 Chirality : 0.039 0.165 2436 Planarity : 0.003 0.039 2714 Dihedral : 8.377 139.132 2452 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.89 % Allowed : 23.14 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.19), residues: 1865 helix: 2.35 (0.14), residues: 1306 sheet: 0.87 (0.53), residues: 110 loop : -0.66 (0.29), residues: 449 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 0.053 0.001 PHE E 250 TRP 0.040 0.002 TRP C 168 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (16858) covalent geometry : angle 0.50087 / 0.27 (22677) SS BOND : bond 0.00243 / 0.16 ( 17) SS BOND : angle 0.97212 / 0.62 ( 34) hydrogen bonds : bond 0.03307 / 2.17 ( 1085) hydrogen bonds : angle 3.78291 / 2.68 ( 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 267 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7438 (tp30) cc_final: 0.7098 (mp0) REVERT: A 245 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8100 (mm-30) REVERT: A 258 ASP cc_start: 0.8159 (p0) cc_final: 0.7816 (p0) REVERT: A 275 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8179 (t80) REVERT: B 162 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6856 (mmpt) REVERT: B 171 ARG cc_start: 0.8142 (ttt-90) cc_final: 0.7916 (ttm-80) REVERT: B 232 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.5917 (mt) REVERT: B 245 GLU cc_start: 0.7719 (tp30) cc_final: 0.7046 (tp30) REVERT: B 320 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8399 (mp) REVERT: B 359 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7553 (pt0) REVERT: C 29 ASP cc_start: 0.7797 (t0) cc_final: 0.7116 (t0) REVERT: C 33 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8148 (mp) REVERT: C 103 ARG cc_start: 0.7987 (ttt-90) cc_final: 0.7386 (tpp-160) REVERT: C 243 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7715 (mm) REVERT: C 280 CYS cc_start: 0.8662 (m) cc_final: 0.8320 (m) REVERT: D 244 PHE cc_start: 0.5137 (OUTLIER) cc_final: 0.4817 (t80) REVERT: D 396 GLU cc_start: 0.6945 (tp30) cc_final: 0.5951 (mt-10) REVERT: D 405 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5909 (pp) REVERT: E 18 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8037 (ttt-90) REVERT: E 164 PHE cc_start: 0.6719 (t80) cc_final: 0.6502 (t80) REVERT: E 266 ARG cc_start: 0.7597 (mpt-90) cc_final: 0.7315 (mpp80) REVERT: E 275 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7389 (t80) REVERT: E 306 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7550 (ttp-110) REVERT: E 375 MET cc_start: 0.7801 (mtm) cc_final: 0.7561 (mpp) REVERT: E 390 PHE cc_start: 0.7931 (t80) cc_final: 0.7341 (t80) REVERT: F 18 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8254 (ttt-90) REVERT: F 58 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7838 (mtm110) REVERT: F 96 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7689 (mtp) REVERT: F 370 PHE cc_start: 0.7148 (t80) cc_final: 0.6885 (t80) REVERT: F 381 ASP cc_start: 0.6535 (t0) cc_final: 0.6302 (t70) REVERT: F 386 LYS cc_start: 0.8379 (mtpp) cc_final: 0.8119 (mmtt) REVERT: F 388 PHE cc_start: 0.6105 (t80) cc_final: 0.5665 (t80) outliers start: 51 outliers final: 35 residues processed: 253 average time/residue: 0.4604 time to fit residues: 134.3462 Evaluate side-chains 255 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR 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 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 49 GLN 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 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 352 SER 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 392 VAL 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 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 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 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 45 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 305 ASN ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.174941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123022 restraints weight = 19595.064| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.46 r_work: 0.3468 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3487 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= 0.150 Angle : 0.511 9.766 22711 Z= 0.270 Chirality : 0.039 0.170 2436 Planarity : 0.003 0.040 2714 Dihedral : 8.325 138.249 2452 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.78 % Allowed : 23.43 % 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 are not related in a simple way. whole: 2.30 (0.19), residues: 1865 helix: 2.31 (0.14), residues: 1310 sheet: 0.87 (0.53), residues: 110 loop : -0.72 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 118 TYR 0.019 0.001 TYR C 284 PHE 0.054 0.001 PHE E 250 TRP 0.048 0.002 TRP C 168 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (16858) covalent geometry : angle 0.51005 / 0.27 (22677) SS BOND : bond 0.00263 / 0.17 ( 17) SS BOND : angle 0.99632 / 0.64 ( 34) hydrogen bonds : bond 0.03345 / 2.19 ( 1085) hydrogen bonds : angle 3.80790 / 2.70 ( 3201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5600.67 seconds wall clock time: 96 minutes 31.30 seconds (5791.30 seconds total)