Starting phenix.real_space_refine on Sun Aug 24 19:00:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i1t_35121/08_2025/8i1t_35121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i1t_35121/08_2025/8i1t_35121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i1t_35121/08_2025/8i1t_35121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i1t_35121/08_2025/8i1t_35121.map" model { file = "/net/cci-nas-00/data/ceres_data/8i1t_35121/08_2025/8i1t_35121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i1t_35121/08_2025/8i1t_35121.cif" } resolution = 2.8 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 1.022 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 91 5.16 5 C 14371 2.51 5 N 3976 2.21 5 O 4501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 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: 22939 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "C" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "E" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "F" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "B" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "D" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Time building chain proxies: 4.96, per 1000 atoms: 0.22 Number of scatterers: 22939 At special positions: 0 Unit cell: (131.44, 178.08, 196.1, 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 91 16.00 O 4501 8.00 N 3976 7.00 C 14371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 990.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5614 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 51 sheets defined 23.5% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'G' and resid 24 through 29 removed outlier: 3.556A pdb=" N LYS G 29 " --> pdb=" O PRO G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 43 removed outlier: 3.619A pdb=" N ARG G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 95 Processing helix chain 'G' and resid 98 through 126 removed outlier: 3.660A pdb=" N ARG G 102 " --> pdb=" O THR G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 158 removed outlier: 3.860A pdb=" N ALA G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 185 removed outlier: 3.759A pdb=" N LYS G 177 " --> pdb=" O GLN G 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR G 180 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS G 184 " --> pdb=" O TYR G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 199 Processing helix chain 'G' and resid 321 through 326 Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.607A pdb=" N GLN A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 43 removed outlier: 3.611A pdb=" N ARG A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 95 Processing helix chain 'A' and resid 97 through 127 Processing helix chain 'A' and resid 142 through 158 Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 189 through 198 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'C' and resid 24 through 30 Processing helix chain 'C' and resid 36 through 43 removed outlier: 3.686A pdb=" N ARG C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 95 removed outlier: 3.697A pdb=" N ARG C 95 " --> pdb=" O ASP C 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 95' Processing helix chain 'C' and resid 97 through 127 Processing helix chain 'C' and resid 142 through 158 removed outlier: 3.503A pdb=" N MET C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 184 Processing helix chain 'C' and resid 190 through 199 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'E' and resid 24 through 30 removed outlier: 3.585A pdb=" N GLN E 28 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 24 through 30' Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 92 through 95 removed outlier: 3.674A pdb=" N ARG E 95 " --> pdb=" O ASP E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 97 through 126 Processing helix chain 'E' and resid 142 through 158 Processing helix chain 'E' and resid 171 through 184 Processing helix chain 'E' and resid 189 through 199 Processing helix chain 'E' and resid 321 through 326 Processing helix chain 'E' and resid 417 through 420 Processing helix chain 'F' and resid 24 through 30 Processing helix chain 'F' and resid 36 through 43 Processing helix chain 'F' and resid 92 through 95 removed outlier: 4.013A pdb=" N ARG F 95 " --> pdb=" O ASP F 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 95' Processing helix chain 'F' and resid 97 through 127 Processing helix chain 'F' and resid 142 through 158 Processing helix chain 'F' and resid 171 through 184 Processing helix chain 'F' and resid 189 through 198 Processing helix chain 'F' and resid 245 through 247 No H-bonds generated for 'chain 'F' and resid 245 through 247' Processing helix chain 'F' and resid 321 through 326 Processing helix chain 'F' and resid 370 through 374 removed outlier: 3.514A pdb=" N ALA F 374 " --> pdb=" O GLU F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'B' and resid 24 through 30 removed outlier: 3.602A pdb=" N GLN B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 43 removed outlier: 3.749A pdb=" N ARG B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 95 removed outlier: 3.652A pdb=" N ARG B 95 " --> pdb=" O ASP B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 95' Processing helix chain 'B' and resid 97 through 126 Processing helix chain 'B' and resid 142 through 158 removed outlier: 3.563A pdb=" N ALA B 151 " --> pdb=" O PHE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 184 Processing helix chain 'B' and resid 189 through 198 Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'D' and resid 24 through 30 removed outlier: 3.521A pdb=" N GLN D 28 " --> pdb=" O THR D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 43 Processing helix chain 'D' and resid 92 through 95 removed outlier: 4.027A pdb=" N ARG D 95 " --> pdb=" O ASP D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 95' Processing helix chain 'D' and resid 97 through 126 Processing helix chain 'D' and resid 142 through 158 Processing helix chain 'D' and resid 171 through 184 Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.750A pdb=" N ALA D 374 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing sheet with id=AA1, first strand: chain 'G' and resid 31 through 33 removed outlier: 6.413A pdb=" N LYS G 31 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N SER G 363 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR G 33 " --> pdb=" O SER G 363 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP G 410 " --> pdb=" O GLN G 364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 31 through 33 removed outlier: 6.413A pdb=" N LYS G 31 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N SER G 363 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR G 33 " --> pdb=" O SER G 363 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP G 410 " --> pdb=" O GLN G 364 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 402 " --> pdb=" O ASP G 397 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TRP G 410 " --> pdb=" O ASN G 389 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN G 389 " --> pdb=" O TRP G 410 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 47 through 50 Processing sheet with id=AA4, first strand: chain 'G' and resid 70 through 71 removed outlier: 6.271A pdb=" N LEU G 70 " --> pdb=" O ASN B 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 129 through 132 removed outlier: 6.513A pdb=" N LEU G 129 " --> pdb=" O VAL G 423 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU G 425 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE G 131 " --> pdb=" O LEU G 425 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR G 166 " --> pdb=" O ASP G 210 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU G 212 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR G 168 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AA7, first strand: chain 'G' and resid 228 through 229 removed outlier: 4.800A pdb=" N ILE G 228 " --> pdb=" O VAL G 340 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA G 339 " --> pdb=" O ALA G 276 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE G 275 " --> pdb=" O ALA G 293 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA G 293 " --> pdb=" O PHE G 275 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N GLY G 277 " --> pdb=" O GLN G 291 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLN G 291 " --> pdb=" O GLY G 277 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LYS G 279 " --> pdb=" O LEU G 289 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU G 289 " --> pdb=" O LYS G 279 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU G 307 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL G 300 " --> pdb=" O HIS G 305 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N HIS G 305 " --> pdb=" O VAL G 300 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 241 through 242 Processing sheet with id=AA9, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AB1, first strand: chain 'A' and resid 74 through 77 Processing sheet with id=AB2, first strand: chain 'A' and resid 58 through 59 removed outlier: 3.521A pdb=" N SER B 402 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 377 through 383 removed outlier: 4.691A pdb=" N LEU A 388 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 129 through 132 Processing sheet with id=AB5, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AB6, first strand: chain 'A' and resid 241 through 244 removed outlier: 3.809A pdb=" N ASN A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 257 through 260 removed outlier: 7.840A pdb=" N HIS A 305 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL A 300 " --> pdb=" O HIS A 305 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU A 307 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 279 through 281 removed outlier: 6.252A pdb=" N GLN A 291 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.294A pdb=" N LYS C 31 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N SER C 363 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR C 33 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 74 through 77 Processing sheet with id=AC2, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.212A pdb=" N LYS D 31 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER D 363 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR D 33 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 59 removed outlier: 5.041A pdb=" N TRP D 410 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN D 389 " --> pdb=" O TRP D 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 377 through 382 Processing sheet with id=AC5, first strand: chain 'C' and resid 129 through 132 removed outlier: 6.220A pdb=" N LEU C 129 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU C 425 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 131 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AC7, first strand: chain 'C' and resid 241 through 243 Processing sheet with id=AC8, first strand: chain 'C' and resid 257 through 260 removed outlier: 7.369A pdb=" N HIS C 305 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL C 300 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU C 307 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU C 289 " --> pdb=" O LYS C 279 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS C 279 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N GLN C 291 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N GLY C 277 " --> pdb=" O GLN C 291 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ALA C 293 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE C 275 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.376A pdb=" N LYS E 31 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER E 363 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR E 33 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 47 through 50 Processing sheet with id=AD2, first strand: chain 'E' and resid 58 through 59 removed outlier: 4.243A pdb=" N LEU F 388 " --> pdb=" O ILE F 383 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 377 through 383 removed outlier: 3.551A pdb=" N LEU E 388 " --> pdb=" O ILE E 383 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 129 through 132 removed outlier: 6.275A pdb=" N LEU E 129 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU E 425 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE E 131 " --> pdb=" O LEU E 425 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 219 through 220 Processing sheet with id=AD6, first strand: chain 'E' and resid 241 through 243 Processing sheet with id=AD7, first strand: chain 'E' and resid 257 through 260 removed outlier: 7.669A pdb=" N HIS E 305 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL E 300 " --> pdb=" O HIS E 305 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU E 307 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU E 289 " --> pdb=" O LYS E 279 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS E 279 " --> pdb=" O LEU E 289 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N GLN E 291 " --> pdb=" O GLY E 277 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N GLY E 277 " --> pdb=" O GLN E 291 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA E 293 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE E 275 " --> pdb=" O ALA E 293 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.398A pdb=" N LYS F 31 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER F 363 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR F 33 " --> pdb=" O SER F 363 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 47 through 50 Processing sheet with id=AE1, first strand: chain 'F' and resid 129 through 132 removed outlier: 6.086A pdb=" N LEU F 129 " --> pdb=" O VAL F 423 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU F 425 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE F 131 " --> pdb=" O LEU F 425 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 219 through 220 Processing sheet with id=AE3, first strand: chain 'F' and resid 241 through 243 Processing sheet with id=AE4, first strand: chain 'F' and resid 257 through 260 removed outlier: 7.347A pdb=" N HIS F 305 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL F 300 " --> pdb=" O HIS F 305 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU F 307 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE F 280 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN F 291 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL F 278 " --> pdb=" O GLN F 291 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N ALA F 293 " --> pdb=" O ALA F 276 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA F 276 " --> pdb=" O ALA F 293 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE F 295 " --> pdb=" O SER F 274 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER F 274 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL F 297 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS F 272 " --> pdb=" O VAL F 297 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.298A pdb=" N LYS B 31 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER B 363 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR B 33 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 47 through 50 Processing sheet with id=AE7, first strand: chain 'B' and resid 129 through 132 removed outlier: 6.397A pdb=" N LEU B 129 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU B 425 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 131 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AE9, first strand: chain 'B' and resid 241 through 243 Processing sheet with id=AF1, first strand: chain 'B' and resid 257 through 260 removed outlier: 7.180A pdb=" N HIS B 305 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL B 300 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU B 307 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU B 289 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS B 279 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N GLN B 291 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N GLY B 277 " --> pdb=" O GLN B 291 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ALA B 293 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE B 275 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 47 through 50 Processing sheet with id=AF3, first strand: chain 'D' and resid 129 through 132 removed outlier: 6.248A pdb=" N LEU D 129 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU D 425 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE D 131 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP D 210 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 219 through 220 Processing sheet with id=AF5, first strand: chain 'D' and resid 241 through 243 Processing sheet with id=AF6, first strand: chain 'D' and resid 257 through 260 removed outlier: 3.614A pdb=" N ARG D 299 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE D 280 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLN D 291 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL D 278 " --> pdb=" O GLN D 291 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ALA D 293 " --> pdb=" O ALA D 276 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA D 276 " --> pdb=" O ALA D 293 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE D 295 " --> pdb=" O SER D 274 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N SER D 274 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 297 " --> pdb=" O LYS D 272 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS D 272 " --> pdb=" O VAL D 297 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2364 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4422 1.32 - 1.44: 5450 1.44 - 1.57: 13298 1.57 - 1.69: 0 1.69 - 1.81: 175 Bond restraints: 23345 Sorted by residual: bond pdb=" C GLU G 323 " pdb=" O GLU G 323 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.29e+00 bond pdb=" C THR B 200 " pdb=" N ILE B 201 " ideal model delta sigma weight residual 1.332 1.293 0.039 1.73e-02 3.34e+03 5.17e+00 bond pdb=" C LEU G 320 " pdb=" O LEU G 320 " ideal model delta sigma weight residual 1.234 1.207 0.028 1.22e-02 6.72e+03 5.14e+00 bond pdb=" N GLU G 323 " pdb=" CA GLU G 323 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.21e-02 6.83e+03 4.04e+00 bond pdb=" C PRO G 322 " pdb=" N GLU G 323 " ideal model delta sigma weight residual 1.335 1.311 0.024 1.31e-02 5.83e+03 3.26e+00 ... (remaining 23340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 31070 2.01 - 4.03: 597 4.03 - 6.04: 56 6.04 - 8.05: 21 8.05 - 10.07: 1 Bond angle restraints: 31745 Sorted by residual: angle pdb=" C ALA C 136 " pdb=" N ILE C 137 " pdb=" CA ILE C 137 " ideal model delta sigma weight residual 121.97 132.04 -10.07 1.80e+00 3.09e-01 3.13e+01 angle pdb=" N ILE B 201 " pdb=" CA ILE B 201 " pdb=" C ILE B 201 " ideal model delta sigma weight residual 110.05 105.16 4.89 1.09e+00 8.42e-01 2.01e+01 angle pdb=" C ASN G 140 " pdb=" CA ASN G 140 " pdb=" CB ASN G 140 " ideal model delta sigma weight residual 116.34 110.65 5.69 1.40e+00 5.10e-01 1.65e+01 angle pdb=" C SER G 321 " pdb=" N PRO G 322 " pdb=" CA PRO G 322 " ideal model delta sigma weight residual 118.85 114.78 4.07 1.09e+00 8.42e-01 1.39e+01 angle pdb=" N ILE C 137 " pdb=" CA ILE C 137 " pdb=" CB ILE C 137 " ideal model delta sigma weight residual 111.23 117.34 -6.11 1.65e+00 3.67e-01 1.37e+01 ... (remaining 31740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12865 17.98 - 35.96: 1060 35.96 - 53.94: 161 53.94 - 71.92: 43 71.92 - 89.89: 25 Dihedral angle restraints: 14154 sinusoidal: 5488 harmonic: 8666 Sorted by residual: dihedral pdb=" CA THR B 200 " pdb=" C THR B 200 " pdb=" N ILE B 201 " pdb=" CA ILE B 201 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASN C 84 " pdb=" C ASN C 84 " pdb=" N ASP C 85 " pdb=" CA ASP C 85 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA TRP F 354 " pdb=" C TRP F 354 " pdb=" N ALA F 355 " pdb=" CA ALA F 355 " ideal model delta harmonic sigma weight residual 180.00 154.03 25.97 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 14151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2559 0.045 - 0.090: 794 0.090 - 0.135: 292 0.135 - 0.180: 16 0.180 - 0.224: 7 Chirality restraints: 3668 Sorted by residual: chirality pdb=" CA THR D 309 " pdb=" N THR D 309 " pdb=" C THR D 309 " pdb=" CB THR D 309 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA THR F 309 " pdb=" N THR F 309 " pdb=" C THR F 309 " pdb=" CB THR F 309 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA THR E 309 " pdb=" N THR E 309 " pdb=" C THR E 309 " pdb=" CB THR E 309 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3665 not shown) Planarity restraints: 4186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 354 " -0.043 2.00e-02 2.50e+03 3.72e-02 3.46e+01 pdb=" CG TRP F 354 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP F 354 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP F 354 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 354 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP F 354 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 354 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 354 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 354 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 354 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 354 " -0.041 2.00e-02 2.50e+03 3.71e-02 3.43e+01 pdb=" CG TRP C 354 " 0.097 2.00e-02 2.50e+03 pdb=" CD1 TRP C 354 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP C 354 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP C 354 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 354 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 354 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 354 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 354 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 354 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 354 " 0.040 2.00e-02 2.50e+03 3.59e-02 3.22e+01 pdb=" CG TRP A 354 " -0.093 2.00e-02 2.50e+03 pdb=" CD1 TRP A 354 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP A 354 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 354 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 354 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 354 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 354 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 354 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 354 " 0.006 2.00e-02 2.50e+03 ... (remaining 4183 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2189 2.74 - 3.28: 22406 3.28 - 3.82: 39736 3.82 - 4.36: 49074 4.36 - 4.90: 82104 Nonbonded interactions: 195509 Sorted by model distance: nonbonded pdb=" O PRO A 134 " pdb=" OG1 THR A 429 " model vdw 2.196 3.040 nonbonded pdb=" NZ LYS E 176 " pdb=" OD1 ASN D 146 " model vdw 2.212 3.120 nonbonded pdb=" OG1 THR C 229 " pdb=" OG SER C 262 " model vdw 2.219 3.040 nonbonded pdb=" O LEU A 217 " pdb=" NH2 ARG A 349 " model vdw 2.237 3.120 nonbonded pdb=" O VAL F 13 " pdb=" NH2 ARG F 102 " model vdw 2.263 3.120 ... (remaining 195504 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 3.840 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.870 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.007 0.054 23345 Z= 0.303 Angle : 0.696 10.068 31745 Z= 0.382 Chirality : 0.049 0.224 3668 Planarity : 0.005 0.060 4186 Dihedral : 14.073 89.894 8540 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.21 % Favored : 96.62 % Rotamer: Outliers : 0.08 % Allowed : 0.49 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.01 (0.14), residues: 2989 helix: 0.27 (0.20), residues: 670 sheet: -0.20 (0.17), residues: 793 loop : -1.35 (0.14), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 349 TYR 0.016 0.002 TYR D 100 PHE 0.054 0.003 PHE E 147 TRP 0.098 0.005 TRP F 354 HIS 0.005 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00694 (23345) covalent geometry : angle 0.69605 (31745) hydrogen bonds : bond 0.16921 ( 843) hydrogen bonds : angle 7.42084 ( 2364) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.689 Fit side-chains REVERT: G 185 ARG cc_start: 0.5234 (tpt170) cc_final: 0.5030 (tmt-80) REVERT: A 338 MET cc_start: 0.8274 (ttm) cc_final: 0.7735 (ttm) REVERT: B 338 MET cc_start: 0.8600 (ptp) cc_final: 0.8177 (ptp) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.5892 time to fit residues: 114.5631 Evaluate side-chains 139 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 GLN A 248 ASN E 114 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.082660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.073518 restraints weight = 45186.540| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.67 r_work: 0.2856 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23345 Z= 0.166 Angle : 0.574 8.484 31745 Z= 0.311 Chirality : 0.045 0.202 3668 Planarity : 0.004 0.053 4186 Dihedral : 5.320 26.911 3206 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.91 % Favored : 96.92 % Rotamer: Outliers : 1.22 % Allowed : 6.02 % Favored : 92.76 % 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: -0.79 (0.14), residues: 2989 helix: 0.68 (0.20), residues: 677 sheet: -0.10 (0.17), residues: 785 loop : -1.32 (0.14), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 102 TYR 0.015 0.001 TYR A 100 PHE 0.029 0.002 PHE G 208 TRP 0.043 0.002 TRP C 354 HIS 0.003 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00372 (23345) covalent geometry : angle 0.57442 (31745) hydrogen bonds : bond 0.05744 ( 843) hydrogen bonds : angle 5.73615 ( 2364) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.670 Fit side-chains REVERT: G 185 ARG cc_start: 0.5225 (tpt170) cc_final: 0.4829 (tmt-80) REVERT: A 338 MET cc_start: 0.8603 (ttm) cc_final: 0.8089 (ttm) REVERT: E 122 MET cc_start: 0.9066 (tpp) cc_final: 0.8846 (tpt) REVERT: E 246 ASP cc_start: 0.8317 (m-30) cc_final: 0.7425 (t0) REVERT: E 316 ASP cc_start: 0.7778 (t70) cc_final: 0.7192 (t0) REVERT: B 336 ASP cc_start: 0.8333 (t0) cc_final: 0.8013 (t0) REVERT: B 338 MET cc_start: 0.8839 (ptp) cc_final: 0.8468 (ptp) REVERT: D 49 MET cc_start: 0.9115 (mtp) cc_final: 0.8891 (mtt) REVERT: D 188 PHE cc_start: 0.7460 (t80) cc_final: 0.7234 (t80) outliers start: 30 outliers final: 11 residues processed: 177 average time/residue: 0.5606 time to fit residues: 114.5266 Evaluate side-chains 161 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 211 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 94 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 273 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 264 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN E 53 GLN E 114 ASN B 248 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.073559 restraints weight = 45190.255| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.66 r_work: 0.2858 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23345 Z= 0.164 Angle : 0.551 7.935 31745 Z= 0.296 Chirality : 0.045 0.190 3668 Planarity : 0.004 0.050 4186 Dihedral : 5.163 25.298 3206 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.94 % Favored : 96.89 % Rotamer: Outliers : 1.67 % Allowed : 7.98 % Favored : 90.35 % 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 (0.14), residues: 2989 helix: 0.83 (0.20), residues: 678 sheet: -0.16 (0.17), residues: 794 loop : -1.28 (0.14), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 102 TYR 0.014 0.001 TYR A 100 PHE 0.026 0.002 PHE G 208 TRP 0.028 0.002 TRP F 354 HIS 0.002 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00370 (23345) covalent geometry : angle 0.55077 (31745) hydrogen bonds : bond 0.05400 ( 843) hydrogen bonds : angle 5.43858 ( 2364) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.793 Fit side-chains REVERT: G 79 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8105 (mtm) REVERT: G 185 ARG cc_start: 0.5206 (tpt170) cc_final: 0.4743 (tmt-80) REVERT: G 209 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8374 (m-30) REVERT: G 316 ASP cc_start: 0.8278 (p0) cc_final: 0.7973 (p0) REVERT: A 338 MET cc_start: 0.8593 (ttm) cc_final: 0.8131 (ttm) REVERT: E 122 MET cc_start: 0.9036 (tpp) cc_final: 0.8789 (tpt) REVERT: E 246 ASP cc_start: 0.8192 (m-30) cc_final: 0.7421 (t0) REVERT: F 317 ASP cc_start: 0.7708 (t0) cc_final: 0.7494 (t0) REVERT: B 15 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6986 (tp30) REVERT: B 336 ASP cc_start: 0.8330 (t0) cc_final: 0.8025 (t0) REVERT: B 338 MET cc_start: 0.8801 (ptp) cc_final: 0.8493 (ptp) outliers start: 41 outliers final: 14 residues processed: 181 average time/residue: 0.5534 time to fit residues: 115.7591 Evaluate side-chains 163 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 105 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 262 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.073373 restraints weight = 44977.429| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.66 r_work: 0.2854 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23345 Z= 0.172 Angle : 0.553 7.710 31745 Z= 0.296 Chirality : 0.045 0.198 3668 Planarity : 0.004 0.050 4186 Dihedral : 5.114 25.428 3206 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.88 % Favored : 96.96 % Rotamer: Outliers : 1.55 % Allowed : 9.61 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.14), residues: 2989 helix: 0.91 (0.20), residues: 673 sheet: -0.20 (0.17), residues: 794 loop : -1.29 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 255 TYR 0.015 0.001 TYR G 175 PHE 0.022 0.002 PHE G 208 TRP 0.024 0.002 TRP G 354 HIS 0.002 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00391 (23345) covalent geometry : angle 0.55255 (31745) hydrogen bonds : bond 0.05283 ( 843) hydrogen bonds : angle 5.34515 ( 2364) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.807 Fit side-chains REVERT: G 79 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8114 (mtm) REVERT: G 185 ARG cc_start: 0.5166 (tpt170) cc_final: 0.4648 (tmt-80) REVERT: G 209 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8329 (m-30) REVERT: A 338 MET cc_start: 0.8526 (ttm) cc_final: 0.8061 (ttm) REVERT: C 307 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: E 122 MET cc_start: 0.9031 (tpp) cc_final: 0.8791 (tpt) REVERT: E 246 ASP cc_start: 0.8200 (m-30) cc_final: 0.7416 (t0) REVERT: E 376 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8274 (ptm) REVERT: F 203 ARG cc_start: 0.8759 (mmp80) cc_final: 0.8463 (mmp80) REVERT: F 317 ASP cc_start: 0.7699 (t0) cc_final: 0.7486 (t0) REVERT: F 338 MET cc_start: 0.8682 (ttm) cc_final: 0.8223 (ttm) REVERT: B 15 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6911 (tp30) REVERT: B 336 ASP cc_start: 0.8360 (t0) cc_final: 0.8071 (t0) REVERT: B 338 MET cc_start: 0.8770 (ptp) cc_final: 0.8471 (ptp) outliers start: 38 outliers final: 21 residues processed: 174 average time/residue: 0.5213 time to fit residues: 104.8655 Evaluate side-chains 175 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 138 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 86 optimal weight: 10.0000 chunk 148 optimal weight: 0.4980 chunk 254 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.073196 restraints weight = 45062.072| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.60 r_work: 0.2852 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23345 Z= 0.187 Angle : 0.560 7.565 31745 Z= 0.299 Chirality : 0.045 0.195 3668 Planarity : 0.004 0.049 4186 Dihedral : 5.160 25.883 3206 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.91 % Favored : 96.92 % Rotamer: Outliers : 1.91 % Allowed : 10.22 % Favored : 87.87 % 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: -0.76 (0.14), residues: 2989 helix: 0.89 (0.20), residues: 673 sheet: -0.25 (0.17), residues: 794 loop : -1.29 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 102 TYR 0.015 0.001 TYR A 100 PHE 0.019 0.002 PHE G 208 TRP 0.022 0.002 TRP G 354 HIS 0.003 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00429 (23345) covalent geometry : angle 0.55968 (31745) hydrogen bonds : bond 0.05335 ( 843) hydrogen bonds : angle 5.34423 ( 2364) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.611 Fit side-chains REVERT: G 79 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8151 (mtm) REVERT: G 185 ARG cc_start: 0.5243 (tpt170) cc_final: 0.4715 (tmt-80) REVERT: G 271 ASP cc_start: 0.7981 (p0) cc_final: 0.7381 (m-30) REVERT: A 164 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8217 (mmp) REVERT: A 338 MET cc_start: 0.8517 (ttm) cc_final: 0.8097 (ttm) REVERT: C 307 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: E 122 MET cc_start: 0.9088 (tpp) cc_final: 0.8857 (tpt) REVERT: E 246 ASP cc_start: 0.8127 (m-30) cc_final: 0.7341 (t0) REVERT: E 376 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8199 (ptm) REVERT: E 377 LYS cc_start: 0.6262 (OUTLIER) cc_final: 0.5733 (mttp) REVERT: F 122 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8676 (tpp) REVERT: F 203 ARG cc_start: 0.8721 (mmp80) cc_final: 0.8475 (mmp80) REVERT: F 317 ASP cc_start: 0.7658 (t0) cc_final: 0.7440 (t0) REVERT: F 338 MET cc_start: 0.8587 (ttm) cc_final: 0.8246 (ttm) REVERT: B 15 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: B 336 ASP cc_start: 0.8342 (t0) cc_final: 0.8045 (t0) REVERT: B 338 MET cc_start: 0.8763 (ptp) cc_final: 0.8473 (ptp) outliers start: 47 outliers final: 22 residues processed: 184 average time/residue: 0.5281 time to fit residues: 112.8076 Evaluate side-chains 177 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 203 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 282 optimal weight: 0.9990 chunk 143 optimal weight: 0.0980 chunk 132 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 49 optimal weight: 30.0000 chunk 144 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 263 optimal weight: 7.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.085725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.076907 restraints weight = 45138.135| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.60 r_work: 0.2927 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23345 Z= 0.102 Angle : 0.489 7.928 31745 Z= 0.261 Chirality : 0.043 0.169 3668 Planarity : 0.003 0.038 4186 Dihedral : 4.590 23.492 3206 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.74 % Favored : 97.09 % Rotamer: Outliers : 1.42 % Allowed : 11.56 % Favored : 87.02 % 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: -0.52 (0.14), residues: 2989 helix: 1.20 (0.20), residues: 675 sheet: -0.07 (0.17), residues: 796 loop : -1.21 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 102 TYR 0.012 0.001 TYR E 100 PHE 0.014 0.001 PHE A 147 TRP 0.015 0.001 TRP E 354 HIS 0.001 0.000 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00224 (23345) covalent geometry : angle 0.48941 (31745) hydrogen bonds : bond 0.04385 ( 843) hydrogen bonds : angle 4.98391 ( 2364) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.647 Fit side-chains REVERT: G 185 ARG cc_start: 0.5122 (tpt170) cc_final: 0.4623 (tmt-80) REVERT: G 271 ASP cc_start: 0.7886 (p0) cc_final: 0.7366 (m-30) REVERT: A 180 TYR cc_start: 0.8571 (t80) cc_final: 0.8367 (t80) REVERT: A 338 MET cc_start: 0.8614 (ttm) cc_final: 0.8174 (ttm) REVERT: E 122 MET cc_start: 0.9038 (tpp) cc_final: 0.8775 (tpt) REVERT: E 246 ASP cc_start: 0.8085 (m-30) cc_final: 0.7270 (t0) REVERT: E 376 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8127 (ptm) REVERT: E 377 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.5980 (mttp) REVERT: F 203 ARG cc_start: 0.8650 (mmp80) cc_final: 0.8415 (mmp80) REVERT: F 317 ASP cc_start: 0.7469 (t0) cc_final: 0.7253 (t0) REVERT: B 15 GLU cc_start: 0.7264 (tp30) cc_final: 0.6969 (tp30) REVERT: B 336 ASP cc_start: 0.8282 (t0) cc_final: 0.7972 (t0) REVERT: B 338 MET cc_start: 0.8729 (ptp) cc_final: 0.8488 (ptp) outliers start: 35 outliers final: 13 residues processed: 199 average time/residue: 0.4940 time to fit residues: 114.6492 Evaluate side-chains 174 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 50 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 285 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 175 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 ASN ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.071290 restraints weight = 45470.637| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.60 r_work: 0.2813 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 23345 Z= 0.325 Angle : 0.671 8.752 31745 Z= 0.356 Chirality : 0.049 0.214 3668 Planarity : 0.005 0.051 4186 Dihedral : 5.522 27.896 3206 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.94 % Favored : 96.86 % Rotamer: Outliers : 2.32 % Allowed : 11.44 % Favored : 86.24 % 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: -0.92 (0.14), residues: 2989 helix: 0.68 (0.19), residues: 677 sheet: -0.35 (0.17), residues: 785 loop : -1.34 (0.14), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 255 TYR 0.017 0.002 TYR C 100 PHE 0.022 0.003 PHE F 188 TRP 0.023 0.002 TRP G 354 HIS 0.005 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00758 (23345) covalent geometry : angle 0.67121 (31745) hydrogen bonds : bond 0.06134 ( 843) hydrogen bonds : angle 5.53384 ( 2364) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 0.820 Fit side-chains REVERT: G 14 ASP cc_start: 0.7958 (p0) cc_final: 0.7728 (p0) REVERT: G 185 ARG cc_start: 0.5275 (tpt170) cc_final: 0.4825 (tmt-80) REVERT: A 338 MET cc_start: 0.8487 (ttm) cc_final: 0.8105 (ttm) REVERT: E 246 ASP cc_start: 0.8083 (m-30) cc_final: 0.7267 (t0) REVERT: E 376 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8199 (ptm) REVERT: E 377 LYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5579 (mptt) REVERT: F 122 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8725 (tpp) REVERT: F 203 ARG cc_start: 0.8810 (mmp80) cc_final: 0.8578 (mmp80) REVERT: F 317 ASP cc_start: 0.7731 (t0) cc_final: 0.7519 (t0) REVERT: B 336 ASP cc_start: 0.8372 (t0) cc_final: 0.8080 (t0) REVERT: B 338 MET cc_start: 0.8700 (ptp) cc_final: 0.8409 (ptp) outliers start: 57 outliers final: 29 residues processed: 186 average time/residue: 0.4929 time to fit residues: 107.1696 Evaluate side-chains 175 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 137 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 269 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.083251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.074339 restraints weight = 45096.622| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.60 r_work: 0.2875 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23345 Z= 0.129 Angle : 0.527 7.922 31745 Z= 0.281 Chirality : 0.044 0.196 3668 Planarity : 0.004 0.044 4186 Dihedral : 4.967 25.049 3206 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.64 % Favored : 97.16 % Rotamer: Outliers : 1.42 % Allowed : 12.86 % Favored : 85.71 % 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: -0.70 (0.14), residues: 2989 helix: 0.97 (0.19), residues: 675 sheet: -0.24 (0.17), residues: 794 loop : -1.26 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 102 TYR 0.014 0.001 TYR A 100 PHE 0.015 0.002 PHE F 188 TRP 0.019 0.001 TRP G 354 HIS 0.002 0.000 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00284 (23345) covalent geometry : angle 0.52675 (31745) hydrogen bonds : bond 0.04886 ( 843) hydrogen bonds : angle 5.17121 ( 2364) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.853 Fit side-chains REVERT: G 185 ARG cc_start: 0.5217 (tpt170) cc_final: 0.4698 (tmt-80) REVERT: G 271 ASP cc_start: 0.8017 (p0) cc_final: 0.7506 (m-30) REVERT: A 338 MET cc_start: 0.8536 (ttm) cc_final: 0.8096 (ttm) REVERT: C 376 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8792 (ptt) REVERT: E 122 MET cc_start: 0.9058 (tpp) cc_final: 0.8793 (tpt) REVERT: E 246 ASP cc_start: 0.8119 (m-30) cc_final: 0.7285 (t0) REVERT: E 376 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8174 (ptm) REVERT: E 377 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5673 (mttp) REVERT: F 194 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8467 (mt-10) REVERT: F 203 ARG cc_start: 0.8664 (mmp80) cc_final: 0.8438 (mmp80) REVERT: F 317 ASP cc_start: 0.7604 (t0) cc_final: 0.7368 (t0) REVERT: B 15 GLU cc_start: 0.7226 (tp30) cc_final: 0.6921 (tp30) REVERT: B 126 MET cc_start: 0.8709 (mmt) cc_final: 0.8442 (tpp) REVERT: B 164 MET cc_start: 0.7608 (pmm) cc_final: 0.7382 (pmm) REVERT: B 336 ASP cc_start: 0.8341 (t0) cc_final: 0.8000 (t0) REVERT: B 338 MET cc_start: 0.8697 (ptp) cc_final: 0.8446 (ptp) REVERT: D 147 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8538 (t80) outliers start: 35 outliers final: 18 residues processed: 176 average time/residue: 0.5218 time to fit residues: 107.2665 Evaluate side-chains 172 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 301 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 121 optimal weight: 0.4980 chunk 244 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.082229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.073273 restraints weight = 45141.567| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.60 r_work: 0.2852 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23345 Z= 0.186 Angle : 0.563 7.761 31745 Z= 0.299 Chirality : 0.045 0.190 3668 Planarity : 0.004 0.047 4186 Dihedral : 5.084 25.925 3206 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.88 % Favored : 96.92 % Rotamer: Outliers : 1.38 % Allowed : 13.02 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.14), residues: 2989 helix: 0.98 (0.20), residues: 669 sheet: -0.29 (0.17), residues: 794 loop : -1.27 (0.14), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.014 0.002 TYR A 100 PHE 0.021 0.002 PHE F 188 TRP 0.018 0.001 TRP G 354 HIS 0.003 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00428 (23345) covalent geometry : angle 0.56299 (31745) hydrogen bonds : bond 0.05214 ( 843) hydrogen bonds : angle 5.23427 ( 2364) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.807 Fit side-chains REVERT: G 185 ARG cc_start: 0.5251 (tpt170) cc_final: 0.4777 (tmt-80) REVERT: G 271 ASP cc_start: 0.8046 (p0) cc_final: 0.7527 (m-30) REVERT: G 316 ASP cc_start: 0.8262 (p0) cc_final: 0.8049 (p0) REVERT: A 338 MET cc_start: 0.8523 (ttm) cc_final: 0.8119 (ttm) REVERT: E 122 MET cc_start: 0.9072 (tpp) cc_final: 0.8812 (tpt) REVERT: E 246 ASP cc_start: 0.8097 (m-30) cc_final: 0.7242 (t0) REVERT: E 376 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8184 (ptm) REVERT: E 377 LYS cc_start: 0.6240 (OUTLIER) cc_final: 0.5707 (mttp) REVERT: F 203 ARG cc_start: 0.8703 (mmp80) cc_final: 0.8491 (mmp80) REVERT: F 317 ASP cc_start: 0.7667 (t0) cc_final: 0.7451 (t0) REVERT: B 15 GLU cc_start: 0.7239 (tp30) cc_final: 0.6938 (tp30) REVERT: B 126 MET cc_start: 0.8760 (mmt) cc_final: 0.8470 (tpp) REVERT: B 164 MET cc_start: 0.7664 (pmm) cc_final: 0.7411 (pmm) REVERT: B 336 ASP cc_start: 0.8339 (t0) cc_final: 0.8036 (t0) REVERT: B 338 MET cc_start: 0.8687 (ptp) cc_final: 0.8445 (ptp) outliers start: 34 outliers final: 22 residues processed: 176 average time/residue: 0.5176 time to fit residues: 106.0300 Evaluate side-chains 172 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 242 optimal weight: 2.9990 chunk 253 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 236 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.073420 restraints weight = 45061.034| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.60 r_work: 0.2857 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 23345 Z= 0.166 Angle : 0.705 59.198 31745 Z= 0.398 Chirality : 0.045 0.406 3668 Planarity : 0.004 0.046 4186 Dihedral : 5.094 30.678 3206 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.91 % Favored : 96.89 % Rotamer: Outliers : 1.30 % Allowed : 13.23 % Favored : 85.47 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.73 (0.14), residues: 2989 helix: 0.99 (0.19), residues: 669 sheet: -0.28 (0.17), residues: 794 loop : -1.27 (0.14), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.014 0.001 TYR A 100 PHE 0.019 0.002 PHE F 188 TRP 0.017 0.001 TRP G 354 HIS 0.002 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00374 (23345) covalent geometry : angle 0.70477 (31745) hydrogen bonds : bond 0.05208 ( 843) hydrogen bonds : angle 5.25822 ( 2364) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.984 Fit side-chains REVERT: G 185 ARG cc_start: 0.5248 (tpt170) cc_final: 0.4774 (tmt-80) REVERT: G 271 ASP cc_start: 0.8045 (p0) cc_final: 0.7530 (m-30) REVERT: G 316 ASP cc_start: 0.8256 (p0) cc_final: 0.8041 (p0) REVERT: A 338 MET cc_start: 0.8522 (ttm) cc_final: 0.8122 (ttm) REVERT: E 122 MET cc_start: 0.9073 (tpp) cc_final: 0.8814 (tpt) REVERT: E 246 ASP cc_start: 0.8084 (m-30) cc_final: 0.7235 (t0) REVERT: E 377 LYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5701 (mttp) REVERT: F 203 ARG cc_start: 0.8690 (mmp80) cc_final: 0.8478 (mmp80) REVERT: F 317 ASP cc_start: 0.7656 (t0) cc_final: 0.7441 (t0) REVERT: B 15 GLU cc_start: 0.7240 (tp30) cc_final: 0.6942 (tp30) REVERT: B 126 MET cc_start: 0.8752 (mmt) cc_final: 0.8460 (tpp) REVERT: B 164 MET cc_start: 0.7663 (pmm) cc_final: 0.7407 (pmm) REVERT: B 336 ASP cc_start: 0.8336 (t0) cc_final: 0.8034 (t0) REVERT: B 338 MET cc_start: 0.8682 (ptp) cc_final: 0.8440 (ptp) outliers start: 32 outliers final: 24 residues processed: 171 average time/residue: 0.6409 time to fit residues: 127.0508 Evaluate side-chains 173 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 150 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 67 optimal weight: 0.4980 chunk 235 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 281 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.082366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.073396 restraints weight = 45127.340| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.60 r_work: 0.2856 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 23345 Z= 0.166 Angle : 0.705 59.198 31745 Z= 0.398 Chirality : 0.045 0.406 3668 Planarity : 0.004 0.046 4186 Dihedral : 5.094 30.678 3206 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.91 % Favored : 96.89 % Rotamer: Outliers : 1.06 % Allowed : 13.43 % Favored : 85.51 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.73 (0.14), residues: 2989 helix: 0.99 (0.19), residues: 669 sheet: -0.28 (0.17), residues: 794 loop : -1.27 (0.14), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.014 0.001 TYR A 100 PHE 0.019 0.002 PHE F 188 TRP 0.017 0.001 TRP G 354 HIS 0.002 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00374 (23345) covalent geometry : angle 0.70477 (31745) hydrogen bonds : bond 0.05208 ( 843) hydrogen bonds : angle 5.25822 ( 2364) =============================================================================== Job complete usr+sys time: 6527.22 seconds wall clock time: 112 minutes 4.50 seconds (6724.50 seconds total)