Starting phenix.real_space_refine on Thu Jun 19 07:23:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i1t_35121/06_2025/8i1t_35121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i1t_35121/06_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_35121/06_2025/8i1t_35121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i1t_35121/06_2025/8i1t_35121.map" model { file = "/net/cci-nas-00/data/ceres_data/8i1t_35121/06_2025/8i1t_35121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i1t_35121/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.91, per 1000 atoms: 0.61 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: 5.23 Conformation dependent library (CDL) restraints added in 2.8 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: 3.41 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: 8.04 Time building geometry restraints manager: 6.31 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 52.070 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.110 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:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.260 ------------------------------------------------------------------------------- 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 : 2.631 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: 1.3875 time to fit residues: 271.3991 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 : 2.392 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075565 restraints weight = 44483.900| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.65 r_work: 0.2892 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 25.927 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 5.58930 ( 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 : 2.758 Fit side-chains REVERT: G 185 ARG cc_start: 0.5193 (tpt170) cc_final: 0.4753 (tmt-80) REVERT: A 338 MET cc_start: 0.8601 (ttm) cc_final: 0.8110 (ttm) REVERT: E 122 MET cc_start: 0.9046 (tpp) cc_final: 0.8825 (tpt) REVERT: E 246 ASP cc_start: 0.8325 (m-30) cc_final: 0.7442 (t0) REVERT: E 316 ASP cc_start: 0.7668 (t70) cc_final: 0.7143 (t0) REVERT: B 336 ASP cc_start: 0.8301 (t0) cc_final: 0.7971 (t0) REVERT: B 338 MET cc_start: 0.8808 (ptp) cc_final: 0.8453 (ptp) REVERT: D 49 MET cc_start: 0.9080 (mtp) cc_final: 0.8875 (mtt) REVERT: D 188 PHE cc_start: 0.7425 (t80) cc_final: 0.7224 (t80) outliers start: 24 outliers final: 9 residues processed: 183 average time/residue: 1.3091 time to fit residues: 277.4579 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 : 2.803 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 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: 9.9990 chunk 30 optimal weight: 0.6980 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.079847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.070668 restraints weight = 44964.575| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.64 r_work: 0.2800 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 23345 Z= 0.348 Angle : 0.694 9.038 31745 Z= 0.370 Chirality : 0.050 0.220 3668 Planarity : 0.005 0.059 4186 Dihedral : 5.741 28.051 3206 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.11 % Favored : 96.72 % Rotamer: Outliers : 2.28 % Allowed : 8.18 % Favored : 89.54 % 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: -0.99 (0.14), residues: 2989 helix: 0.51 (0.19), residues: 676 sheet: -0.31 (0.17), residues: 785 loop : -1.39 (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 0.044 0.003 PHE G 208 TYR 0.017 0.002 TYR G 175 ARG 0.006 0.001 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.06561 ( 843) hydrogen bonds : angle 5.76243 ( 2364) covalent geometry : bond 0.00812 (23345) covalent geometry : angle 0.69390 (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 208 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 2.388 Fit side-chains REVERT: G 14 ASP cc_start: 0.7960 (p0) cc_final: 0.7718 (p0) REVERT: G 15 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7877 (mm-30) REVERT: G 79 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8153 (mtm) REVERT: G 185 ARG cc_start: 0.5391 (tpt170) cc_final: 0.4930 (tmt-80) REVERT: G 209 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8277 (m-30) REVERT: A 164 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8240 (mmp) REVERT: A 242 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8525 (pt0) REVERT: A 338 MET cc_start: 0.8480 (ttm) cc_final: 0.8103 (ttm) REVERT: C 307 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8523 (tt0) REVERT: E 246 ASP cc_start: 0.8249 (m-30) cc_final: 0.7391 (t0) REVERT: E 377 LYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5520 (mptt) REVERT: F 122 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8683 (tpp) REVERT: F 194 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8349 (mt-10) REVERT: B 15 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6969 (tp30) REVERT: B 122 MET cc_start: 0.9246 (tpp) cc_final: 0.8807 (tpt) REVERT: B 246 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.6947 (p0) REVERT: B 248 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8517 (m110) REVERT: B 336 ASP cc_start: 0.8396 (t0) cc_final: 0.8126 (t0) REVERT: B 338 MET cc_start: 0.8836 (ptp) cc_final: 0.8504 (ptp) REVERT: D 219 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.9002 (t) outliers start: 56 outliers final: 20 residues processed: 183 average time/residue: 1.2913 time to fit residues: 272.0001 Evaluate side-chains 175 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 2.400 ------------------------------------------------------------------------------- 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 242 GLN 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: 0.7980 chunk 146 optimal weight: 8.9990 chunk 220 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 280 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 242 GLN A 248 ASN E 84 ASN E 114 ASN B 58 GLN ** D 84 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 = 0.3145 r_free = 0.3145 target = 0.084217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.075324 restraints weight = 45345.324| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.61 r_work: 0.2895 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23345 Z= 0.114 Angle : 0.516 7.825 31745 Z= 0.277 Chirality : 0.043 0.189 3668 Planarity : 0.004 0.051 4186 Dihedral : 4.932 24.783 3206 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.26 % Rotamer: Outliers : 1.18 % Allowed : 10.38 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 2989 helix: 0.91 (0.20), residues: 678 sheet: -0.17 (0.17), residues: 794 loop : -1.28 (0.14), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 354 HIS 0.001 0.000 HIS C 370 PHE 0.016 0.002 PHE A 147 TYR 0.013 0.001 TYR A 100 ARG 0.003 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 843) hydrogen bonds : angle 5.21566 ( 2364) covalent geometry : bond 0.00249 (23345) covalent geometry : angle 0.51593 (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 188 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 2.709 Fit side-chains REVERT: G 79 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8061 (mtm) REVERT: G 185 ARG cc_start: 0.5126 (tpt170) cc_final: 0.4635 (tmt-80) REVERT: G 271 ASP cc_start: 0.7933 (p0) cc_final: 0.7228 (m-30) REVERT: A 338 MET cc_start: 0.8621 (ttm) cc_final: 0.8155 (ttm) REVERT: C 307 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8434 (tm-30) REVERT: E 122 MET cc_start: 0.9068 (tpp) cc_final: 0.8827 (tpt) REVERT: E 246 ASP cc_start: 0.8140 (m-30) cc_final: 0.7344 (t0) REVERT: F 203 ARG cc_start: 0.8710 (mmp80) cc_final: 0.8391 (mmp80) REVERT: F 338 MET cc_start: 0.8651 (ttm) cc_final: 0.8221 (ttm) REVERT: B 15 GLU cc_start: 0.7277 (tp30) cc_final: 0.6973 (tp30) REVERT: B 336 ASP cc_start: 0.8379 (t0) cc_final: 0.8054 (t0) REVERT: B 338 MET cc_start: 0.8774 (ptp) cc_final: 0.8490 (ptp) outliers start: 29 outliers final: 12 residues processed: 178 average time/residue: 1.3310 time to fit residues: 274.2454 Evaluate side-chains 163 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 2.767 ------------------------------------------------------------------------------- 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 191 ILE 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: 0.2980 chunk 96 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 ** 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 = 0.3095 r_free = 0.3095 target = 0.081484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.072498 restraints weight = 45399.974| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.61 r_work: 0.2837 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23345 Z= 0.222 Angle : 0.587 7.558 31745 Z= 0.313 Chirality : 0.046 0.195 3668 Planarity : 0.004 0.054 4186 Dihedral : 5.253 26.501 3206 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.71 % Favored : 97.12 % Rotamer: Outliers : 2.08 % Allowed : 10.54 % Favored : 87.38 % 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: -0.82 (0.14), residues: 2989 helix: 0.85 (0.20), residues: 674 sheet: -0.29 (0.17), residues: 785 loop : -1.33 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 354 HIS 0.003 0.001 HIS C 370 PHE 0.020 0.002 PHE G 208 TYR 0.015 0.002 TYR G 175 ARG 0.004 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.05546 ( 843) hydrogen bonds : angle 5.38457 ( 2364) covalent geometry : bond 0.00512 (23345) covalent geometry : angle 0.58683 (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 201 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 2.422 Fit side-chains REVERT: G 79 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8154 (mtm) REVERT: G 185 ARG cc_start: 0.5238 (tpt170) cc_final: 0.4705 (tmt-80) REVERT: A 338 MET cc_start: 0.8528 (ttm) cc_final: 0.8088 (ttm) REVERT: C 307 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: E 122 MET cc_start: 0.9099 (tpp) cc_final: 0.8871 (tpt) REVERT: E 246 ASP cc_start: 0.8144 (m-30) cc_final: 0.7348 (t0) REVERT: E 376 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8197 (ptm) REVERT: E 377 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5676 (mptt) REVERT: F 203 ARG cc_start: 0.8733 (mmp80) cc_final: 0.8465 (mmp80) REVERT: F 338 MET cc_start: 0.8724 (ttm) cc_final: 0.8257 (ttm) REVERT: B 15 GLU cc_start: 0.7284 (tp30) cc_final: 0.6967 (tp30) REVERT: B 336 ASP cc_start: 0.8370 (t0) cc_final: 0.8074 (t0) REVERT: B 338 MET cc_start: 0.8767 (ptp) cc_final: 0.8461 (ptp) REVERT: D 219 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.8969 (t) outliers start: 51 outliers final: 25 residues processed: 186 average time/residue: 1.3102 time to fit residues: 283.2071 Evaluate side-chains 173 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 2.568 ------------------------------------------------------------------------------- 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 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 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 72 GLU 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 278 VAL Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 198 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 247 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ** 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 = 0.3124 r_free = 0.3124 target = 0.083060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.074139 restraints weight = 45023.700| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.60 r_work: 0.2871 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23345 Z= 0.143 Angle : 0.530 7.862 31745 Z= 0.283 Chirality : 0.044 0.194 3668 Planarity : 0.004 0.051 4186 Dihedral : 4.979 25.177 3206 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.61 % Favored : 97.19 % Rotamer: Outliers : 2.24 % Allowed : 11.36 % Favored : 86.41 % 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: -0.70 (0.14), residues: 2989 helix: 0.98 (0.20), residues: 675 sheet: -0.21 (0.17), residues: 794 loop : -1.27 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 354 HIS 0.002 0.001 HIS C 370 PHE 0.016 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 0.04982 ( 843) hydrogen bonds : angle 5.20554 ( 2364) covalent geometry : bond 0.00323 (23345) covalent geometry : angle 0.53023 (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 207 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 2.735 Fit side-chains REVERT: G 79 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8129 (mtm) REVERT: G 185 ARG cc_start: 0.5206 (tpt170) cc_final: 0.4712 (tmt-80) REVERT: G 209 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: G 271 ASP cc_start: 0.8035 (p0) cc_final: 0.7455 (m-30) REVERT: A 338 MET cc_start: 0.8563 (ttm) cc_final: 0.8144 (ttm) REVERT: C 307 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8435 (tm-30) REVERT: E 122 MET cc_start: 0.9062 (tpp) cc_final: 0.8824 (tpt) REVERT: E 246 ASP cc_start: 0.8120 (m-30) cc_final: 0.7303 (t0) REVERT: E 376 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8191 (ptm) REVERT: E 377 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.6076 (mttp) REVERT: F 122 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8393 (tpp) REVERT: F 203 ARG cc_start: 0.8679 (mmp80) cc_final: 0.8409 (mmp80) REVERT: B 15 GLU cc_start: 0.7299 (tp30) cc_final: 0.6968 (tp30) REVERT: B 336 ASP cc_start: 0.8347 (t0) cc_final: 0.8012 (t0) REVERT: B 338 MET cc_start: 0.8752 (ptp) cc_final: 0.8483 (ptp) REVERT: D 219 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8959 (t) outliers start: 55 outliers final: 22 residues processed: 190 average time/residue: 1.4387 time to fit residues: 320.6983 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 : 2.429 ------------------------------------------------------------------------------- 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 137 ILE 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 298 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 3 LEU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain D residue 219 VAL 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: 6.9990 chunk 149 optimal weight: 0.7980 chunk 291 optimal weight: 9.9990 chunk 9 optimal weight: 0.0970 chunk 194 optimal weight: 9.9990 chunk 139 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 13 optimal weight: 0.0980 chunk 154 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** E 305 HIS B 58 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.084994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.076124 restraints weight = 45150.089| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.61 r_work: 0.2913 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23345 Z= 0.109 Angle : 0.499 7.939 31745 Z= 0.266 Chirality : 0.043 0.170 3668 Planarity : 0.004 0.043 4186 Dihedral : 4.652 23.479 3206 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.74 % Favored : 97.06 % Rotamer: Outliers : 1.95 % Allowed : 11.80 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.54 (0.14), residues: 2989 helix: 1.24 (0.20), residues: 670 sheet: -0.10 (0.17), residues: 807 loop : -1.24 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 354 HIS 0.001 0.000 HIS C 370 PHE 0.015 0.001 PHE B 188 TYR 0.012 0.001 TYR G 175 ARG 0.003 0.000 ARG B 162 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 843) hydrogen bonds : angle 4.98887 ( 2364) covalent geometry : bond 0.00240 (23345) covalent geometry : angle 0.49934 (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 212 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 2.484 Fit side-chains REVERT: G 185 ARG cc_start: 0.5196 (tpt170) cc_final: 0.4704 (tmt-80) REVERT: G 209 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: G 271 ASP cc_start: 0.7936 (p0) cc_final: 0.7456 (m-30) REVERT: A 338 MET cc_start: 0.8614 (ttm) cc_final: 0.8123 (ttm) REVERT: E 122 MET cc_start: 0.9039 (tpp) cc_final: 0.8788 (tpt) REVERT: E 246 ASP cc_start: 0.8091 (m-30) cc_final: 0.7267 (t0) REVERT: E 377 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6315 (mttp) REVERT: F 122 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8356 (tpp) REVERT: F 203 ARG cc_start: 0.8663 (mmp80) cc_final: 0.8357 (mmp80) REVERT: B 15 GLU cc_start: 0.7334 (tp30) cc_final: 0.7022 (tp30) REVERT: B 336 ASP cc_start: 0.8295 (t0) cc_final: 0.7947 (t0) REVERT: B 338 MET cc_start: 0.8675 (ptp) cc_final: 0.8424 (ptp) outliers start: 48 outliers final: 25 residues processed: 201 average time/residue: 1.2116 time to fit residues: 283.5467 Evaluate side-chains 179 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 2.447 ------------------------------------------------------------------------------- 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 C residue 376 MET 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 72 GLU Chi-restraints excluded: chain F residue 122 MET 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 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: 10.0000 chunk 234 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 0.0370 chunk 254 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN 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 = 0.3173 r_free = 0.3173 target = 0.085755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.076929 restraints weight = 45090.616| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.60 r_work: 0.2929 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23345 Z= 0.106 Angle : 0.498 7.953 31745 Z= 0.264 Chirality : 0.043 0.171 3668 Planarity : 0.003 0.041 4186 Dihedral : 4.480 22.610 3206 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.54 % Favored : 97.26 % Rotamer: Outliers : 1.71 % Allowed : 12.70 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 2989 helix: 1.36 (0.20), residues: 669 sheet: -0.08 (0.17), residues: 809 loop : -1.18 (0.14), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 354 HIS 0.001 0.000 HIS C 370 PHE 0.016 0.001 PHE F 188 TYR 0.013 0.001 TYR E 100 ARG 0.002 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 843) hydrogen bonds : angle 4.87581 ( 2364) covalent geometry : bond 0.00236 (23345) covalent geometry : angle 0.49797 (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 199 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 2.570 Fit side-chains REVERT: G 185 ARG cc_start: 0.5122 (tpt170) cc_final: 0.4624 (tmt-80) REVERT: G 209 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8279 (m-30) REVERT: G 271 ASP cc_start: 0.7907 (p0) cc_final: 0.7482 (m-30) REVERT: A 338 MET cc_start: 0.8607 (ttm) cc_final: 0.8101 (ttm) REVERT: C 376 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8671 (ptt) REVERT: E 122 MET cc_start: 0.9041 (tpp) cc_final: 0.8783 (tpt) REVERT: E 246 ASP cc_start: 0.8146 (m-30) cc_final: 0.7265 (t0) REVERT: E 377 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.5514 (mptt) REVERT: F 122 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8316 (tpp) REVERT: F 203 ARG cc_start: 0.8621 (mmp80) cc_final: 0.8296 (mmp80) REVERT: B 15 GLU cc_start: 0.7321 (tp30) cc_final: 0.7035 (tp30) REVERT: B 122 MET cc_start: 0.9112 (tpp) cc_final: 0.8233 (tpp) REVERT: B 126 MET cc_start: 0.8698 (mmt) cc_final: 0.8405 (tpp) REVERT: B 164 MET cc_start: 0.7565 (pmm) cc_final: 0.7336 (pmm) REVERT: B 338 MET cc_start: 0.8640 (ptp) cc_final: 0.8421 (ptp) outliers start: 42 outliers final: 28 residues processed: 191 average time/residue: 1.2317 time to fit residues: 273.8019 Evaluate side-chains 184 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 2.428 ------------------------------------------------------------------------------- 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 C residue 347 ASP 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 377 LYS Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 376 MET 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 B residue 291 GLN Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 219 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 101 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 238 optimal weight: 0.1980 chunk 178 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- 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 ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 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 = 0.3102 r_free = 0.3102 target = 0.081822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.072863 restraints weight = 45249.197| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.60 r_work: 0.2845 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23345 Z= 0.233 Angle : 0.597 7.718 31745 Z= 0.317 Chirality : 0.046 0.194 3668 Planarity : 0.004 0.049 4186 Dihedral : 5.096 26.523 3206 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.81 % Favored : 96.99 % Rotamer: Outliers : 1.71 % Allowed : 13.11 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.73 (0.14), residues: 2989 helix: 0.97 (0.19), residues: 675 sheet: -0.27 (0.17), residues: 785 loop : -1.26 (0.14), residues: 1529 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 0.024 0.002 PHE F 188 TYR 0.017 0.002 TYR C 100 ARG 0.007 0.001 ARG F 190 Details of bonding type rmsd hydrogen bonds : bond 0.05439 ( 843) hydrogen bonds : angle 5.23986 ( 2364) covalent geometry : bond 0.00540 (23345) covalent geometry : angle 0.59735 (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 191 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 2.753 Fit side-chains REVERT: G 185 ARG cc_start: 0.5314 (tpt170) cc_final: 0.4787 (tmt-80) REVERT: G 271 ASP cc_start: 0.8078 (p0) cc_final: 0.7597 (m-30) REVERT: G 316 ASP cc_start: 0.8279 (p0) cc_final: 0.7929 (p0) REVERT: A 338 MET cc_start: 0.8499 (ttm) cc_final: 0.8052 (ttm) REVERT: E 122 MET cc_start: 0.9097 (tpp) cc_final: 0.8870 (tpt) REVERT: E 246 ASP cc_start: 0.8123 (m-30) cc_final: 0.7249 (t0) REVERT: E 377 LYS cc_start: 0.6250 (OUTLIER) cc_final: 0.5752 (mttp) REVERT: B 15 GLU cc_start: 0.7378 (tp30) cc_final: 0.7046 (tp30) REVERT: B 336 ASP cc_start: 0.8300 (t0) cc_final: 0.7973 (t0) REVERT: B 338 MET cc_start: 0.8686 (ptp) cc_final: 0.8409 (ptp) outliers start: 42 outliers final: 28 residues processed: 180 average time/residue: 1.2329 time to fit residues: 259.8913 Evaluate side-chains 172 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR 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 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 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 B residue 291 GLN Chi-restraints excluded: chain D residue 219 VAL 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: 7.9990 chunk 219 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 292 optimal weight: 0.7980 chunk 195 optimal weight: 0.2980 chunk 110 optimal weight: 0.2980 chunk 112 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.082981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.074053 restraints weight = 45279.561| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.60 r_work: 0.2869 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23345 Z= 0.155 Angle : 0.545 7.794 31745 Z= 0.289 Chirality : 0.044 0.194 3668 Planarity : 0.004 0.049 4186 Dihedral : 4.938 25.230 3206 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.81 % Favored : 96.99 % Rotamer: Outliers : 1.42 % Allowed : 13.47 % 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: -0.70 (0.14), residues: 2989 helix: 1.03 (0.19), residues: 676 sheet: -0.27 (0.17), residues: 785 loop : -1.26 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 354 HIS 0.002 0.001 HIS C 370 PHE 0.021 0.002 PHE F 188 TYR 0.014 0.001 TYR A 100 ARG 0.004 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.04995 ( 843) hydrogen bonds : angle 5.13856 ( 2364) covalent geometry : bond 0.00354 (23345) covalent geometry : angle 0.54492 (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 189 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 2.474 Fit side-chains revert: symmetry clash REVERT: G 185 ARG cc_start: 0.5248 (tpt170) cc_final: 0.4763 (tmt-80) REVERT: G 271 ASP cc_start: 0.8013 (p0) cc_final: 0.7550 (m-30) REVERT: G 289 LEU cc_start: 0.9213 (mt) cc_final: 0.8991 (mp) REVERT: G 291 GLN cc_start: 0.8267 (mp10) cc_final: 0.8060 (mp10) REVERT: A 79 MET cc_start: 0.8047 (mtp) cc_final: 0.7833 (ttp) REVERT: A 338 MET cc_start: 0.8549 (ttm) cc_final: 0.8131 (ttm) REVERT: E 122 MET cc_start: 0.9066 (tpp) cc_final: 0.8822 (tpt) REVERT: E 246 ASP cc_start: 0.8073 (m-30) cc_final: 0.7228 (t0) REVERT: E 377 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5744 (mttp) REVERT: B 15 GLU cc_start: 0.7307 (tp30) cc_final: 0.7019 (tp30) REVERT: B 126 MET cc_start: 0.8813 (mmt) cc_final: 0.8534 (tpp) REVERT: B 336 ASP cc_start: 0.8317 (t0) cc_final: 0.7995 (t0) REVERT: B 338 MET cc_start: 0.8676 (ptp) cc_final: 0.8449 (ptp) REVERT: D 219 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8925 (t) outliers start: 35 outliers final: 29 residues processed: 182 average time/residue: 1.3411 time to fit residues: 285.7514 Evaluate side-chains 184 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR 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 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 377 LYS Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 141 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 B residue 291 GLN Chi-restraints excluded: chain D residue 219 VAL 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: 7.9990 chunk 255 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 226 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 chunk 231 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 214 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN B 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.086233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.077419 restraints weight = 45100.914| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.61 r_work: 0.2939 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1838 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= 0.101 Angle : 0.497 7.923 31745 Z= 0.263 Chirality : 0.043 0.164 3668 Planarity : 0.004 0.041 4186 Dihedral : 4.483 22.660 3206 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.78 % Favored : 97.02 % Rotamer: Outliers : 1.51 % Allowed : 13.51 % Favored : 84.98 % 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: -0.47 (0.14), residues: 2989 helix: 1.36 (0.20), residues: 664 sheet: -0.15 (0.17), residues: 798 loop : -1.16 (0.14), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 354 HIS 0.001 0.000 HIS C 370 PHE 0.021 0.001 PHE F 188 TYR 0.012 0.001 TYR G 100 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 843) hydrogen bonds : angle 4.86096 ( 2364) covalent geometry : bond 0.00225 (23345) covalent geometry : angle 0.49653 (31745) =============================================================================== Job complete usr+sys time: 16995.82 seconds wall clock time: 297 minutes 1.79 seconds (17821.79 seconds total)