Starting phenix.real_space_refine on Mon Jan 20 13:19:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v62_42987/01_2025/8v62_42987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v62_42987/01_2025/8v62_42987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v62_42987/01_2025/8v62_42987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v62_42987/01_2025/8v62_42987.map" model { file = "/net/cci-nas-00/data/ceres_data/8v62_42987/01_2025/8v62_42987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v62_42987/01_2025/8v62_42987.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 9585 2.51 5 N 2622 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15234 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3327 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain breaks: 5 Chain: "E" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 874 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "G" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Restraints were copied for chains: D, F, I, H, C, B Time building chain proxies: 8.33, per 1000 atoms: 0.55 Number of scatterers: 15234 At special positions: 0 Unit cell: (135.36, 132.54, 127.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 2958 8.00 N 2622 7.00 C 9585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " 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: 3.59 Conformation dependent library (CDL) restraints added in 2.0 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 29.1% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.538A pdb=" N GLN A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 88 removed outlier: 4.263A pdb=" N ARG A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 124 through 137 Processing helix chain 'A' and resid 137 through 154 removed outlier: 4.027A pdb=" N LYS A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.617A pdb=" N ILE A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.548A pdb=" N CYS A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 481 Processing helix chain 'B' and resid 21 through 28 removed outlier: 3.538A pdb=" N GLN B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 88 removed outlier: 4.263A pdb=" N ARG B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 137 through 154 removed outlier: 4.027A pdb=" N LYS B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 182 through 190 removed outlier: 3.617A pdb=" N ILE B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 215 removed outlier: 3.547A pdb=" N CYS B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 235 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 452 through 481 Processing helix chain 'C' and resid 21 through 28 removed outlier: 3.538A pdb=" N GLN C 26 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 4.263A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Proline residue: C 81 - end of helix Processing helix chain 'C' and resid 124 through 137 Processing helix chain 'C' and resid 137 through 154 removed outlier: 4.027A pdb=" N LYS C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 182 through 190 removed outlier: 3.617A pdb=" N ILE C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 215 removed outlier: 3.547A pdb=" N CYS C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 452 through 481 Processing helix chain 'D' and resid 69 through 72 removed outlier: 3.718A pdb=" N LYS D 72 " --> pdb=" O ASP D 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 69 through 72' Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'E' and resid 69 through 72 removed outlier: 3.718A pdb=" N LYS E 72 " --> pdb=" O ASP E 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 69 through 72' Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'F' and resid 69 through 72 removed outlier: 3.717A pdb=" N LYS F 72 " --> pdb=" O ASP F 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 69 through 72' Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.901A pdb=" N THR G 99 " --> pdb=" O PRO G 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.901A pdb=" N THR H 99 " --> pdb=" O PRO H 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 99 removed outlier: 3.901A pdb=" N THR I 99 " --> pdb=" O PRO I 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 4.577A pdb=" N HIS A 315 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 160 removed outlier: 5.549A pdb=" N SER A 41 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR A 286 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN A 43 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 268 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN A 279 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 266 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ARG A 281 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL A 264 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE A 226 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 32 removed outlier: 4.577A pdb=" N HIS B 315 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 158 through 160 removed outlier: 5.548A pdb=" N SER B 41 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR B 286 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN B 43 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 268 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN B 279 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL B 266 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ARG B 281 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL B 264 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 226 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 158 through 160 Processing sheet with id=AB3, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AB4, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=AB5, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB6, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AB7, first strand: chain 'C' and resid 30 through 32 removed outlier: 4.577A pdb=" N HIS C 315 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 158 through 160 removed outlier: 5.549A pdb=" N SER C 41 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR C 286 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN C 43 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 268 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN C 279 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL C 266 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ARG C 281 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL C 264 " --> pdb=" O ARG C 281 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE C 226 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 160 Processing sheet with id=AC1, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AC3, first strand: chain 'C' and resid 392 through 394 Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.635A pdb=" N GLY D 11 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER D 127 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 13 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 38 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET D 39 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG D 55 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP D 41 " --> pdb=" O VAL D 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.635A pdb=" N GLY D 11 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER D 127 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 13 " --> pdb=" O SER D 127 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.634A pdb=" N GLY E 11 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER E 127 " --> pdb=" O GLY E 11 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL E 13 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 38 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET E 39 " --> pdb=" O ARG E 55 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG E 55 " --> pdb=" O MET E 39 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TRP E 41 " --> pdb=" O VAL E 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.634A pdb=" N GLY E 11 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER E 127 " --> pdb=" O GLY E 11 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL E 13 " --> pdb=" O SER E 127 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'F' and resid 11 through 14 removed outlier: 6.635A pdb=" N GLY F 11 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER F 127 " --> pdb=" O GLY F 11 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL F 13 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA F 38 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET F 39 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG F 55 " --> pdb=" O MET F 39 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP F 41 " --> pdb=" O VAL F 53 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 11 through 14 removed outlier: 6.635A pdb=" N GLY F 11 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER F 127 " --> pdb=" O GLY F 11 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL F 13 " --> pdb=" O SER F 127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 2 through 7 removed outlier: 3.534A pdb=" N THR G 77 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.169A pdb=" N GLY G 11 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LYS G 37 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR G 57 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU G 39 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER G 55 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP G 41 " --> pdb=" O VAL G 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.169A pdb=" N GLY G 11 " --> pdb=" O THR G 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 2 through 7 removed outlier: 3.534A pdb=" N THR H 77 " --> pdb=" O ARG H 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.168A pdb=" N GLY H 11 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS H 37 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR H 57 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU H 39 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER H 55 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.168A pdb=" N GLY H 11 " --> pdb=" O THR H 125 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 2 through 7 removed outlier: 3.535A pdb=" N THR I 77 " --> pdb=" O ARG I 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.168A pdb=" N GLY I 11 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LYS I 37 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR I 57 " --> pdb=" O LYS I 37 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU I 39 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER I 55 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP I 41 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.168A pdb=" N GLY I 11 " --> pdb=" O THR I 125 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2061 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: 6.12 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5055 1.35 - 1.46: 3372 1.46 - 1.58: 6933 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 15450 Sorted by residual: bond pdb=" CB CYS A 195 " pdb=" SG CYS A 195 " ideal model delta sigma weight residual 1.808 1.785 0.023 3.30e-02 9.18e+02 4.85e-01 bond pdb=" CB CYS C 195 " pdb=" SG CYS C 195 " ideal model delta sigma weight residual 1.808 1.785 0.023 3.30e-02 9.18e+02 4.85e-01 bond pdb=" CB CYS B 195 " pdb=" SG CYS B 195 " ideal model delta sigma weight residual 1.808 1.785 0.023 3.30e-02 9.18e+02 4.84e-01 bond pdb=" CB VAL B 92 " pdb=" CG2 VAL B 92 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.45e-01 bond pdb=" CB VAL A 92 " pdb=" CG2 VAL A 92 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.20e-01 ... (remaining 15445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 20089 1.26 - 2.52: 683 2.52 - 3.79: 115 3.79 - 5.05: 26 5.05 - 6.31: 6 Bond angle restraints: 20919 Sorted by residual: angle pdb=" N SER A 174 " pdb=" CA SER A 174 " pdb=" C SER A 174 " ideal model delta sigma weight residual 111.02 114.60 -3.58 1.22e+00 6.72e-01 8.62e+00 angle pdb=" N SER C 174 " pdb=" CA SER C 174 " pdb=" C SER C 174 " ideal model delta sigma weight residual 111.02 114.58 -3.56 1.22e+00 6.72e-01 8.51e+00 angle pdb=" N SER B 174 " pdb=" CA SER B 174 " pdb=" C SER B 174 " ideal model delta sigma weight residual 111.02 114.53 -3.51 1.22e+00 6.72e-01 8.29e+00 angle pdb=" N VAL B 328 " pdb=" CA VAL B 328 " pdb=" CB VAL B 328 " ideal model delta sigma weight residual 111.82 105.51 6.31 2.75e+00 1.32e-01 5.26e+00 angle pdb=" N VAL C 328 " pdb=" CA VAL C 328 " pdb=" CB VAL C 328 " ideal model delta sigma weight residual 111.82 105.53 6.29 2.75e+00 1.32e-01 5.24e+00 ... (remaining 20914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 8822 16.89 - 33.78: 434 33.78 - 50.66: 71 50.66 - 67.55: 12 67.55 - 84.44: 9 Dihedral angle restraints: 9348 sinusoidal: 3669 harmonic: 5679 Sorted by residual: dihedral pdb=" CA PHE C 111 " pdb=" CB PHE C 111 " pdb=" CG PHE C 111 " pdb=" CD1 PHE C 111 " ideal model delta sinusoidal sigma weight residual 90.00 37.84 52.16 2 2.00e+01 2.50e-03 7.48e+00 dihedral pdb=" CA PHE A 111 " pdb=" CB PHE A 111 " pdb=" CG PHE A 111 " pdb=" CD1 PHE A 111 " ideal model delta sinusoidal sigma weight residual 90.00 37.88 52.12 2 2.00e+01 2.50e-03 7.48e+00 dihedral pdb=" CA PHE B 111 " pdb=" CB PHE B 111 " pdb=" CG PHE B 111 " pdb=" CD1 PHE B 111 " ideal model delta sinusoidal sigma weight residual 90.00 37.88 52.12 2 2.00e+01 2.50e-03 7.48e+00 ... (remaining 9345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1546 0.031 - 0.063: 547 0.063 - 0.094: 212 0.094 - 0.126: 140 0.126 - 0.157: 24 Chirality restraints: 2469 Sorted by residual: chirality pdb=" CA CYS C 195 " pdb=" N CYS C 195 " pdb=" C CYS C 195 " pdb=" CB CYS C 195 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA CYS A 195 " pdb=" N CYS A 195 " pdb=" C CYS A 195 " pdb=" CB CYS A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA CYS B 195 " pdb=" N CYS B 195 " pdb=" C CYS B 195 " pdb=" CB CYS B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 2466 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 43 " 0.163 9.50e-02 1.11e+02 7.38e-02 4.36e+00 pdb=" NE ARG I 43 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG I 43 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG I 43 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG I 43 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 43 " 0.162 9.50e-02 1.11e+02 7.32e-02 4.33e+00 pdb=" NE ARG G 43 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG G 43 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG G 43 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G 43 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 43 " -0.162 9.50e-02 1.11e+02 7.33e-02 4.32e+00 pdb=" NE ARG H 43 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG H 43 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG H 43 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG H 43 " 0.000 2.00e-02 2.50e+03 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 111 2.60 - 3.18: 12720 3.18 - 3.75: 21662 3.75 - 4.33: 31118 4.33 - 4.90: 51966 Nonbonded interactions: 117577 Sorted by model distance: nonbonded pdb=" SG CYS C 355 " pdb=" SG CYS C 363 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS B 331 " pdb=" SG CYS B 340 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS C 331 " pdb=" SG CYS C 340 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS B 355 " pdb=" SG CYS B 363 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C 186 " pdb=" SG CYS C 195 " model vdw 2.028 3.760 ... (remaining 117572 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: 0.08 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 35.810 Find NCS groups from input model: 0.260 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 42.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 : 0.002 0.027 15450 Z= 0.145 Angle : 0.561 6.308 20919 Z= 0.317 Chirality : 0.044 0.157 2469 Planarity : 0.007 0.074 2673 Dihedral : 10.429 84.440 5682 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1932 helix: 0.32 (0.23), residues: 441 sheet: 0.57 (0.21), residues: 594 loop : 0.53 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 118 HIS 0.001 0.000 HIS C 350 PHE 0.014 0.001 PHE A 346 TYR 0.020 0.004 TYR B 338 ARG 0.018 0.003 ARG G 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8360 (mttt) cc_final: 0.7951 (mttt) REVERT: A 49 LEU cc_start: 0.8748 (tp) cc_final: 0.8518 (tt) REVERT: A 57 ILE cc_start: 0.8670 (mm) cc_final: 0.8273 (mm) REVERT: A 65 ASP cc_start: 0.7940 (p0) cc_final: 0.7732 (p0) REVERT: A 69 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8596 (ttmm) REVERT: A 70 GLN cc_start: 0.8498 (tp40) cc_final: 0.8196 (tp-100) REVERT: A 73 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7817 (ttm110) REVERT: A 74 LEU cc_start: 0.8668 (tp) cc_final: 0.8229 (tp) REVERT: A 139 GLN cc_start: 0.7704 (tp40) cc_final: 0.7390 (tp-100) REVERT: A 175 VAL cc_start: 0.8395 (m) cc_final: 0.7999 (t) REVERT: A 182 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 193 GLU cc_start: 0.8459 (pm20) cc_final: 0.8192 (pm20) REVERT: A 205 GLN cc_start: 0.8069 (mt0) cc_final: 0.7796 (mt0) REVERT: A 207 TYR cc_start: 0.8533 (t80) cc_final: 0.8176 (t80) REVERT: A 212 ASN cc_start: 0.8082 (t0) cc_final: 0.7869 (t0) REVERT: A 229 GLN cc_start: 0.8155 (tp40) cc_final: 0.7841 (tp40) REVERT: A 263 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7964 (mtpt) REVERT: A 270 ASP cc_start: 0.7785 (t0) cc_final: 0.7484 (t0) REVERT: A 294 TYR cc_start: 0.8197 (m-80) cc_final: 0.7971 (m-80) REVERT: A 333 GLU cc_start: 0.7810 (tt0) cc_final: 0.7412 (tt0) REVERT: A 432 GLU cc_start: 0.7454 (mp0) cc_final: 0.7075 (mp0) REVERT: B 36 LYS cc_start: 0.8337 (mttt) cc_final: 0.8135 (mttt) REVERT: B 70 GLN cc_start: 0.8595 (tp40) cc_final: 0.8227 (tp40) REVERT: B 73 ARG cc_start: 0.8250 (ttm110) cc_final: 0.8003 (ttm110) REVERT: B 74 LEU cc_start: 0.8671 (tp) cc_final: 0.8406 (tp) REVERT: B 90 LYS cc_start: 0.7416 (mmtt) cc_final: 0.7148 (mmtt) REVERT: B 139 GLN cc_start: 0.7748 (tp40) cc_final: 0.7510 (tp40) REVERT: B 151 ILE cc_start: 0.8469 (mt) cc_final: 0.8242 (tp) REVERT: B 158 VAL cc_start: 0.8657 (t) cc_final: 0.8272 (p) REVERT: B 175 VAL cc_start: 0.8304 (m) cc_final: 0.8017 (t) REVERT: B 212 ASN cc_start: 0.8066 (t0) cc_final: 0.7417 (t0) REVERT: B 214 PHE cc_start: 0.8303 (m-80) cc_final: 0.7997 (m-80) REVERT: B 238 ASN cc_start: 0.7680 (m-40) cc_final: 0.7449 (m-40) REVERT: B 256 LEU cc_start: 0.7921 (mm) cc_final: 0.7641 (mm) REVERT: B 263 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7783 (mtpt) REVERT: B 281 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7627 (mtm-85) REVERT: B 332 ILE cc_start: 0.8427 (mm) cc_final: 0.8226 (mt) REVERT: B 375 ARG cc_start: 0.8483 (mtt90) cc_final: 0.8268 (mtt90) REVERT: B 431 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7550 (mmtt) REVERT: B 432 GLU cc_start: 0.7207 (mp0) cc_final: 0.6613 (mp0) REVERT: B 464 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8026 (mtpp) REVERT: B 468 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7455 (mt-10) REVERT: B 469 GLU cc_start: 0.8244 (tt0) cc_final: 0.7941 (tt0) REVERT: B 471 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7424 (ttmm) REVERT: C 36 LYS cc_start: 0.8386 (mttt) cc_final: 0.8142 (mttt) REVERT: C 38 MET cc_start: 0.8401 (ttp) cc_final: 0.8090 (ttp) REVERT: C 69 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8560 (ttmm) REVERT: C 73 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7841 (ttm110) REVERT: C 83 TYR cc_start: 0.8287 (t80) cc_final: 0.8016 (t80) REVERT: C 89 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7001 (pt0) REVERT: C 177 ASP cc_start: 0.8273 (t70) cc_final: 0.8073 (t0) REVERT: C 212 ASN cc_start: 0.8194 (t0) cc_final: 0.7711 (t0) REVERT: C 262 ILE cc_start: 0.8156 (mt) cc_final: 0.7916 (mm) REVERT: C 275 SER cc_start: 0.8646 (t) cc_final: 0.8416 (p) REVERT: C 297 ASP cc_start: 0.7745 (m-30) cc_final: 0.7494 (m-30) REVERT: C 307 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7491 (mt-10) REVERT: C 314 SER cc_start: 0.8516 (m) cc_final: 0.8291 (p) REVERT: C 375 ARG cc_start: 0.8426 (mtt90) cc_final: 0.7987 (mtt90) REVERT: C 464 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7973 (mttm) REVERT: E 64 THR cc_start: 0.8707 (m) cc_final: 0.8292 (p) REVERT: H 28 SER cc_start: 0.8513 (m) cc_final: 0.8229 (p) REVERT: I 28 SER cc_start: 0.8546 (m) cc_final: 0.8178 (p) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.3174 time to fit residues: 214.5071 Evaluate side-chains 431 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 77 optimal weight: 0.0060 chunk 150 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 0.0770 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 27 HIS A 89 GLN A 305 ASN A 380 ASN A 446 ASN A 479 GLN B 19 GLN B 89 GLN B 127 GLN B 159 GLN B 305 ASN B 380 ASN B 479 GLN C 19 GLN C 89 GLN C 127 GLN C 238 ASN C 305 ASN C 380 ASN C 479 GLN D 116 ASN E 116 ASN F 116 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107388 restraints weight = 22711.590| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.48 r_work: 0.3140 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15450 Z= 0.239 Angle : 0.558 6.483 20919 Z= 0.299 Chirality : 0.045 0.153 2469 Planarity : 0.004 0.035 2673 Dihedral : 4.883 83.640 2136 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.36 % Allowed : 7.98 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1932 helix: 1.08 (0.24), residues: 450 sheet: 0.55 (0.21), residues: 585 loop : 0.59 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 118 HIS 0.002 0.000 HIS B 315 PHE 0.012 0.002 PHE A 346 TYR 0.020 0.002 TYR B 207 ARG 0.003 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 429 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8726 (tp) cc_final: 0.8524 (tt) REVERT: A 57 ILE cc_start: 0.8690 (mm) cc_final: 0.8311 (mm) REVERT: A 66 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 70 GLN cc_start: 0.8611 (tp40) cc_final: 0.8323 (tp-100) REVERT: A 73 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7769 (ttm110) REVERT: A 190 LEU cc_start: 0.8796 (mt) cc_final: 0.8543 (mp) REVERT: A 205 GLN cc_start: 0.7927 (mt0) cc_final: 0.7717 (mt0) REVERT: A 229 GLN cc_start: 0.8280 (tp40) cc_final: 0.7838 (tp40) REVERT: A 263 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7954 (mtpt) REVERT: A 270 ASP cc_start: 0.7650 (t0) cc_final: 0.7412 (t0) REVERT: A 432 GLU cc_start: 0.7494 (mp0) cc_final: 0.7149 (mp0) REVERT: A 462 LYS cc_start: 0.8035 (tptt) cc_final: 0.7831 (tptt) REVERT: B 63 CYS cc_start: 0.8631 (t) cc_final: 0.8363 (t) REVERT: B 65 ASP cc_start: 0.7775 (p0) cc_final: 0.7567 (p0) REVERT: B 70 GLN cc_start: 0.8607 (tp40) cc_final: 0.8262 (tp-100) REVERT: B 73 ARG cc_start: 0.8070 (ttm110) cc_final: 0.7702 (ttm110) REVERT: B 192 CYS cc_start: 0.8194 (t) cc_final: 0.7805 (t) REVERT: B 212 ASN cc_start: 0.8128 (t0) cc_final: 0.7573 (t0) REVERT: B 214 PHE cc_start: 0.8331 (m-80) cc_final: 0.8113 (m-80) REVERT: B 263 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7785 (mtpt) REVERT: B 272 ASN cc_start: 0.8009 (m-40) cc_final: 0.7756 (m-40) REVERT: B 281 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7667 (mtm-85) REVERT: B 331 CYS cc_start: 0.8201 (m) cc_final: 0.7921 (m) REVERT: B 432 GLU cc_start: 0.7260 (mp0) cc_final: 0.6676 (mp0) REVERT: B 469 GLU cc_start: 0.8270 (tt0) cc_final: 0.7975 (tt0) REVERT: B 471 LYS cc_start: 0.7702 (mtpp) cc_final: 0.7395 (ttmm) REVERT: C 63 CYS cc_start: 0.8590 (t) cc_final: 0.8224 (t) REVERT: C 69 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8645 (ttmm) REVERT: C 76 ASP cc_start: 0.8035 (m-30) cc_final: 0.7607 (m-30) REVERT: C 83 TYR cc_start: 0.8346 (t80) cc_final: 0.8070 (t80) REVERT: C 212 ASN cc_start: 0.8295 (t0) cc_final: 0.7899 (t0) REVERT: C 262 ILE cc_start: 0.8245 (mt) cc_final: 0.7991 (mm) REVERT: C 263 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7933 (mtpt) REVERT: C 274 TYR cc_start: 0.8715 (m-80) cc_final: 0.8039 (m-80) REVERT: C 297 ASP cc_start: 0.7558 (m-30) cc_final: 0.7297 (m-30) REVERT: C 331 CYS cc_start: 0.8345 (m) cc_final: 0.8132 (m) REVERT: C 353 GLU cc_start: 0.7223 (tt0) cc_final: 0.6864 (tt0) REVERT: C 417 CYS cc_start: 0.8312 (m) cc_final: 0.8028 (m) REVERT: C 464 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8072 (mttm) REVERT: C 469 GLU cc_start: 0.8289 (tt0) cc_final: 0.8048 (tp30) REVERT: G 118 TRP cc_start: 0.8527 (m100) cc_final: 0.7863 (m100) REVERT: H 28 SER cc_start: 0.8516 (m) cc_final: 0.8075 (p) outliers start: 40 outliers final: 22 residues processed: 444 average time/residue: 0.3396 time to fit residues: 213.6340 Evaluate side-chains 430 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 408 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 380 ASN B 205 GLN B 380 ASN C 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.133101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.107050 restraints weight = 22587.022| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.47 r_work: 0.3146 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15450 Z= 0.231 Angle : 0.533 6.764 20919 Z= 0.281 Chirality : 0.044 0.149 2469 Planarity : 0.003 0.043 2673 Dihedral : 4.921 83.036 2136 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.07 % Allowed : 10.70 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 1932 helix: 1.37 (0.25), residues: 450 sheet: 0.49 (0.21), residues: 576 loop : 0.49 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 118 HIS 0.001 0.000 HIS C 315 PHE 0.012 0.001 PHE A 346 TYR 0.015 0.002 TYR B 294 ARG 0.006 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 417 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7775 (mm-30) REVERT: A 57 ILE cc_start: 0.8709 (mm) cc_final: 0.8346 (mm) REVERT: A 66 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A 70 GLN cc_start: 0.8607 (tp40) cc_final: 0.8116 (tp-100) REVERT: A 73 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7733 (ttm110) REVERT: A 263 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7944 (mtpt) REVERT: A 270 ASP cc_start: 0.7576 (t0) cc_final: 0.7367 (t0) REVERT: A 432 GLU cc_start: 0.7491 (mp0) cc_final: 0.7158 (mp0) REVERT: A 462 LYS cc_start: 0.8038 (tptt) cc_final: 0.7822 (tptt) REVERT: B 63 CYS cc_start: 0.8676 (t) cc_final: 0.8310 (t) REVERT: B 70 GLN cc_start: 0.8559 (tp40) cc_final: 0.8308 (tp-100) REVERT: B 73 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7717 (ttm110) REVERT: B 192 CYS cc_start: 0.8043 (t) cc_final: 0.7646 (t) REVERT: B 212 ASN cc_start: 0.8198 (t0) cc_final: 0.7646 (t0) REVERT: B 214 PHE cc_start: 0.8320 (m-80) cc_final: 0.8052 (m-80) REVERT: B 238 ASN cc_start: 0.7799 (m-40) cc_final: 0.7508 (m-40) REVERT: B 263 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7769 (mtpt) REVERT: B 281 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7665 (mtm-85) REVERT: B 331 CYS cc_start: 0.8182 (m) cc_final: 0.7871 (m) REVERT: B 365 ARG cc_start: 0.8425 (ptt90) cc_final: 0.8188 (ptt-90) REVERT: B 432 GLU cc_start: 0.7229 (mp0) cc_final: 0.6644 (mp0) REVERT: B 469 GLU cc_start: 0.8247 (tt0) cc_final: 0.8002 (tt0) REVERT: C 21 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: C 69 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8651 (ttmm) REVERT: C 83 TYR cc_start: 0.8332 (t80) cc_final: 0.8104 (t80) REVERT: C 89 GLN cc_start: 0.7679 (tp40) cc_final: 0.7247 (pt0) REVERT: C 212 ASN cc_start: 0.8285 (t0) cc_final: 0.7916 (t0) REVERT: C 263 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7924 (mtpt) REVERT: C 297 ASP cc_start: 0.7575 (m-30) cc_final: 0.7295 (m-30) REVERT: C 331 CYS cc_start: 0.8338 (m) cc_final: 0.8120 (m) REVERT: C 394 CYS cc_start: 0.7741 (t) cc_final: 0.7435 (t) REVERT: C 469 GLU cc_start: 0.8301 (tt0) cc_final: 0.8055 (tp30) REVERT: H 28 SER cc_start: 0.8524 (m) cc_final: 0.8108 (p) outliers start: 35 outliers final: 24 residues processed: 429 average time/residue: 0.3166 time to fit residues: 191.2721 Evaluate side-chains 423 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 398 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 123 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 380 ASN B 305 ASN B 380 ASN B 446 ASN C 279 GLN C 386 ASN C 446 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104758 restraints weight = 22612.353| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.47 r_work: 0.3101 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15450 Z= 0.365 Angle : 0.582 7.208 20919 Z= 0.305 Chirality : 0.046 0.179 2469 Planarity : 0.004 0.038 2673 Dihedral : 5.171 82.102 2136 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.25 % Allowed : 11.47 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1932 helix: 1.18 (0.25), residues: 450 sheet: 0.23 (0.21), residues: 585 loop : 0.30 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 118 HIS 0.003 0.001 HIS B 206 PHE 0.021 0.002 PHE B 427 TYR 0.022 0.002 TYR B 294 ARG 0.006 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 420 time to evaluate : 1.769 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 57 ILE cc_start: 0.8724 (mm) cc_final: 0.8448 (mm) REVERT: A 66 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 73 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7868 (ttm110) REVERT: A 263 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7957 (mtpt) REVERT: A 270 ASP cc_start: 0.7584 (t0) cc_final: 0.7348 (t0) REVERT: A 432 GLU cc_start: 0.7521 (mp0) cc_final: 0.7190 (mp0) REVERT: A 459 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7606 (mt-10) REVERT: B 63 CYS cc_start: 0.8670 (t) cc_final: 0.8313 (t) REVERT: B 70 GLN cc_start: 0.8641 (tp40) cc_final: 0.8384 (tp-100) REVERT: B 73 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7942 (ttm110) REVERT: B 148 LYS cc_start: 0.8237 (mtmt) cc_final: 0.8031 (mtmt) REVERT: B 184 VAL cc_start: 0.8999 (t) cc_final: 0.8786 (t) REVERT: B 192 CYS cc_start: 0.8234 (t) cc_final: 0.7847 (t) REVERT: B 212 ASN cc_start: 0.8229 (t0) cc_final: 0.7741 (t0) REVERT: B 238 ASN cc_start: 0.7822 (m-40) cc_final: 0.7544 (m-40) REVERT: B 331 CYS cc_start: 0.8192 (m) cc_final: 0.7860 (m) REVERT: B 428 ASN cc_start: 0.7964 (t0) cc_final: 0.7617 (t0) REVERT: B 469 GLU cc_start: 0.8256 (tt0) cc_final: 0.8009 (tt0) REVERT: C 69 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8696 (ttmm) REVERT: C 89 GLN cc_start: 0.7668 (tp40) cc_final: 0.7281 (pt0) REVERT: C 182 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7638 (mt-10) REVERT: C 212 ASN cc_start: 0.8317 (t0) cc_final: 0.7923 (t0) REVERT: C 239 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8290 (mt) REVERT: C 263 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7880 (mtpt) REVERT: C 278 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8242 (mt) REVERT: C 297 ASP cc_start: 0.7587 (m-30) cc_final: 0.7306 (m-30) REVERT: C 331 CYS cc_start: 0.8377 (m) cc_final: 0.8152 (m) REVERT: C 394 CYS cc_start: 0.7796 (t) cc_final: 0.7576 (t) REVERT: C 469 GLU cc_start: 0.8289 (tt0) cc_final: 0.8045 (tp30) REVERT: D 64 THR cc_start: 0.8598 (m) cc_final: 0.8392 (m) REVERT: D 91 MET cc_start: 0.7872 (mtm) cc_final: 0.7651 (mtp) REVERT: G 28 SER cc_start: 0.8771 (m) cc_final: 0.8285 (p) REVERT: H 28 SER cc_start: 0.8577 (m) cc_final: 0.8193 (p) REVERT: H 118 TRP cc_start: 0.8470 (m100) cc_final: 0.7955 (m100) REVERT: I 28 SER cc_start: 0.8757 (m) cc_final: 0.8288 (p) outliers start: 55 outliers final: 33 residues processed: 445 average time/residue: 0.3005 time to fit residues: 190.4189 Evaluate side-chains 443 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 408 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 59 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 chunk 165 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 380 ASN B 305 ASN B 380 ASN B 446 ASN C 305 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107571 restraints weight = 22887.482| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.48 r_work: 0.3146 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15450 Z= 0.150 Angle : 0.496 7.351 20919 Z= 0.263 Chirality : 0.043 0.152 2469 Planarity : 0.003 0.051 2673 Dihedral : 4.939 81.110 2136 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.60 % Allowed : 13.59 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1932 helix: 1.49 (0.26), residues: 450 sheet: 0.32 (0.21), residues: 576 loop : 0.32 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 118 HIS 0.003 0.001 HIS C 206 PHE 0.012 0.001 PHE C 346 TYR 0.014 0.001 TYR B 207 ARG 0.005 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 410 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 57 ILE cc_start: 0.8726 (mm) cc_final: 0.8412 (mm) REVERT: A 66 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 73 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7799 (ttm110) REVERT: A 263 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7935 (mtpt) REVERT: A 270 ASP cc_start: 0.7564 (t0) cc_final: 0.7302 (t0) REVERT: A 432 GLU cc_start: 0.7491 (mp0) cc_final: 0.7180 (mp0) REVERT: A 459 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7499 (mt-10) REVERT: B 63 CYS cc_start: 0.8702 (t) cc_final: 0.8342 (t) REVERT: B 70 GLN cc_start: 0.8593 (tp40) cc_final: 0.8356 (tp-100) REVERT: B 73 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7815 (ttm110) REVERT: B 92 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7089 (m) REVERT: B 184 VAL cc_start: 0.8947 (t) cc_final: 0.8719 (t) REVERT: B 192 CYS cc_start: 0.7975 (t) cc_final: 0.7441 (t) REVERT: B 212 ASN cc_start: 0.8216 (t0) cc_final: 0.7695 (t0) REVERT: B 238 ASN cc_start: 0.7770 (m-40) cc_final: 0.7466 (t0) REVERT: B 331 CYS cc_start: 0.8158 (m) cc_final: 0.7825 (m) REVERT: B 400 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7631 (ttm-80) REVERT: B 428 ASN cc_start: 0.7897 (t0) cc_final: 0.7530 (t0) REVERT: B 469 GLU cc_start: 0.8237 (tt0) cc_final: 0.7999 (tt0) REVERT: C 47 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7898 (mmt-90) REVERT: C 53 LEU cc_start: 0.8743 (mt) cc_final: 0.8436 (mp) REVERT: C 69 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8637 (ttmm) REVERT: C 89 GLN cc_start: 0.7698 (tp40) cc_final: 0.7325 (pt0) REVERT: C 92 VAL cc_start: 0.7318 (m) cc_final: 0.6908 (p) REVERT: C 182 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7575 (mt-10) REVERT: C 212 ASN cc_start: 0.8317 (t0) cc_final: 0.8061 (t0) REVERT: C 239 ILE cc_start: 0.8528 (mm) cc_final: 0.8298 (mt) REVERT: C 263 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7861 (mtpt) REVERT: C 297 ASP cc_start: 0.7599 (m-30) cc_final: 0.7311 (m-30) REVERT: C 412 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8205 (mt) REVERT: C 469 GLU cc_start: 0.8285 (tt0) cc_final: 0.8060 (tp30) REVERT: G 28 SER cc_start: 0.8773 (m) cc_final: 0.8313 (p) REVERT: H 28 SER cc_start: 0.8600 (m) cc_final: 0.8254 (p) REVERT: H 118 TRP cc_start: 0.8513 (m100) cc_final: 0.7980 (m100) REVERT: I 28 SER cc_start: 0.8718 (m) cc_final: 0.8220 (p) outliers start: 44 outliers final: 26 residues processed: 428 average time/residue: 0.3124 time to fit residues: 188.0933 Evaluate side-chains 431 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 402 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 87 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 380 ASN A 399 ASN B 305 ASN B 380 ASN B 446 ASN C 70 GLN C 305 ASN C 446 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104535 restraints weight = 23035.721| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.49 r_work: 0.3108 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15450 Z= 0.353 Angle : 0.573 7.666 20919 Z= 0.299 Chirality : 0.045 0.206 2469 Planarity : 0.004 0.045 2673 Dihedral : 5.072 80.163 2136 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.37 % Allowed : 14.54 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1932 helix: 1.34 (0.25), residues: 450 sheet: 0.19 (0.21), residues: 585 loop : 0.20 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 118 HIS 0.003 0.001 HIS B 206 PHE 0.019 0.002 PHE B 427 TYR 0.022 0.002 TYR C 338 ARG 0.006 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 425 time to evaluate : 1.726 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 66 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 73 ARG cc_start: 0.8089 (ttm110) cc_final: 0.7839 (ttm110) REVERT: A 263 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7979 (mtpt) REVERT: A 270 ASP cc_start: 0.7558 (t0) cc_final: 0.7299 (t0) REVERT: A 294 TYR cc_start: 0.8689 (m-80) cc_final: 0.8404 (m-80) REVERT: A 432 GLU cc_start: 0.7503 (mp0) cc_final: 0.7202 (mp0) REVERT: A 459 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7548 (mt-10) REVERT: B 63 CYS cc_start: 0.8717 (t) cc_final: 0.8383 (t) REVERT: B 67 GLN cc_start: 0.8063 (mp10) cc_final: 0.7751 (mp10) REVERT: B 70 GLN cc_start: 0.8659 (tp40) cc_final: 0.8446 (tp-100) REVERT: B 73 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7903 (ttm110) REVERT: B 169 ILE cc_start: 0.8467 (mt) cc_final: 0.8222 (mt) REVERT: B 192 CYS cc_start: 0.8169 (t) cc_final: 0.7774 (t) REVERT: B 212 ASN cc_start: 0.8226 (t0) cc_final: 0.7745 (t0) REVERT: B 238 ASN cc_start: 0.7779 (m-40) cc_final: 0.7505 (m-40) REVERT: B 331 CYS cc_start: 0.8243 (m) cc_final: 0.7901 (m) REVERT: B 365 ARG cc_start: 0.8455 (ptt90) cc_final: 0.8141 (ptt-90) REVERT: B 400 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7685 (ttm-80) REVERT: B 428 ASN cc_start: 0.7967 (t0) cc_final: 0.7596 (t0) REVERT: B 469 GLU cc_start: 0.8230 (tt0) cc_final: 0.8000 (tt0) REVERT: C 42 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7778 (mm-40) REVERT: C 53 LEU cc_start: 0.8733 (mt) cc_final: 0.8452 (mp) REVERT: C 78 LEU cc_start: 0.8547 (tp) cc_final: 0.8272 (tt) REVERT: C 169 ILE cc_start: 0.8184 (mt) cc_final: 0.7831 (mt) REVERT: C 182 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7619 (mt-10) REVERT: C 212 ASN cc_start: 0.8364 (t0) cc_final: 0.7950 (t0) REVERT: C 239 ILE cc_start: 0.8512 (mm) cc_final: 0.8283 (mt) REVERT: C 263 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7832 (mtpt) REVERT: C 297 ASP cc_start: 0.7606 (m-30) cc_final: 0.7314 (m-30) REVERT: C 426 LEU cc_start: 0.8289 (mt) cc_final: 0.8079 (mt) REVERT: C 469 GLU cc_start: 0.8281 (tt0) cc_final: 0.8039 (tp30) REVERT: G 28 SER cc_start: 0.8834 (m) cc_final: 0.8367 (p) REVERT: H 28 SER cc_start: 0.8749 (m) cc_final: 0.8359 (p) REVERT: H 118 TRP cc_start: 0.8527 (m100) cc_final: 0.7955 (m100) REVERT: I 28 SER cc_start: 0.8713 (m) cc_final: 0.8231 (p) outliers start: 57 outliers final: 39 residues processed: 448 average time/residue: 0.3116 time to fit residues: 197.3967 Evaluate side-chains 452 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 412 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 113 optimal weight: 0.0060 chunk 3 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 191 optimal weight: 0.0980 chunk 128 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 380 ASN B 380 ASN C 305 ASN C 386 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.132488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106604 restraints weight = 22824.529| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.48 r_work: 0.3125 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15450 Z= 0.209 Angle : 0.515 7.077 20919 Z= 0.272 Chirality : 0.043 0.170 2469 Planarity : 0.003 0.042 2673 Dihedral : 4.967 78.951 2136 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.13 % Allowed : 15.43 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1932 helix: 1.30 (0.25), residues: 471 sheet: 0.19 (0.21), residues: 585 loop : 0.20 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 118 HIS 0.001 0.000 HIS A 350 PHE 0.013 0.001 PHE C 346 TYR 0.015 0.002 TYR C 338 ARG 0.006 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 420 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8041 (mp10) cc_final: 0.7708 (mp10) REVERT: A 73 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7803 (ttm110) REVERT: A 169 ILE cc_start: 0.8377 (mt) cc_final: 0.8124 (mt) REVERT: A 260 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 263 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7979 (mtpt) REVERT: A 270 ASP cc_start: 0.7549 (t0) cc_final: 0.7303 (t0) REVERT: A 294 TYR cc_start: 0.8664 (m-80) cc_final: 0.8398 (m-80) REVERT: A 362 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8015 (mm-40) REVERT: A 432 GLU cc_start: 0.7531 (mp0) cc_final: 0.7228 (mp0) REVERT: A 459 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7487 (mt-10) REVERT: B 67 GLN cc_start: 0.8008 (mp10) cc_final: 0.7743 (mp10) REVERT: B 70 GLN cc_start: 0.8647 (tp40) cc_final: 0.8436 (tp-100) REVERT: B 73 ARG cc_start: 0.8066 (ttm110) cc_final: 0.7843 (ttm170) REVERT: B 169 ILE cc_start: 0.8443 (mt) cc_final: 0.8175 (mt) REVERT: B 212 ASN cc_start: 0.8216 (t0) cc_final: 0.7732 (t0) REVERT: B 238 ASN cc_start: 0.7773 (m-40) cc_final: 0.7488 (t0) REVERT: B 288 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7868 (mt) REVERT: B 375 ARG cc_start: 0.8486 (mtt90) cc_final: 0.8268 (mpt90) REVERT: B 400 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7680 (ttm-80) REVERT: B 428 ASN cc_start: 0.7926 (t0) cc_final: 0.7534 (t0) REVERT: B 469 GLU cc_start: 0.8231 (tt0) cc_final: 0.7998 (tt0) REVERT: C 42 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7754 (mm-40) REVERT: C 53 LEU cc_start: 0.8723 (mt) cc_final: 0.8451 (mp) REVERT: C 169 ILE cc_start: 0.8120 (mt) cc_final: 0.7758 (mt) REVERT: C 182 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7630 (mt-10) REVERT: C 212 ASN cc_start: 0.8365 (t0) cc_final: 0.7959 (t0) REVERT: C 239 ILE cc_start: 0.8494 (mm) cc_final: 0.8276 (mt) REVERT: C 263 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7825 (mtpt) REVERT: C 278 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8227 (mt) REVERT: C 297 ASP cc_start: 0.7585 (m-30) cc_final: 0.7282 (m-30) REVERT: C 412 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8199 (mt) REVERT: C 426 LEU cc_start: 0.8281 (mt) cc_final: 0.8080 (mt) REVERT: C 469 GLU cc_start: 0.8267 (tt0) cc_final: 0.8037 (tp30) REVERT: G 28 SER cc_start: 0.8804 (m) cc_final: 0.8354 (p) REVERT: H 28 SER cc_start: 0.8759 (m) cc_final: 0.8385 (p) REVERT: H 118 TRP cc_start: 0.8541 (m100) cc_final: 0.7929 (m100) REVERT: I 28 SER cc_start: 0.8704 (m) cc_final: 0.8223 (p) outliers start: 53 outliers final: 39 residues processed: 442 average time/residue: 0.3063 time to fit residues: 192.2271 Evaluate side-chains 447 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 404 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 117 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 305 ASN A 380 ASN B 380 ASN C 305 ASN C 446 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104852 restraints weight = 22769.855| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.48 r_work: 0.3096 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15450 Z= 0.352 Angle : 0.577 7.323 20919 Z= 0.301 Chirality : 0.045 0.198 2469 Planarity : 0.004 0.046 2673 Dihedral : 5.069 77.025 2136 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.01 % Allowed : 16.02 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1932 helix: 1.15 (0.25), residues: 471 sheet: 0.14 (0.21), residues: 636 loop : 0.10 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 118 HIS 0.002 0.001 HIS C 315 PHE 0.019 0.002 PHE B 427 TYR 0.022 0.002 TYR C 338 ARG 0.007 0.001 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 420 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7809 (ttm110) REVERT: A 169 ILE cc_start: 0.8354 (mt) cc_final: 0.8102 (mt) REVERT: A 263 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7970 (mtpt) REVERT: A 270 ASP cc_start: 0.7603 (t0) cc_final: 0.7338 (t0) REVERT: A 294 TYR cc_start: 0.8693 (m-80) cc_final: 0.8430 (m-80) REVERT: A 432 GLU cc_start: 0.7560 (mp0) cc_final: 0.7263 (mp0) REVERT: A 459 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7530 (mt-10) REVERT: B 73 ARG cc_start: 0.8089 (ttm110) cc_final: 0.7884 (ttm170) REVERT: B 169 ILE cc_start: 0.8463 (mt) cc_final: 0.8196 (mt) REVERT: B 212 ASN cc_start: 0.8226 (t0) cc_final: 0.7772 (t0) REVERT: B 238 ASN cc_start: 0.7812 (m-40) cc_final: 0.7536 (m-40) REVERT: B 331 CYS cc_start: 0.8239 (m) cc_final: 0.7854 (m) REVERT: B 375 ARG cc_start: 0.8489 (mtt90) cc_final: 0.8248 (mpt90) REVERT: B 400 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7649 (ttm-80) REVERT: B 428 ASN cc_start: 0.7969 (t0) cc_final: 0.7574 (t0) REVERT: B 469 GLU cc_start: 0.8213 (tt0) cc_final: 0.7985 (tt0) REVERT: C 53 LEU cc_start: 0.8726 (mt) cc_final: 0.8456 (mp) REVERT: C 169 ILE cc_start: 0.8173 (mt) cc_final: 0.7827 (mt) REVERT: C 182 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7640 (mt-10) REVERT: C 212 ASN cc_start: 0.8384 (t0) cc_final: 0.7995 (t0) REVERT: C 239 ILE cc_start: 0.8500 (mm) cc_final: 0.8279 (mt) REVERT: C 278 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8273 (mt) REVERT: C 297 ASP cc_start: 0.7631 (m-30) cc_final: 0.7338 (m-30) REVERT: C 469 GLU cc_start: 0.8263 (tt0) cc_final: 0.8033 (tp30) REVERT: D 65 LEU cc_start: 0.8587 (mp) cc_final: 0.8346 (mp) REVERT: G 28 SER cc_start: 0.8817 (m) cc_final: 0.8375 (p) REVERT: H 28 SER cc_start: 0.8703 (m) cc_final: 0.8330 (p) REVERT: H 118 TRP cc_start: 0.8532 (m100) cc_final: 0.7878 (m100) REVERT: I 28 SER cc_start: 0.8768 (m) cc_final: 0.8295 (p) outliers start: 51 outliers final: 44 residues processed: 441 average time/residue: 0.3099 time to fit residues: 193.5356 Evaluate side-chains 471 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 425 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 107 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN B 70 GLN B 302 ASN B 380 ASN C 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105329 restraints weight = 22853.360| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.49 r_work: 0.3121 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15450 Z= 0.261 Angle : 0.551 8.043 20919 Z= 0.287 Chirality : 0.044 0.186 2469 Planarity : 0.004 0.043 2673 Dihedral : 4.959 74.618 2136 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.13 % Allowed : 16.61 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1932 helix: 1.15 (0.25), residues: 471 sheet: -0.02 (0.21), residues: 606 loop : 0.18 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 118 HIS 0.001 0.000 HIS C 315 PHE 0.013 0.002 PHE C 346 TYR 0.020 0.002 TYR C 338 ARG 0.008 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 417 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7793 (ttm110) REVERT: A 169 ILE cc_start: 0.8324 (mt) cc_final: 0.8020 (mt) REVERT: A 263 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7946 (mtpt) REVERT: A 270 ASP cc_start: 0.7608 (t0) cc_final: 0.7325 (t0) REVERT: A 294 TYR cc_start: 0.8673 (m-80) cc_final: 0.8394 (m-80) REVERT: A 362 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8065 (mm-40) REVERT: A 432 GLU cc_start: 0.7531 (mp0) cc_final: 0.7233 (mp0) REVERT: A 459 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7482 (mt-10) REVERT: B 169 ILE cc_start: 0.8445 (mt) cc_final: 0.8167 (mt) REVERT: B 195 CYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7117 (m) REVERT: B 212 ASN cc_start: 0.8243 (t0) cc_final: 0.7758 (t0) REVERT: B 238 ASN cc_start: 0.7784 (m-40) cc_final: 0.7512 (m-40) REVERT: B 331 CYS cc_start: 0.8237 (m) cc_final: 0.7847 (m) REVERT: B 375 ARG cc_start: 0.8460 (mtt90) cc_final: 0.8253 (mpt90) REVERT: B 400 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7660 (ttm-80) REVERT: B 428 ASN cc_start: 0.7959 (t0) cc_final: 0.7546 (t0) REVERT: B 469 GLU cc_start: 0.8216 (tt0) cc_final: 0.7992 (tt0) REVERT: C 53 LEU cc_start: 0.8711 (mt) cc_final: 0.8448 (mp) REVERT: C 169 ILE cc_start: 0.8130 (mt) cc_final: 0.7767 (mt) REVERT: C 182 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 204 ASP cc_start: 0.7834 (t0) cc_final: 0.7578 (t0) REVERT: C 212 ASN cc_start: 0.8396 (t0) cc_final: 0.7998 (t0) REVERT: C 237 THR cc_start: 0.8181 (m) cc_final: 0.7803 (p) REVERT: C 239 ILE cc_start: 0.8505 (mm) cc_final: 0.8293 (mt) REVERT: C 278 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8233 (mt) REVERT: C 297 ASP cc_start: 0.7630 (m-30) cc_final: 0.7340 (m-30) REVERT: C 469 GLU cc_start: 0.8255 (tt0) cc_final: 0.8020 (tp30) REVERT: G 28 SER cc_start: 0.8778 (m) cc_final: 0.8343 (p) REVERT: H 28 SER cc_start: 0.8701 (m) cc_final: 0.8336 (p) REVERT: I 28 SER cc_start: 0.8768 (m) cc_final: 0.8295 (p) outliers start: 53 outliers final: 45 residues processed: 440 average time/residue: 0.3019 time to fit residues: 188.6831 Evaluate side-chains 448 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 400 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 187 optimal weight: 0.0000 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 380 ASN A 407 GLN B 70 GLN B 380 ASN C 446 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106500 restraints weight = 22929.718| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.50 r_work: 0.3140 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15450 Z= 0.210 Angle : 0.534 8.696 20919 Z= 0.278 Chirality : 0.043 0.153 2469 Planarity : 0.004 0.059 2673 Dihedral : 4.789 70.644 2136 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.60 % Allowed : 17.32 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 1932 helix: 1.28 (0.25), residues: 480 sheet: 0.06 (0.21), residues: 576 loop : 0.16 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 118 HIS 0.002 0.000 HIS C 206 PHE 0.013 0.001 PHE C 346 TYR 0.020 0.002 TYR C 338 ARG 0.008 0.000 ARG A 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 411 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8383 (mtpp) REVERT: A 73 ARG cc_start: 0.7999 (ttm110) cc_final: 0.7758 (ttm110) REVERT: A 237 THR cc_start: 0.8258 (m) cc_final: 0.7721 (p) REVERT: A 263 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7944 (mtpt) REVERT: A 270 ASP cc_start: 0.7603 (t0) cc_final: 0.7316 (t0) REVERT: A 294 TYR cc_start: 0.8661 (m-80) cc_final: 0.8373 (m-80) REVERT: A 354 SER cc_start: 0.8075 (m) cc_final: 0.7605 (p) REVERT: A 431 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7772 (mmtt) REVERT: A 432 GLU cc_start: 0.7469 (mp0) cc_final: 0.7197 (mp0) REVERT: B 92 VAL cc_start: 0.7545 (OUTLIER) cc_final: 0.7153 (p) REVERT: B 169 ILE cc_start: 0.8402 (mt) cc_final: 0.8106 (mt) REVERT: B 195 CYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7077 (m) REVERT: B 212 ASN cc_start: 0.8209 (t0) cc_final: 0.7725 (t0) REVERT: B 237 THR cc_start: 0.8387 (m) cc_final: 0.7883 (p) REVERT: B 238 ASN cc_start: 0.7774 (m-40) cc_final: 0.7542 (t0) REVERT: B 331 CYS cc_start: 0.8251 (m) cc_final: 0.7876 (m) REVERT: B 400 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7631 (ttm-80) REVERT: B 428 ASN cc_start: 0.7943 (t0) cc_final: 0.7517 (t0) REVERT: B 469 GLU cc_start: 0.8218 (tt0) cc_final: 0.8008 (tt0) REVERT: C 47 ARG cc_start: 0.8261 (mtt90) cc_final: 0.7974 (mmt-90) REVERT: C 53 LEU cc_start: 0.8699 (mt) cc_final: 0.8445 (mp) REVERT: C 169 ILE cc_start: 0.8064 (mt) cc_final: 0.7675 (mt) REVERT: C 182 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7587 (mt-10) REVERT: C 212 ASN cc_start: 0.8352 (t0) cc_final: 0.7992 (t0) REVERT: C 237 THR cc_start: 0.8144 (m) cc_final: 0.7758 (p) REVERT: C 239 ILE cc_start: 0.8521 (mm) cc_final: 0.8235 (mt) REVERT: C 278 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8221 (mt) REVERT: C 297 ASP cc_start: 0.7620 (m-30) cc_final: 0.7333 (m-30) REVERT: C 469 GLU cc_start: 0.8264 (tt0) cc_final: 0.8027 (tp30) REVERT: G 28 SER cc_start: 0.8784 (m) cc_final: 0.8336 (p) REVERT: H 28 SER cc_start: 0.8692 (m) cc_final: 0.8337 (p) REVERT: I 28 SER cc_start: 0.8765 (m) cc_final: 0.8302 (p) outliers start: 44 outliers final: 34 residues processed: 432 average time/residue: 0.3372 time to fit residues: 209.0420 Evaluate side-chains 435 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 397 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 121 optimal weight: 0.1980 chunk 127 optimal weight: 1.9990 chunk 29 optimal weight: 0.0170 chunk 61 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 380 ASN B 305 ASN B 380 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107857 restraints weight = 22651.681| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.48 r_work: 0.3158 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15450 Z= 0.163 Angle : 0.520 8.821 20919 Z= 0.269 Chirality : 0.042 0.145 2469 Planarity : 0.003 0.038 2673 Dihedral : 4.569 65.500 2136 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.30 % Allowed : 18.26 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1932 helix: 1.50 (0.25), residues: 471 sheet: 0.15 (0.21), residues: 582 loop : 0.18 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 118 HIS 0.002 0.001 HIS C 206 PHE 0.012 0.001 PHE C 346 TYR 0.018 0.002 TYR C 178 ARG 0.007 0.000 ARG A 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8124.25 seconds wall clock time: 145 minutes 7.69 seconds (8707.69 seconds total)