Starting phenix.real_space_refine on Thu May 22 01:36:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i1t_35121/05_2025/8i1t_35121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i1t_35121/05_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_35121/05_2025/8i1t_35121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i1t_35121/05_2025/8i1t_35121.map" model { file = "/net/cci-nas-00/data/ceres_data/8i1t_35121/05_2025/8i1t_35121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i1t_35121/05_2025/8i1t_35121.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.03, per 1000 atoms: 0.57 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: 5.32 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 3.25 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: 9.23 Time building geometry restraints manager: 6.25 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: 0.04 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: 2.230 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: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 51.050 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.130 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:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.098 0.005 TRP F 354 HIS 0.005 0.001 HIS C 370 PHE 0.054 0.003 PHE E 147 TYR 0.016 0.002 TYR D 100 ARG 0.007 0.001 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.16921 ( 843) hydrogen bonds : angle 7.42084 ( 2364) covalent geometry : bond 0.00694 (23345) covalent geometry : angle 0.69605 (31745) *********************** 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 : 2.625 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: 1.3893 time to fit residues: 271.5001 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 : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.4980 chunk 222 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 150 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 171 ASN A 248 ASN E 53 GLN E 114 ASN E 305 HIS ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.084609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075567 restraints weight = 44484.370| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.65 r_work: 0.2893 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23345 Z= 0.125 Angle : 0.540 8.600 31745 Z= 0.293 Chirality : 0.044 0.188 3668 Planarity : 0.004 0.048 4186 Dihedral : 5.081 25.925 3206 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 0.98 % Allowed : 5.78 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 2989 helix: 0.68 (0.20), residues: 687 sheet: -0.03 (0.17), residues: 794 loop : -1.23 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 354 HIS 0.002 0.001 HIS G 305 PHE 0.024 0.002 PHE A 147 TYR 0.014 0.001 TYR A 100 ARG 0.003 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.05309 ( 843) hydrogen bonds : angle 5.58942 ( 2364) covalent geometry : bond 0.00269 (23345) covalent geometry : angle 0.54016 (31745) *********************** 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 197 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 2.527 Fit side-chains REVERT: G 185 ARG cc_start: 0.5189 (tpt170) cc_final: 0.4748 (tmt-80) REVERT: A 338 MET cc_start: 0.8600 (ttm) cc_final: 0.8110 (ttm) REVERT: E 122 MET cc_start: 0.9047 (tpp) cc_final: 0.8826 (tpt) REVERT: E 246 ASP cc_start: 0.8333 (m-30) cc_final: 0.7449 (t0) REVERT: E 316 ASP cc_start: 0.7675 (t70) cc_final: 0.7150 (t0) REVERT: B 336 ASP cc_start: 0.8311 (t0) cc_final: 0.7974 (t0) REVERT: B 338 MET cc_start: 0.8808 (ptp) cc_final: 0.8451 (ptp) REVERT: D 49 MET cc_start: 0.9092 (mtp) cc_final: 0.8887 (mtt) REVERT: D 188 PHE cc_start: 0.7428 (t80) cc_final: 0.7225 (t80) outliers start: 24 outliers final: 9 residues processed: 183 average time/residue: 1.2462 time to fit residues: 264.4996 Evaluate side-chains 160 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 2.381 ------------------------------------------------------------------------------- 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 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 B residue 141 THR 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 42 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 11 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 overall best weight: 5.4586 ------------------------------------------------------------------------------- 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN B 58 GLN B 248 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.080043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.070868 restraints weight = 44916.102| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.64 r_work: 0.2804 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 23345 Z= 0.327 Angle : 0.679 8.646 31745 Z= 0.362 Chirality : 0.049 0.217 3668 Planarity : 0.005 0.058 4186 Dihedral : 5.702 27.883 3206 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.08 % Favored : 96.75 % Rotamer: Outliers : 2.28 % Allowed : 8.06 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 2989 helix: 0.54 (0.19), residues: 676 sheet: -0.29 (0.17), residues: 785 loop : -1.38 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP F 354 HIS 0.005 0.002 HIS C 370 PHE 0.045 0.003 PHE G 208 TYR 0.017 0.002 TYR G 175 ARG 0.005 0.001 ARG G 255 Details of bonding type rmsd hydrogen bonds : bond 0.06478 ( 843) hydrogen bonds : angle 5.74345 ( 2364) covalent geometry : bond 0.00761 (23345) covalent geometry : angle 0.67936 (31745) *********************** 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 209 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 2.475 Fit side-chains REVERT: G 14 ASP cc_start: 0.7958 (p0) cc_final: 0.7717 (p0) REVERT: G 15 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7868 (mm-30) REVERT: G 79 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8155 (mtm) REVERT: G 185 ARG cc_start: 0.5382 (tpt170) cc_final: 0.4923 (tmt-80) REVERT: G 209 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8272 (m-30) REVERT: G 316 ASP cc_start: 0.8393 (p0) cc_final: 0.8132 (p0) REVERT: A 164 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8240 (mmp) REVERT: A 338 MET cc_start: 0.8474 (ttm) cc_final: 0.8094 (ttm) REVERT: C 307 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: E 246 ASP cc_start: 0.8247 (m-30) cc_final: 0.7392 (t0) REVERT: E 377 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5518 (mptt) REVERT: F 122 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8726 (tpp) REVERT: F 194 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: B 15 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6964 (tp30) REVERT: B 122 MET cc_start: 0.9239 (tpp) cc_final: 0.8795 (tpt) REVERT: B 246 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6957 (p0) REVERT: B 248 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8507 (m110) REVERT: B 336 ASP cc_start: 0.8352 (t0) cc_final: 0.8063 (t0) REVERT: B 338 MET cc_start: 0.8833 (ptp) cc_final: 0.8478 (ptp) REVERT: D 219 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.9002 (t) outliers start: 56 outliers final: 20 residues processed: 184 average time/residue: 1.3476 time to fit residues: 285.2456 Evaluate side-chains 176 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 209 ASP 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 278 VAL 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 26 MET Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 246 ASP 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 B residue 246 ASP Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain D residue 219 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 36 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 220 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 280 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 248 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.084057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.075170 restraints weight = 45344.094| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.61 r_work: 0.2891 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23345 Z= 0.114 Angle : 0.517 7.829 31745 Z= 0.278 Chirality : 0.044 0.187 3668 Planarity : 0.004 0.051 4186 Dihedral : 4.953 24.919 3206 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.26 % Rotamer: Outliers : 1.18 % Allowed : 10.26 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 2989 helix: 0.92 (0.20), residues: 678 sheet: -0.19 (0.17), residues: 794 loop : -1.27 (0.14), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 354 HIS 0.002 0.000 HIS C 370 PHE 0.017 0.002 PHE A 147 TYR 0.013 0.001 TYR G 175 ARG 0.003 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 843) hydrogen bonds : angle 5.23051 ( 2364) covalent geometry : bond 0.00244 (23345) covalent geometry : angle 0.51677 (31745) *********************** 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 189 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 2.752 Fit side-chains REVERT: G 79 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8075 (mtm) REVERT: G 185 ARG cc_start: 0.5134 (tpt170) cc_final: 0.4647 (tmt-80) REVERT: G 271 ASP cc_start: 0.7938 (p0) cc_final: 0.7225 (m-30) REVERT: G 316 ASP cc_start: 0.8293 (p0) cc_final: 0.7954 (p0) REVERT: A 338 MET cc_start: 0.8618 (ttm) cc_final: 0.8145 (ttm) REVERT: C 307 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: E 122 MET cc_start: 0.9080 (tpp) cc_final: 0.8837 (tpt) REVERT: E 246 ASP cc_start: 0.8138 (m-30) cc_final: 0.7371 (t0) REVERT: F 203 ARG cc_start: 0.8715 (mmp80) cc_final: 0.8395 (mmp80) REVERT: F 338 MET cc_start: 0.8629 (ttm) cc_final: 0.8332 (ttm) REVERT: B 15 GLU cc_start: 0.7240 (tp30) cc_final: 0.6923 (tp30) REVERT: B 336 ASP cc_start: 0.8371 (t0) cc_final: 0.8052 (t0) REVERT: B 338 MET cc_start: 0.8779 (ptp) cc_final: 0.8473 (ptp) outliers start: 29 outliers final: 14 residues processed: 178 average time/residue: 1.2721 time to fit residues: 262.6366 Evaluate side-chains 165 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 2.634 ------------------------------------------------------------------------------- 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 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 309 THR Chi-restraints excluded: chain C residue 126 MET 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 F residue 72 GLU Chi-restraints excluded: chain D residue 301 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 85 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 241 optimal weight: 8.9990 chunk 64 optimal weight: 0.1980 overall best weight: 6.0388 ------------------------------------------------------------------------------- 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** A 245 ASN E 84 ASN B 58 GLN ** D 84 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 = 0.3061 r_free = 0.3061 target = 0.079674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.070667 restraints weight = 45589.898| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.60 r_work: 0.2803 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 23345 Z= 0.359 Angle : 0.696 9.425 31745 Z= 0.370 Chirality : 0.050 0.225 3668 Planarity : 0.005 0.060 4186 Dihedral : 5.739 28.194 3206 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.14 % Favored : 96.69 % Rotamer: Outliers : 2.69 % Allowed : 10.26 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 2989 helix: 0.53 (0.19), residues: 676 sheet: -0.41 (0.17), residues: 785 loop : -1.42 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 354 HIS 0.005 0.002 HIS C 370 PHE 0.021 0.003 PHE B 87 TYR 0.017 0.002 TYR G 175 ARG 0.007 0.001 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.06424 ( 843) hydrogen bonds : angle 5.67208 ( 2364) covalent geometry : bond 0.00837 (23345) covalent geometry : angle 0.69579 (31745) *********************** 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 210 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 144 time to evaluate : 2.583 Fit side-chains REVERT: G 79 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8185 (mtm) REVERT: G 185 ARG cc_start: 0.5307 (tpt170) cc_final: 0.4806 (tmt-80) REVERT: A 164 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8222 (mmp) REVERT: A 338 MET cc_start: 0.8495 (ttm) cc_final: 0.8105 (ttm) REVERT: C 122 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8690 (tpp) REVERT: C 307 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: E 246 ASP cc_start: 0.8139 (m-30) cc_final: 0.7338 (t0) REVERT: E 376 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8251 (ptm) REVERT: E 377 LYS cc_start: 0.6319 (OUTLIER) cc_final: 0.5685 (mptt) REVERT: F 122 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8671 (tpp) REVERT: F 203 ARG cc_start: 0.8765 (mmp80) cc_final: 0.8523 (mmp80) REVERT: B 122 MET cc_start: 0.9287 (tpp) cc_final: 0.8901 (tpt) REVERT: B 246 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6826 (p0) REVERT: B 248 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8444 (p0) REVERT: B 336 ASP cc_start: 0.8402 (t0) cc_final: 0.8116 (t0) REVERT: B 338 MET cc_start: 0.8802 (ptp) cc_final: 0.8466 (ptp) outliers start: 66 outliers final: 33 residues processed: 188 average time/residue: 1.2076 time to fit residues: 264.4805 Evaluate side-chains 185 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 284 MET Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 PHE 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 122 MET Chi-restraints excluded: chain C residue 126 MET 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 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 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 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 246 ASP Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain D residue 219 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 388 LEU Chi-restraints excluded: chain D residue 423 VAL 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 198 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 120 optimal weight: 0.0670 chunk 247 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- 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 245 ASN E 84 ASN E 305 HIS B 58 GLN D 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.082349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.073440 restraints weight = 45105.297| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.60 r_work: 0.2858 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23345 Z= 0.144 Angle : 0.545 7.831 31745 Z= 0.292 Chirality : 0.045 0.200 3668 Planarity : 0.004 0.056 4186 Dihedral : 5.197 26.354 3206 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.78 % Favored : 97.02 % Rotamer: Outliers : 2.12 % Allowed : 11.56 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 2989 helix: 0.81 (0.20), residues: 675 sheet: -0.30 (0.17), residues: 785 loop : -1.36 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 354 HIS 0.002 0.000 HIS C 370 PHE 0.015 0.002 PHE A 147 TYR 0.015 0.001 TYR D 100 ARG 0.003 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.05157 ( 843) hydrogen bonds : angle 5.32858 ( 2364) covalent geometry : bond 0.00324 (23345) covalent geometry : angle 0.54497 (31745) *********************** 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 206 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 2.865 Fit side-chains REVERT: G 79 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8142 (mtm) REVERT: G 185 ARG cc_start: 0.5261 (tpt170) cc_final: 0.4741 (tmt-80) REVERT: G 209 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: G 271 ASP cc_start: 0.8032 (p0) cc_final: 0.7397 (m-30) REVERT: A 338 MET cc_start: 0.8567 (ttm) cc_final: 0.8168 (ttm) REVERT: E 122 MET cc_start: 0.9073 (tpp) cc_final: 0.8844 (tpt) REVERT: E 246 ASP cc_start: 0.8141 (m-30) cc_final: 0.7320 (t0) REVERT: E 376 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8175 (ptm) REVERT: B 15 GLU cc_start: 0.7330 (tp30) cc_final: 0.6990 (tp30) REVERT: B 336 ASP cc_start: 0.8320 (t0) cc_final: 0.7976 (t0) REVERT: B 338 MET cc_start: 0.8767 (ptp) cc_final: 0.8466 (ptp) REVERT: D 84 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8671 (m110) outliers start: 52 outliers final: 22 residues processed: 189 average time/residue: 1.2608 time to fit residues: 281.9951 Evaluate side-chains 169 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 2.667 ------------------------------------------------------------------------------- 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 280 PHE 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 126 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 376 MET 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 F residue 72 GLU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 78 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 291 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 A 245 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN D 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.081014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.072022 restraints weight = 45283.687| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.61 r_work: 0.2828 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23345 Z= 0.231 Angle : 0.599 7.690 31745 Z= 0.319 Chirality : 0.046 0.202 3668 Planarity : 0.004 0.057 4186 Dihedral : 5.367 26.989 3206 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.94 % Favored : 96.86 % Rotamer: Outliers : 2.32 % Allowed : 12.01 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 2989 helix: 0.74 (0.19), residues: 674 sheet: -0.37 (0.17), residues: 785 loop : -1.37 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 354 HIS 0.003 0.001 HIS C 370 PHE 0.017 0.002 PHE B 87 TYR 0.016 0.002 TYR D 100 ARG 0.004 0.000 ARG G 255 Details of bonding type rmsd hydrogen bonds : bond 0.05618 ( 843) hydrogen bonds : angle 5.41127 ( 2364) covalent geometry : bond 0.00535 (23345) covalent geometry : angle 0.59867 (31745) *********************** 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 204 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 147 time to evaluate : 2.770 Fit side-chains revert: symmetry clash REVERT: G 79 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8197 (mtm) REVERT: G 185 ARG cc_start: 0.5301 (tpt170) cc_final: 0.4781 (tmt-80) REVERT: G 209 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: G 271 ASP cc_start: 0.8082 (p0) cc_final: 0.7468 (m-30) REVERT: A 338 MET cc_start: 0.8544 (ttm) cc_final: 0.8092 (ttm) REVERT: E 246 ASP cc_start: 0.8132 (m-30) cc_final: 0.7306 (t0) REVERT: E 376 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8190 (ptm) REVERT: E 377 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5738 (mttp) REVERT: B 15 GLU cc_start: 0.7276 (tp30) cc_final: 0.6945 (tp30) REVERT: B 336 ASP cc_start: 0.8360 (t0) cc_final: 0.8059 (t0) REVERT: B 338 MET cc_start: 0.8718 (ptp) cc_final: 0.8448 (ptp) REVERT: D 84 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8819 (m110) outliers start: 57 outliers final: 29 residues processed: 189 average time/residue: 1.1792 time to fit residues: 260.4217 Evaluate side-chains 179 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 2.634 ------------------------------------------------------------------------------- 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 280 PHE 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 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 126 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 C residue 376 MET 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 3 LEU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 198 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 25 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** G 414 ASN A 84 ASN A 245 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN B 58 GLN D 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.083078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.074168 restraints weight = 45024.095| |-----------------------------------------------------------------------------| 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: 0.8637 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23345 Z= 0.135 Angle : 0.530 7.848 31745 Z= 0.283 Chirality : 0.044 0.194 3668 Planarity : 0.004 0.051 4186 Dihedral : 4.982 25.347 3206 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.58 % Favored : 97.22 % Rotamer: Outliers : 2.08 % Allowed : 12.45 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 2989 helix: 0.95 (0.20), residues: 675 sheet: -0.28 (0.17), residues: 786 loop : -1.31 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 354 HIS 0.002 0.000 HIS C 370 PHE 0.016 0.002 PHE A 147 TYR 0.013 0.001 TYR D 100 ARG 0.003 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 843) hydrogen bonds : angle 5.17113 ( 2364) covalent geometry : bond 0.00305 (23345) covalent geometry : angle 0.53024 (31745) *********************** 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 202 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 2.550 Fit side-chains revert: symmetry clash REVERT: G 79 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8194 (mtm) REVERT: G 185 ARG cc_start: 0.5239 (tpt170) cc_final: 0.4741 (tmt-80) REVERT: G 209 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8263 (m-30) REVERT: G 271 ASP cc_start: 0.8005 (p0) cc_final: 0.7487 (m-30) REVERT: A 338 MET cc_start: 0.8592 (ttm) cc_final: 0.8204 (ttm) REVERT: E 122 MET cc_start: 0.9040 (tpp) cc_final: 0.8756 (tpt) REVERT: E 246 ASP cc_start: 0.8111 (m-30) cc_final: 0.7277 (t0) REVERT: E 377 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6133 (mttp) REVERT: B 15 GLU cc_start: 0.7258 (tp30) cc_final: 0.6964 (tp30) REVERT: B 336 ASP cc_start: 0.8334 (t0) cc_final: 0.8036 (t0) REVERT: B 338 MET cc_start: 0.8703 (ptp) cc_final: 0.8435 (ptp) REVERT: D 84 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8630 (m110) outliers start: 51 outliers final: 29 residues processed: 191 average time/residue: 1.1445 time to fit residues: 256.1330 Evaluate side-chains 177 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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 280 PHE 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 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 126 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 376 MET Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 VAL 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 84 ASN Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 101 optimal weight: 0.7980 chunk 176 optimal weight: 8.9990 chunk 238 optimal weight: 0.0060 chunk 178 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 272 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 237 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 B 45 ASN B 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.084767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.075915 restraints weight = 45126.835| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.60 r_work: 0.2906 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23345 Z= 0.106 Angle : 0.507 7.918 31745 Z= 0.270 Chirality : 0.043 0.171 3668 Planarity : 0.004 0.044 4186 Dihedral : 4.692 23.700 3206 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.68 % Favored : 97.12 % Rotamer: Outliers : 1.67 % Allowed : 13.23 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 2989 helix: 1.17 (0.20), residues: 669 sheet: -0.20 (0.17), residues: 786 loop : -1.27 (0.14), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 354 HIS 0.001 0.000 HIS C 370 PHE 0.015 0.001 PHE A 147 TYR 0.013 0.001 TYR E 100 ARG 0.002 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 843) hydrogen bonds : angle 4.98601 ( 2364) covalent geometry : bond 0.00234 (23345) covalent geometry : angle 0.50733 (31745) *********************** 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 200 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 2.721 Fit side-chains REVERT: G 79 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8154 (mtm) REVERT: G 132 THR cc_start: 0.8814 (m) cc_final: 0.8177 (p) REVERT: G 185 ARG cc_start: 0.5201 (tpt170) cc_final: 0.4642 (tmt-80) REVERT: G 209 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8267 (m-30) REVERT: G 271 ASP cc_start: 0.7944 (p0) cc_final: 0.7481 (m-30) REVERT: A 338 MET cc_start: 0.8628 (ttm) cc_final: 0.8157 (ttm) REVERT: E 122 MET cc_start: 0.9034 (tpp) cc_final: 0.8721 (tpt) REVERT: E 246 ASP cc_start: 0.8094 (m-30) cc_final: 0.7251 (t0) REVERT: E 377 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6297 (mttp) REVERT: B 15 GLU cc_start: 0.7310 (tp30) cc_final: 0.6990 (tp30) REVERT: B 126 MET cc_start: 0.8717 (mmt) cc_final: 0.8446 (tpp) REVERT: B 336 ASP cc_start: 0.8323 (t0) cc_final: 0.7987 (t0) REVERT: B 338 MET cc_start: 0.8687 (ptp) cc_final: 0.8425 (ptp) REVERT: D 147 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8506 (t80) outliers start: 41 outliers final: 25 residues processed: 189 average time/residue: 1.1473 time to fit residues: 256.0088 Evaluate side-chains 179 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 2.717 ------------------------------------------------------------------------------- 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 280 PHE 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 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 126 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 E residue 94 LEU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 VAL 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 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain D residue 147 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 131 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 173 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 292 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 274 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 B 58 GLN D 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.080728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.071710 restraints weight = 45410.915| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.61 r_work: 0.2822 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 23345 Z= 0.282 Angle : 0.644 8.012 31745 Z= 0.341 Chirality : 0.048 0.215 3668 Planarity : 0.004 0.054 4186 Dihedral : 5.389 27.179 3206 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.98 % Favored : 96.82 % Rotamer: Outliers : 1.71 % Allowed : 13.35 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 2989 helix: 0.77 (0.19), residues: 673 sheet: -0.38 (0.17), residues: 787 loop : -1.36 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 354 HIS 0.004 0.001 HIS A 305 PHE 0.021 0.003 PHE F 188 TYR 0.017 0.002 TYR D 100 ARG 0.004 0.001 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.05830 ( 843) hydrogen bonds : angle 5.40632 ( 2364) covalent geometry : bond 0.00658 (23345) covalent geometry : angle 0.64442 (31745) ********************** 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 190 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 2.624 Fit side-chains REVERT: G 185 ARG cc_start: 0.5292 (tpt170) cc_final: 0.4814 (tmt-80) REVERT: G 209 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8331 (m-30) REVERT: G 271 ASP cc_start: 0.8130 (p0) cc_final: 0.7605 (m-30) REVERT: A 338 MET cc_start: 0.8511 (ttm) cc_final: 0.8129 (ttm) REVERT: E 122 MET cc_start: 0.9095 (tpp) cc_final: 0.8846 (tpt) REVERT: E 246 ASP cc_start: 0.8101 (m-30) cc_final: 0.7251 (t0) REVERT: E 376 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8195 (ptm) REVERT: E 377 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5798 (mttp) REVERT: B 15 GLU cc_start: 0.7279 (tp30) cc_final: 0.6935 (tp30) REVERT: B 336 ASP cc_start: 0.8397 (t0) cc_final: 0.8092 (t0) REVERT: B 338 MET cc_start: 0.8694 (ptp) cc_final: 0.8396 (ptp) REVERT: D 84 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8811 (m110) REVERT: D 147 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8578 (t80) outliers start: 42 outliers final: 26 residues processed: 179 average time/residue: 1.2248 time to fit residues: 255.0943 Evaluate side-chains 176 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 280 PHE 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 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 126 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 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 84 ASN Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 147 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 194 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 226 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** B 58 GLN D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.080881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.071859 restraints weight = 45218.036| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.60 r_work: 0.2827 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 23345 Z= 0.276 Angle : 0.903 59.200 31745 Z= 0.524 Chirality : 0.048 0.568 3668 Planarity : 0.005 0.054 4186 Dihedral : 5.435 29.136 3206 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.01 % Favored : 96.79 % Rotamer: Outliers : 1.51 % Allowed : 13.59 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 2989 helix: 0.76 (0.19), residues: 673 sheet: -0.40 (0.17), residues: 787 loop : -1.36 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 354 HIS 0.004 0.001 HIS A 305 PHE 0.020 0.002 PHE B 256 TYR 0.017 0.002 TYR D 100 ARG 0.004 0.000 ARG C 299 Details of bonding type rmsd hydrogen bonds : bond 0.05861 ( 843) hydrogen bonds : angle 5.48699 ( 2364) covalent geometry : bond 0.00598 (23345) covalent geometry : angle 0.90328 (31745) =============================================================================== Job complete usr+sys time: 13772.37 seconds wall clock time: 239 minutes 54.15 seconds (14394.15 seconds total)