Starting phenix.real_space_refine on Sat Aug 23 23:03:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v62_42987/08_2025/8v62_42987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v62_42987/08_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_42987/08_2025/8v62_42987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v62_42987/08_2025/8v62_42987.map" model { file = "/net/cci-nas-00/data/ceres_data/8v62_42987/08_2025/8v62_42987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v62_42987/08_2025/8v62_42987.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: "D" 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: B, C, E, F, H, I Time building chain proxies: 2.78, per 1000 atoms: 0.18 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=18, 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 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 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: 0.87 Conformation dependent library (CDL) restraints added in 710.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.62 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: 2.63 Time building geometry restraints manager: 1.26 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: 8848 16.89 - 33.78: 442 33.78 - 50.66: 73 50.66 - 67.55: 12 67.55 - 84.44: 9 Dihedral angle restraints: 9384 sinusoidal: 3705 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 9381 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 - 2.61: 99 2.61 - 3.18: 12779 3.18 - 3.75: 21635 3.75 - 4.33: 31120 4.33 - 4.90: 51908 Nonbonded interactions: 117541 Sorted by model distance: nonbonded pdb=" SG CYS E 23 " pdb=" SG CYS E 104 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS F 23 " pdb=" SG CYS F 104 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS D 23 " pdb=" SG CYS D 104 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS I 23 " pdb=" SG CYS I 104 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS G 23 " pdb=" SG CYS G 104 " model vdw 2.035 3.760 ... (remaining 117536 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.880 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.670 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.890 ------------------------------------------------------------------------------- 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 15468 Z= 0.099 Angle : 0.562 6.308 20955 Z= 0.318 Chirality : 0.044 0.157 2469 Planarity : 0.007 0.074 2673 Dihedral : 10.429 84.440 5682 Min Nonbonded Distance : 2.032 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (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 ARG 0.018 0.003 ARG G 43 TYR 0.020 0.004 TYR B 338 PHE 0.014 0.001 PHE A 346 TRP 0.021 0.002 TRP G 118 HIS 0.001 0.000 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00223 (15450) covalent geometry : angle 0.56065 (20919) SS BOND : bond 0.00248 ( 18) SS BOND : angle 1.21078 ( 36) hydrogen bonds : bond 0.20215 ( 738) hydrogen bonds : angle 7.92714 ( 2061) *********************** 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 : 0.426 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: 0.1093 time to fit residues: 74.4069 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 : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0060 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 302 ASN 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 Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108111 restraints weight = 22505.390| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.48 r_work: 0.3152 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15468 Z= 0.153 Angle : 0.549 6.353 20955 Z= 0.295 Chirality : 0.044 0.150 2469 Planarity : 0.004 0.034 2673 Dihedral : 4.789 83.651 2136 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.25 % Allowed : 7.86 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.19), residues: 1932 helix: 1.19 (0.25), residues: 450 sheet: 0.61 (0.22), residues: 585 loop : 0.59 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 236 TYR 0.019 0.002 TYR B 207 PHE 0.011 0.001 PHE A 346 TRP 0.012 0.001 TRP G 118 HIS 0.002 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00330 (15450) covalent geometry : angle 0.54623 (20919) SS BOND : bond 0.00433 ( 18) SS BOND : angle 1.43951 ( 36) hydrogen bonds : bond 0.05492 ( 738) hydrogen bonds : angle 5.56357 ( 2061) *********************** 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 465 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 427 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.8677 (mm) cc_final: 0.8316 (mm) REVERT: A 65 ASP cc_start: 0.7692 (p0) cc_final: 0.7490 (p0) REVERT: A 66 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 70 GLN cc_start: 0.8571 (tp40) cc_final: 0.8289 (tp-100) REVERT: A 73 ARG cc_start: 0.8072 (ttm110) cc_final: 0.7752 (ttm110) REVERT: A 190 LEU cc_start: 0.8770 (mt) cc_final: 0.8529 (mp) REVERT: A 205 GLN cc_start: 0.7925 (mt0) cc_final: 0.7705 (mt0) REVERT: A 229 GLN cc_start: 0.8283 (tp40) cc_final: 0.7845 (tp40) REVERT: A 263 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7941 (mtpt) REVERT: A 270 ASP cc_start: 0.7622 (t0) cc_final: 0.7288 (t0) REVERT: A 432 GLU cc_start: 0.7499 (mp0) cc_final: 0.7152 (mp0) REVERT: B 63 CYS cc_start: 0.7766 (t) cc_final: 0.7541 (t) REVERT: B 65 ASP cc_start: 0.7859 (p0) cc_final: 0.7615 (p0) REVERT: B 70 GLN cc_start: 0.8606 (tp40) cc_final: 0.8252 (tp-100) REVERT: B 73 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7694 (ttm110) REVERT: B 212 ASN cc_start: 0.8113 (t0) cc_final: 0.7567 (t0) REVERT: B 214 PHE cc_start: 0.8334 (m-80) cc_final: 0.8089 (m-80) REVERT: B 263 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7773 (mtpt) REVERT: B 272 ASN cc_start: 0.7984 (m-40) cc_final: 0.7742 (m-40) REVERT: B 281 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7667 (mtm-85) REVERT: B 296 VAL cc_start: 0.8198 (t) cc_final: 0.7951 (m) REVERT: B 432 GLU cc_start: 0.7225 (mp0) cc_final: 0.6641 (mp0) REVERT: B 469 GLU cc_start: 0.8254 (tt0) cc_final: 0.7956 (tt0) REVERT: B 471 LYS cc_start: 0.7699 (mtpp) cc_final: 0.7386 (ttmm) REVERT: C 69 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8656 (ttmm) REVERT: C 76 ASP cc_start: 0.8029 (m-30) cc_final: 0.7598 (m-30) REVERT: C 83 TYR cc_start: 0.8346 (t80) cc_final: 0.8074 (t80) REVERT: C 212 ASN cc_start: 0.8316 (t0) cc_final: 0.7918 (t0) REVERT: C 262 ILE cc_start: 0.8250 (mt) cc_final: 0.8000 (mm) REVERT: C 274 TYR cc_start: 0.8708 (m-80) cc_final: 0.8049 (m-80) REVERT: C 297 ASP cc_start: 0.7560 (m-30) cc_final: 0.7299 (m-30) REVERT: C 464 LYS cc_start: 0.8363 (mtpp) cc_final: 0.8051 (mttm) REVERT: C 469 GLU cc_start: 0.8299 (tt0) cc_final: 0.8055 (tp30) REVERT: G 118 TRP cc_start: 0.8516 (m100) cc_final: 0.7975 (m100) REVERT: H 28 SER cc_start: 0.8512 (m) cc_final: 0.8069 (p) outliers start: 38 outliers final: 22 residues processed: 442 average time/residue: 0.1240 time to fit residues: 77.2898 Evaluate side-chains 437 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 415 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 186 CYS 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 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 117 optimal weight: 0.1980 chunk 49 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108223 restraints weight = 22666.240| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.49 r_work: 0.3148 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15468 Z= 0.144 Angle : 0.531 6.834 20955 Z= 0.279 Chirality : 0.043 0.148 2469 Planarity : 0.003 0.040 2673 Dihedral : 4.861 83.002 2136 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.07 % Allowed : 10.40 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.19), residues: 1932 helix: 1.51 (0.25), residues: 450 sheet: 0.56 (0.21), residues: 576 loop : 0.51 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 281 TYR 0.021 0.002 TYR B 207 PHE 0.011 0.001 PHE A 346 TRP 0.011 0.001 TRP E 118 HIS 0.001 0.000 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00318 (15450) covalent geometry : angle 0.52808 (20919) SS BOND : bond 0.00291 ( 18) SS BOND : angle 1.34389 ( 36) hydrogen bonds : bond 0.04700 ( 738) hydrogen bonds : angle 5.20905 ( 2061) *********************** 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 453 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 418 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.8699 (mm) cc_final: 0.8335 (mm) REVERT: A 66 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7294 (tm-30) REVERT: A 70 GLN cc_start: 0.8605 (tp40) cc_final: 0.8097 (tp-100) REVERT: A 73 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7728 (ttm110) REVERT: A 178 TYR cc_start: 0.8781 (t80) cc_final: 0.8518 (t80) REVERT: A 190 LEU cc_start: 0.8865 (mt) cc_final: 0.8639 (mp) REVERT: A 270 ASP cc_start: 0.7660 (t0) cc_final: 0.7417 (t0) REVERT: A 432 GLU cc_start: 0.7526 (mp0) cc_final: 0.7191 (mp0) REVERT: A 462 LYS cc_start: 0.8051 (tptt) cc_final: 0.7813 (tptt) REVERT: B 63 CYS cc_start: 0.7946 (t) cc_final: 0.7740 (t) REVERT: B 70 GLN cc_start: 0.8587 (tp40) cc_final: 0.8329 (tp-100) REVERT: B 73 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7760 (ttm110) REVERT: B 212 ASN cc_start: 0.8175 (t0) cc_final: 0.7622 (t0) REVERT: B 214 PHE cc_start: 0.8299 (m-80) cc_final: 0.8038 (m-80) REVERT: B 263 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7772 (mtpt) REVERT: B 281 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7635 (mtm-85) REVERT: B 296 VAL cc_start: 0.8214 (t) cc_final: 0.7975 (m) REVERT: B 365 ARG cc_start: 0.8454 (ptt90) cc_final: 0.8239 (ptt-90) REVERT: B 432 GLU cc_start: 0.7238 (mp0) cc_final: 0.6652 (mp0) REVERT: B 469 GLU cc_start: 0.8252 (tt0) cc_final: 0.7994 (tt0) REVERT: B 471 LYS cc_start: 0.7687 (mtpp) cc_final: 0.7397 (ttmm) REVERT: C 21 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: C 69 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8694 (ttmm) REVERT: C 83 TYR cc_start: 0.8334 (t80) cc_final: 0.8110 (t80) REVERT: C 89 GLN cc_start: 0.7666 (tp40) cc_final: 0.7227 (pt0) REVERT: C 92 VAL cc_start: 0.7447 (m) cc_final: 0.6234 (t) REVERT: C 212 ASN cc_start: 0.8291 (t0) cc_final: 0.7920 (t0) REVERT: C 262 ILE cc_start: 0.8223 (mt) cc_final: 0.7980 (mm) REVERT: C 263 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7937 (mtpt) REVERT: C 297 ASP cc_start: 0.7574 (m-30) cc_final: 0.7326 (m-30) REVERT: C 464 LYS cc_start: 0.8372 (mtpp) cc_final: 0.8032 (mttm) REVERT: C 469 GLU cc_start: 0.8291 (tt0) cc_final: 0.8042 (tp30) REVERT: H 28 SER cc_start: 0.8518 (m) cc_final: 0.8105 (p) outliers start: 35 outliers final: 23 residues processed: 432 average time/residue: 0.1491 time to fit residues: 90.9982 Evaluate side-chains 420 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 396 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 186 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 ILE 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 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 155 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 131 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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 205 GLN B 380 ASN C 305 ASN C 446 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.132836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107074 restraints weight = 22524.176| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.45 r_work: 0.3125 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15468 Z= 0.182 Angle : 0.544 7.129 20955 Z= 0.286 Chirality : 0.044 0.158 2469 Planarity : 0.004 0.045 2673 Dihedral : 4.980 81.859 2136 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.90 % Allowed : 11.52 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.19), residues: 1932 helix: 1.32 (0.25), residues: 474 sheet: 0.35 (0.21), residues: 585 loop : 0.50 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 47 TYR 0.017 0.002 TYR C 338 PHE 0.015 0.002 PHE B 427 TRP 0.013 0.001 TRP E 118 HIS 0.001 0.000 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00407 (15450) covalent geometry : angle 0.54111 (20919) SS BOND : bond 0.00496 ( 18) SS BOND : angle 1.51853 ( 36) hydrogen bonds : bond 0.04528 ( 738) hydrogen bonds : angle 5.06668 ( 2061) *********************** 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 456 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 407 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.8710 (mm) cc_final: 0.8424 (mm) REVERT: A 66 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 70 GLN cc_start: 0.8619 (tp40) cc_final: 0.8138 (tp-100) REVERT: A 73 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7766 (ttm110) REVERT: A 190 LEU cc_start: 0.8942 (mt) cc_final: 0.8720 (mp) REVERT: A 270 ASP cc_start: 0.7627 (t0) cc_final: 0.7368 (t0) REVERT: A 432 GLU cc_start: 0.7502 (mp0) cc_final: 0.7168 (mp0) REVERT: A 459 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7577 (mt-10) REVERT: B 65 ASP cc_start: 0.7789 (p0) cc_final: 0.7548 (p0) REVERT: B 70 GLN cc_start: 0.8609 (tp40) cc_final: 0.8372 (tp-100) REVERT: B 73 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7867 (ttm110) REVERT: B 148 LYS cc_start: 0.8238 (mtmt) cc_final: 0.8020 (mtmt) REVERT: B 169 ILE cc_start: 0.8477 (mt) cc_final: 0.8275 (mt) REVERT: B 212 ASN cc_start: 0.8168 (t0) cc_final: 0.7669 (t0) REVERT: B 238 ASN cc_start: 0.7784 (m-40) cc_final: 0.7504 (m-40) REVERT: B 296 VAL cc_start: 0.8217 (t) cc_final: 0.7957 (m) REVERT: B 365 ARG cc_start: 0.8457 (ptt90) cc_final: 0.8232 (ptt-90) REVERT: B 469 GLU cc_start: 0.8229 (tt0) cc_final: 0.7997 (tt0) REVERT: C 69 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8703 (ttmm) REVERT: C 89 GLN cc_start: 0.7674 (tp40) cc_final: 0.7266 (pt0) REVERT: C 182 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7593 (mt-10) REVERT: C 212 ASN cc_start: 0.8269 (t0) cc_final: 0.8030 (t0) REVERT: C 239 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8252 (mt) REVERT: C 263 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7898 (mtpt) REVERT: C 297 ASP cc_start: 0.7575 (m-30) cc_final: 0.7290 (m-30) REVERT: C 464 LYS cc_start: 0.8382 (mtpp) cc_final: 0.8131 (mtpp) REVERT: C 469 GLU cc_start: 0.8289 (tt0) cc_final: 0.8044 (tp30) REVERT: D 64 THR cc_start: 0.8606 (m) cc_final: 0.8399 (m) REVERT: G 28 SER cc_start: 0.8764 (m) cc_final: 0.8293 (p) REVERT: H 28 SER cc_start: 0.8556 (m) cc_final: 0.8166 (p) REVERT: I 28 SER cc_start: 0.8749 (m) cc_final: 0.8254 (p) outliers start: 49 outliers final: 29 residues processed: 429 average time/residue: 0.1505 time to fit residues: 91.2224 Evaluate side-chains 431 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 401 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 156 LYS 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 A residue 467 LEU Chi-restraints excluded: chain B residue 76 ASP 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 211 THR Chi-restraints excluded: chain B residue 276 ILE 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 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 317 MET Chi-restraints excluded: chain C residue 459 GLU 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 10 optimal weight: 0.6980 chunk 117 optimal weight: 0.0970 chunk 144 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 380 ASN B 414 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107901 restraints weight = 22615.032| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.46 r_work: 0.3143 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15468 Z= 0.125 Angle : 0.514 10.633 20955 Z= 0.269 Chirality : 0.043 0.147 2469 Planarity : 0.003 0.055 2673 Dihedral : 4.872 80.703 2136 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.48 % Allowed : 12.94 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.19), residues: 1932 helix: 1.60 (0.25), residues: 450 sheet: 0.36 (0.21), residues: 585 loop : 0.39 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 189 TYR 0.015 0.002 TYR B 207 PHE 0.010 0.001 PHE C 346 TRP 0.008 0.001 TRP H 118 HIS 0.002 0.000 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00275 (15450) covalent geometry : angle 0.51130 (20919) SS BOND : bond 0.00263 ( 18) SS BOND : angle 1.38421 ( 36) hydrogen bonds : bond 0.04011 ( 738) hydrogen bonds : angle 4.91475 ( 2061) *********************** 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 445 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 403 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.8701 (mm) cc_final: 0.8401 (mm) REVERT: A 66 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 70 GLN cc_start: 0.8620 (tp40) cc_final: 0.8088 (tp-100) REVERT: A 73 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7720 (ttm110) REVERT: A 212 ASN cc_start: 0.8164 (t0) cc_final: 0.7757 (t0) REVERT: A 270 ASP cc_start: 0.7560 (t0) cc_final: 0.7333 (t0) REVERT: A 432 GLU cc_start: 0.7492 (mp0) cc_final: 0.7160 (mp0) REVERT: A 459 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7511 (mt-10) REVERT: B 70 GLN cc_start: 0.8603 (tp40) cc_final: 0.8379 (tp-100) REVERT: B 73 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7833 (ttm110) REVERT: B 169 ILE cc_start: 0.8449 (mt) cc_final: 0.8218 (mt) REVERT: B 212 ASN cc_start: 0.8177 (t0) cc_final: 0.7690 (t0) REVERT: B 238 ASN cc_start: 0.7759 (m-40) cc_final: 0.7457 (t0) REVERT: B 239 ILE cc_start: 0.8477 (mm) cc_final: 0.8269 (mt) REVERT: B 281 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7614 (mtm-85) REVERT: B 400 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7727 (ttm-80) REVERT: B 428 ASN cc_start: 0.7837 (t0) cc_final: 0.7621 (t0) REVERT: C 53 LEU cc_start: 0.8735 (mt) cc_final: 0.8431 (mp) REVERT: C 69 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8682 (ttmm) REVERT: C 169 ILE cc_start: 0.8166 (mt) cc_final: 0.7845 (mt) REVERT: C 182 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7525 (mt-10) REVERT: C 212 ASN cc_start: 0.8288 (t0) cc_final: 0.8072 (t0) REVERT: C 239 ILE cc_start: 0.8494 (mm) cc_final: 0.8276 (mt) REVERT: C 263 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7900 (mtpt) REVERT: C 278 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8213 (mt) REVERT: C 297 ASP cc_start: 0.7575 (m-30) cc_final: 0.7298 (m-30) REVERT: C 464 LYS cc_start: 0.8342 (mtpp) cc_final: 0.8104 (mtpp) REVERT: C 469 GLU cc_start: 0.8269 (tt0) cc_final: 0.8047 (tp30) REVERT: G 28 SER cc_start: 0.8760 (m) cc_final: 0.8313 (p) REVERT: H 28 SER cc_start: 0.8552 (m) cc_final: 0.8198 (p) REVERT: H 118 TRP cc_start: 0.8492 (m100) cc_final: 0.7951 (m100) REVERT: I 28 SER cc_start: 0.8704 (m) cc_final: 0.8220 (p) outliers start: 42 outliers final: 25 residues processed: 419 average time/residue: 0.1504 time to fit residues: 88.5372 Evaluate side-chains 417 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 390 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 B residue 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 ILE 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 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 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 314 SER Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 114 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 174 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 B 446 ASN C 70 GLN C 446 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107398 restraints weight = 22457.532| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.44 r_work: 0.3129 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15468 Z= 0.158 Angle : 0.526 10.608 20955 Z= 0.273 Chirality : 0.043 0.149 2469 Planarity : 0.003 0.039 2673 Dihedral : 4.872 79.369 2136 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.07 % Allowed : 14.01 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.19), residues: 1932 helix: 1.49 (0.25), residues: 456 sheet: 0.29 (0.21), residues: 585 loop : 0.32 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 189 TYR 0.016 0.002 TYR C 338 PHE 0.013 0.001 PHE B 427 TRP 0.009 0.001 TRP E 118 HIS 0.001 0.000 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00356 (15450) covalent geometry : angle 0.52302 (20919) SS BOND : bond 0.00469 ( 18) SS BOND : angle 1.46222 ( 36) hydrogen bonds : bond 0.04121 ( 738) hydrogen bonds : angle 4.91226 ( 2061) *********************** 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 456 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 404 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.8713 (mm) cc_final: 0.8412 (mm) REVERT: A 66 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 70 GLN cc_start: 0.8634 (tp40) cc_final: 0.8136 (tp-100) REVERT: A 73 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7724 (ttm110) REVERT: A 270 ASP cc_start: 0.7519 (t0) cc_final: 0.7272 (t0) REVERT: A 432 GLU cc_start: 0.7495 (mp0) cc_final: 0.7169 (mp0) REVERT: A 459 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7508 (mt-10) REVERT: B 70 GLN cc_start: 0.8631 (tp40) cc_final: 0.8421 (tp-100) REVERT: B 73 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7848 (ttm170) REVERT: B 92 VAL cc_start: 0.7617 (OUTLIER) cc_final: 0.7250 (p) REVERT: B 169 ILE cc_start: 0.8442 (mt) cc_final: 0.8196 (mt) REVERT: B 212 ASN cc_start: 0.8172 (t0) cc_final: 0.7714 (t0) REVERT: B 238 ASN cc_start: 0.7758 (m-40) cc_final: 0.7481 (m-40) REVERT: B 239 ILE cc_start: 0.8497 (mm) cc_final: 0.8278 (mt) REVERT: B 281 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7659 (mtm-85) REVERT: B 288 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7921 (mt) REVERT: B 365 ARG cc_start: 0.8455 (ptt90) cc_final: 0.8252 (ptt-90) REVERT: B 400 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7682 (ttm-80) REVERT: B 428 ASN cc_start: 0.7862 (t0) cc_final: 0.7560 (t0) REVERT: C 53 LEU cc_start: 0.8714 (mt) cc_final: 0.8430 (mp) REVERT: C 69 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8697 (ttmm) REVERT: C 169 ILE cc_start: 0.8124 (mt) cc_final: 0.7787 (mt) REVERT: C 182 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7563 (mt-10) REVERT: C 204 ASP cc_start: 0.7804 (t0) cc_final: 0.7517 (t0) REVERT: C 212 ASN cc_start: 0.8316 (t0) cc_final: 0.8084 (t0) REVERT: C 239 ILE cc_start: 0.8494 (mm) cc_final: 0.8279 (mt) REVERT: C 263 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7869 (mtpt) REVERT: C 278 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8219 (mt) REVERT: C 297 ASP cc_start: 0.7565 (m-30) cc_final: 0.7283 (m-30) REVERT: C 412 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8399 (mt) REVERT: C 464 LYS cc_start: 0.8367 (mtpp) cc_final: 0.8123 (mtpp) REVERT: C 469 GLU cc_start: 0.8251 (tt0) cc_final: 0.8019 (tp30) REVERT: G 28 SER cc_start: 0.8791 (m) cc_final: 0.8332 (p) REVERT: H 28 SER cc_start: 0.8715 (m) cc_final: 0.8345 (p) REVERT: H 118 TRP cc_start: 0.8495 (m100) cc_final: 0.7914 (m100) REVERT: I 28 SER cc_start: 0.8723 (m) cc_final: 0.8241 (p) outliers start: 52 outliers final: 30 residues processed: 428 average time/residue: 0.1448 time to fit residues: 87.7385 Evaluate side-chains 435 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 400 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 409 VAL 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 92 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 73 ARG 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 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 314 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 0.0020 chunk 143 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 169 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 446 ASN B 380 ASN B 446 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108273 restraints weight = 22443.343| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.45 r_work: 0.3149 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15468 Z= 0.131 Angle : 0.519 10.923 20955 Z= 0.270 Chirality : 0.043 0.145 2469 Planarity : 0.003 0.047 2673 Dihedral : 4.804 77.924 2136 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.84 % Allowed : 15.01 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.19), residues: 1932 helix: 1.54 (0.25), residues: 456 sheet: 0.31 (0.21), residues: 585 loop : 0.29 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 189 TYR 0.016 0.002 TYR C 178 PHE 0.011 0.001 PHE C 346 TRP 0.008 0.001 TRP H 118 HIS 0.002 0.000 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00292 (15450) covalent geometry : angle 0.51507 (20919) SS BOND : bond 0.00324 ( 18) SS BOND : angle 1.56285 ( 36) hydrogen bonds : bond 0.03905 ( 738) hydrogen bonds : angle 4.80458 ( 2061) *********************** 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 455 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 407 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.8699 (mm) cc_final: 0.8386 (mm) REVERT: A 70 GLN cc_start: 0.8610 (tp40) cc_final: 0.8041 (tp40) REVERT: A 73 ARG cc_start: 0.7984 (ttm110) cc_final: 0.7712 (ttm110) REVERT: A 212 ASN cc_start: 0.8137 (t0) cc_final: 0.7744 (t0) REVERT: A 270 ASP cc_start: 0.7557 (t0) cc_final: 0.7295 (t0) REVERT: A 362 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7996 (mm-40) REVERT: A 432 GLU cc_start: 0.7494 (mp0) cc_final: 0.7190 (mp0) REVERT: A 459 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7529 (mt-10) REVERT: B 73 ARG cc_start: 0.8047 (ttm110) cc_final: 0.7838 (ttm170) REVERT: B 92 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7134 (p) REVERT: B 169 ILE cc_start: 0.8427 (mt) cc_final: 0.8170 (mt) REVERT: B 212 ASN cc_start: 0.8167 (t0) cc_final: 0.7712 (t0) REVERT: B 238 ASN cc_start: 0.7744 (m-40) cc_final: 0.7463 (t0) REVERT: B 239 ILE cc_start: 0.8491 (mm) cc_final: 0.8287 (mt) REVERT: B 281 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7665 (mtm-85) REVERT: B 375 ARG cc_start: 0.8460 (mtt90) cc_final: 0.8208 (mpt90) REVERT: B 400 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7660 (ttm-80) REVERT: B 428 ASN cc_start: 0.7845 (t0) cc_final: 0.7516 (t0) REVERT: C 39 LYS cc_start: 0.8452 (mttt) cc_final: 0.8242 (mtmt) REVERT: C 53 LEU cc_start: 0.8718 (mt) cc_final: 0.8434 (mp) REVERT: C 69 LYS cc_start: 0.8907 (ttmm) cc_final: 0.8688 (ttmm) REVERT: C 169 ILE cc_start: 0.8094 (mt) cc_final: 0.7747 (mt) REVERT: C 182 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7499 (mt-10) REVERT: C 204 ASP cc_start: 0.7770 (t0) cc_final: 0.7488 (t0) REVERT: C 212 ASN cc_start: 0.8316 (t0) cc_final: 0.8090 (t0) REVERT: C 239 ILE cc_start: 0.8490 (mm) cc_final: 0.8273 (mt) REVERT: C 263 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7854 (mtpt) REVERT: C 278 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8202 (mt) REVERT: C 297 ASP cc_start: 0.7540 (m-30) cc_final: 0.7260 (m-30) REVERT: C 426 LEU cc_start: 0.8266 (mt) cc_final: 0.8043 (mt) REVERT: C 449 VAL cc_start: 0.8565 (m) cc_final: 0.8362 (t) REVERT: C 464 LYS cc_start: 0.8358 (mtpp) cc_final: 0.8119 (mtpp) REVERT: C 469 GLU cc_start: 0.8265 (tt0) cc_final: 0.8027 (tp30) REVERT: G 28 SER cc_start: 0.8802 (m) cc_final: 0.8346 (p) REVERT: H 28 SER cc_start: 0.8717 (m) cc_final: 0.8344 (p) REVERT: H 118 TRP cc_start: 0.8515 (m100) cc_final: 0.7962 (m100) REVERT: I 28 SER cc_start: 0.8701 (m) cc_final: 0.8218 (p) outliers start: 48 outliers final: 33 residues processed: 427 average time/residue: 0.1465 time to fit residues: 88.4241 Evaluate side-chains 437 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 401 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 237 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 318 THR 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 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 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 ILE 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 40 ILE 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 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 314 SER Chi-restraints excluded: chain C residue 317 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 133 optimal weight: 0.0470 chunk 171 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 159 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 A 403 GLN B 380 ASN B 446 ASN C 446 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108720 restraints weight = 22558.780| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.47 r_work: 0.3159 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15468 Z= 0.113 Angle : 0.512 10.308 20955 Z= 0.266 Chirality : 0.043 0.147 2469 Planarity : 0.003 0.044 2673 Dihedral : 4.713 76.085 2136 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.60 % Allowed : 15.19 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.19), residues: 1932 helix: 1.60 (0.25), residues: 465 sheet: 0.34 (0.21), residues: 558 loop : 0.27 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 47 TYR 0.016 0.001 TYR C 178 PHE 0.011 0.001 PHE C 346 TRP 0.007 0.001 TRP H 118 HIS 0.002 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00249 (15450) covalent geometry : angle 0.50820 (20919) SS BOND : bond 0.00299 ( 18) SS BOND : angle 1.51717 ( 36) hydrogen bonds : bond 0.03677 ( 738) hydrogen bonds : angle 4.70424 ( 2061) *********************** 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 437 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 393 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8379 (mtpp) REVERT: A 57 ILE cc_start: 0.8700 (mm) cc_final: 0.8356 (mm) REVERT: A 70 GLN cc_start: 0.8604 (tp40) cc_final: 0.8066 (tp-100) REVERT: A 73 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7688 (ttm110) REVERT: A 270 ASP cc_start: 0.7569 (t0) cc_final: 0.7267 (t0) REVERT: A 432 GLU cc_start: 0.7448 (mp0) cc_final: 0.7154 (mp0) REVERT: A 459 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7506 (mt-10) REVERT: B 92 VAL cc_start: 0.7389 (OUTLIER) cc_final: 0.6968 (p) REVERT: B 169 ILE cc_start: 0.8410 (mt) cc_final: 0.8139 (mt) REVERT: B 212 ASN cc_start: 0.8151 (t0) cc_final: 0.7696 (t0) REVERT: B 237 THR cc_start: 0.8308 (m) cc_final: 0.7795 (p) REVERT: B 238 ASN cc_start: 0.7749 (m-40) cc_final: 0.7529 (t0) REVERT: B 296 VAL cc_start: 0.8223 (t) cc_final: 0.7976 (m) REVERT: B 375 ARG cc_start: 0.8430 (mtt90) cc_final: 0.8192 (mpt90) REVERT: B 400 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7638 (ttm-80) REVERT: B 428 ASN cc_start: 0.7797 (t0) cc_final: 0.7492 (t0) REVERT: C 53 LEU cc_start: 0.8724 (mt) cc_final: 0.8431 (mp) REVERT: C 69 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8686 (ttmm) REVERT: C 169 ILE cc_start: 0.8074 (mt) cc_final: 0.7699 (mt) REVERT: C 182 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7517 (mt-10) REVERT: C 204 ASP cc_start: 0.7758 (t0) cc_final: 0.7455 (t0) REVERT: C 212 ASN cc_start: 0.8312 (t0) cc_final: 0.8105 (t0) REVERT: C 239 ILE cc_start: 0.8497 (mm) cc_final: 0.8283 (mt) REVERT: C 263 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7848 (mtpt) REVERT: C 278 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8169 (mt) REVERT: C 297 ASP cc_start: 0.7564 (m-30) cc_final: 0.7285 (m-30) REVERT: C 426 LEU cc_start: 0.8242 (mt) cc_final: 0.8021 (mt) REVERT: C 469 GLU cc_start: 0.8232 (tt0) cc_final: 0.7997 (tp30) REVERT: G 28 SER cc_start: 0.8790 (m) cc_final: 0.8336 (p) REVERT: H 28 SER cc_start: 0.8721 (m) cc_final: 0.8357 (p) REVERT: I 28 SER cc_start: 0.8699 (m) cc_final: 0.8230 (p) outliers start: 44 outliers final: 31 residues processed: 409 average time/residue: 0.1435 time to fit residues: 82.9562 Evaluate side-chains 424 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 390 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU 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 409 VAL 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 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 ILE 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 134 LEU Chi-restraints excluded: chain C residue 172 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 288 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 409 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 52 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 380 ASN B 70 GLN B 380 ASN B 446 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108116 restraints weight = 22426.095| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.46 r_work: 0.3140 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15468 Z= 0.150 Angle : 0.537 10.259 20955 Z= 0.279 Chirality : 0.044 0.212 2469 Planarity : 0.004 0.059 2673 Dihedral : 4.700 73.698 2136 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.07 % Allowed : 16.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.19), residues: 1932 helix: 1.55 (0.25), residues: 465 sheet: 0.32 (0.21), residues: 558 loop : 0.21 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 189 TYR 0.016 0.002 TYR C 178 PHE 0.012 0.001 PHE C 346 TRP 0.007 0.001 TRP E 118 HIS 0.001 0.000 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00343 (15450) covalent geometry : angle 0.53382 (20919) SS BOND : bond 0.00310 ( 18) SS BOND : angle 1.54855 ( 36) hydrogen bonds : bond 0.03888 ( 738) hydrogen bonds : angle 4.70109 ( 2061) *********************** 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 444 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 409 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.8702 (mm) cc_final: 0.8371 (mm) REVERT: A 70 GLN cc_start: 0.8638 (tp40) cc_final: 0.8102 (tp40) REVERT: A 73 ARG cc_start: 0.8008 (ttm110) cc_final: 0.7712 (ttm110) REVERT: A 182 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7918 (mt-10) REVERT: A 270 ASP cc_start: 0.7629 (t0) cc_final: 0.7334 (t0) REVERT: A 362 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7992 (mm-40) REVERT: A 431 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7798 (mmtt) REVERT: A 432 GLU cc_start: 0.7513 (mp0) cc_final: 0.7220 (mp0) REVERT: A 459 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 92 VAL cc_start: 0.7521 (OUTLIER) cc_final: 0.7075 (p) REVERT: B 212 ASN cc_start: 0.8203 (t0) cc_final: 0.7746 (t0) REVERT: B 237 THR cc_start: 0.8302 (m) cc_final: 0.7807 (p) REVERT: B 238 ASN cc_start: 0.7777 (m-40) cc_final: 0.7550 (t0) REVERT: B 281 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7692 (mtm-85) REVERT: B 296 VAL cc_start: 0.8244 (t) cc_final: 0.7971 (m) REVERT: B 400 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7635 (ttm-80) REVERT: B 428 ASN cc_start: 0.7853 (t0) cc_final: 0.7525 (t0) REVERT: C 53 LEU cc_start: 0.8718 (mt) cc_final: 0.8432 (mp) REVERT: C 69 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8684 (ttmm) REVERT: C 169 ILE cc_start: 0.8099 (mt) cc_final: 0.7746 (mt) REVERT: C 182 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7484 (mt-10) REVERT: C 204 ASP cc_start: 0.7730 (t0) cc_final: 0.7458 (t0) REVERT: C 212 ASN cc_start: 0.8311 (t0) cc_final: 0.7974 (t0) REVERT: C 239 ILE cc_start: 0.8494 (mm) cc_final: 0.8284 (mt) REVERT: C 263 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7848 (mtpt) REVERT: C 278 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8202 (mt) REVERT: C 297 ASP cc_start: 0.7598 (m-30) cc_final: 0.7331 (m-30) REVERT: C 469 GLU cc_start: 0.8245 (tt0) cc_final: 0.8017 (tp30) REVERT: D 65 LEU cc_start: 0.8631 (mp) cc_final: 0.8374 (mp) REVERT: G 28 SER cc_start: 0.8786 (m) cc_final: 0.8344 (p) REVERT: H 28 SER cc_start: 0.8758 (m) cc_final: 0.8408 (p) REVERT: I 28 SER cc_start: 0.8772 (m) cc_final: 0.8318 (p) outliers start: 35 outliers final: 28 residues processed: 424 average time/residue: 0.1417 time to fit residues: 84.9183 Evaluate side-chains 417 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 386 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU 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 318 THR 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 B residue 68 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 ILE 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 134 LEU Chi-restraints excluded: chain C residue 172 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 314 SER Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 409 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 58 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 184 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 70 GLN B 380 ASN B 446 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 = 0.3677 r_free = 0.3677 target = 0.133441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107785 restraints weight = 22603.981| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.47 r_work: 0.3143 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15468 Z= 0.150 Angle : 0.541 10.226 20955 Z= 0.280 Chirality : 0.044 0.202 2469 Planarity : 0.004 0.056 2673 Dihedral : 4.648 70.099 2136 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.13 % Allowed : 17.26 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.19), residues: 1932 helix: 1.54 (0.25), residues: 465 sheet: 0.29 (0.21), residues: 558 loop : 0.20 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 47 TYR 0.031 0.002 TYR B 207 PHE 0.012 0.001 PHE B 427 TRP 0.007 0.001 TRP E 118 HIS 0.001 0.000 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00341 (15450) covalent geometry : angle 0.53800 (20919) SS BOND : bond 0.00316 ( 18) SS BOND : angle 1.49962 ( 36) hydrogen bonds : bond 0.03909 ( 738) hydrogen bonds : angle 4.68818 ( 2061) ********************** 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 426 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 390 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.8720 (mm) cc_final: 0.8411 (mm) REVERT: A 70 GLN cc_start: 0.8611 (tp40) cc_final: 0.8091 (tp-100) REVERT: A 73 ARG cc_start: 0.7990 (ttm110) cc_final: 0.7712 (ttm110) REVERT: A 237 THR cc_start: 0.8302 (m) cc_final: 0.7767 (p) REVERT: A 270 ASP cc_start: 0.7636 (t0) cc_final: 0.7332 (t0) REVERT: A 431 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7782 (mmtt) REVERT: A 432 GLU cc_start: 0.7529 (mp0) cc_final: 0.7241 (mp0) REVERT: A 459 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7518 (mt-10) REVERT: B 92 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.7122 (p) REVERT: B 169 ILE cc_start: 0.8286 (mt) cc_final: 0.7893 (mt) REVERT: B 212 ASN cc_start: 0.8201 (t0) cc_final: 0.7729 (t0) REVERT: B 238 ASN cc_start: 0.7714 (m-40) cc_final: 0.7456 (t0) REVERT: B 281 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7697 (mtm-85) REVERT: B 296 VAL cc_start: 0.8240 (t) cc_final: 0.7963 (m) REVERT: B 400 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7739 (ttm-80) REVERT: B 428 ASN cc_start: 0.7841 (t0) cc_final: 0.7524 (t0) REVERT: C 53 LEU cc_start: 0.8726 (mt) cc_final: 0.8439 (mp) REVERT: C 69 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8685 (ttmm) REVERT: C 169 ILE cc_start: 0.8105 (mt) cc_final: 0.7744 (mt) REVERT: C 182 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7495 (mt-10) REVERT: C 204 ASP cc_start: 0.7736 (t0) cc_final: 0.7464 (t0) REVERT: C 212 ASN cc_start: 0.8315 (t0) cc_final: 0.7989 (t0) REVERT: C 239 ILE cc_start: 0.8500 (mm) cc_final: 0.8292 (mt) REVERT: C 263 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7818 (mtpt) REVERT: C 278 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8206 (mt) REVERT: C 297 ASP cc_start: 0.7574 (m-30) cc_final: 0.7298 (m-30) REVERT: C 469 GLU cc_start: 0.8228 (tt0) cc_final: 0.7994 (tp30) REVERT: D 65 LEU cc_start: 0.8627 (mp) cc_final: 0.8373 (mp) REVERT: G 28 SER cc_start: 0.8770 (m) cc_final: 0.8334 (p) REVERT: H 28 SER cc_start: 0.8762 (m) cc_final: 0.8417 (p) REVERT: I 28 SER cc_start: 0.8780 (m) cc_final: 0.8283 (p) outliers start: 36 outliers final: 29 residues processed: 406 average time/residue: 0.1431 time to fit residues: 82.0934 Evaluate side-chains 420 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 388 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU 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 318 THR 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 B residue 68 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 276 ILE 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 76 ASP 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 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 314 SER Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 409 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 61 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 0.0670 chunk 91 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 380 ASN B 446 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108185 restraints weight = 22375.761| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.44 r_work: 0.3153 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15468 Z= 0.131 Angle : 0.532 10.056 20955 Z= 0.275 Chirality : 0.043 0.145 2469 Planarity : 0.004 0.052 2673 Dihedral : 4.531 65.725 2136 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.07 % Allowed : 17.49 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.19), residues: 1932 helix: 1.58 (0.25), residues: 465 sheet: 0.33 (0.21), residues: 558 loop : 0.20 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 47 TYR 0.052 0.002 TYR B 207 PHE 0.011 0.001 PHE C 346 TRP 0.006 0.001 TRP H 118 HIS 0.001 0.000 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00298 (15450) covalent geometry : angle 0.52970 (20919) SS BOND : bond 0.00270 ( 18) SS BOND : angle 1.37161 ( 36) hydrogen bonds : bond 0.03755 ( 738) hydrogen bonds : angle 4.64074 ( 2061) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4002.69 seconds wall clock time: 69 minutes 14.68 seconds (4154.68 seconds total)