Starting phenix.real_space_refine on Thu Feb 5 09:08:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kub_62575/02_2026/9kub_62575.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kub_62575/02_2026/9kub_62575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kub_62575/02_2026/9kub_62575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kub_62575/02_2026/9kub_62575.map" model { file = "/net/cci-nas-00/data/ceres_data/9kub_62575/02_2026/9kub_62575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kub_62575/02_2026/9kub_62575.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 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 48 5.16 5 C 10295 2.51 5 N 2739 2.21 5 O 3034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16116 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2617 Classifications: {'peptide': 341} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 322} Chain breaks: 3 Chain: "C" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2747 Classifications: {'peptide': 357} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 337} Chain breaks: 2 Chain: "F" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2617 Classifications: {'peptide': 341} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 322} Chain breaks: 3 Chain: "A" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2759 Classifications: {'peptide': 359} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 339} Chain breaks: 2 Chain: "D" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2617 Classifications: {'peptide': 341} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 322} Chain breaks: 3 Chain: "E" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2759 Classifications: {'peptide': 359} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 339} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N GLY B 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 261 " occ=0.00 residue: pdb=" N GLY B 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 281 " occ=0.00 residue: pdb=" N GLY C 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY C 261 " occ=0.00 residue: pdb=" N GLY C 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY C 281 " occ=0.00 residue: pdb=" N GLY F 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY F 261 " occ=0.00 residue: pdb=" N GLY F 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY F 281 " occ=0.00 residue: pdb=" N GLY A 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 261 " occ=0.00 residue: pdb=" N GLY A 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 281 " occ=0.00 residue: pdb=" N GLY D 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 261 " occ=0.00 residue: pdb=" N GLY D 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 281 " occ=0.00 residue: pdb=" N GLY E 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY E 261 " occ=0.00 residue: pdb=" N GLY E 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY E 281 " occ=0.00 Time building chain proxies: 4.06, per 1000 atoms: 0.25 Number of scatterers: 16116 At special positions: 0 Unit cell: (153.55, 156.04, 85.49, 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 48 16.00 O 3034 8.00 N 2739 7.00 C 10295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 718.7 milliseconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 38 sheets defined 34.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'B' and resid 47 through 61 removed outlier: 3.571A pdb=" N VAL B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 83 removed outlier: 3.520A pdb=" N THR B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 134 removed outlier: 4.244A pdb=" N LYS B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 246 through 258 removed outlier: 3.529A pdb=" N LEU B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.678A pdb=" N ALA B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 426 removed outlier: 3.977A pdb=" N ILE B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 426 " --> pdb=" O MET B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 447 removed outlier: 3.852A pdb=" N LYS B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 58 removed outlier: 3.547A pdb=" N GLU C 56 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 83 removed outlier: 3.987A pdb=" N ASP C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.643A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 96 " --> pdb=" O LYS C 92 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN C 98 " --> pdb=" O PHE C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 134 removed outlier: 3.931A pdb=" N LYS C 132 " --> pdb=" O THR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 217 through 228 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.785A pdb=" N GLY C 252 " --> pdb=" O ASN C 248 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 256 " --> pdb=" O GLY C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 Processing helix chain 'C' and resid 419 through 426 removed outlier: 3.519A pdb=" N ILE C 423 " --> pdb=" O THR C 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP C 426 " --> pdb=" O MET C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 446 removed outlier: 3.716A pdb=" N LYS C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 60 removed outlier: 4.084A pdb=" N VAL F 53 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU F 58 " --> pdb=" O VAL F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 removed outlier: 4.208A pdb=" N ASP F 83 " --> pdb=" O LEU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 134 removed outlier: 4.128A pdb=" N LYS F 132 " --> pdb=" O THR F 128 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY F 134 " --> pdb=" O ALA F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 162 Processing helix chain 'F' and resid 217 through 228 Processing helix chain 'F' and resid 246 through 256 Processing helix chain 'F' and resid 300 through 312 removed outlier: 3.584A pdb=" N ALA F 306 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 426 removed outlier: 3.629A pdb=" N ILE F 423 " --> pdb=" O THR F 419 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP F 426 " --> pdb=" O MET F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 447 removed outlier: 3.985A pdb=" N LYS F 430 " --> pdb=" O ASP F 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 60 removed outlier: 3.546A pdb=" N GLU A 56 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 83 removed outlier: 3.586A pdb=" N ASP A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.816A pdb=" N GLU A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 134 removed outlier: 3.814A pdb=" N LYS A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.735A pdb=" N VAL A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 4.294A pdb=" N LYS A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 425 removed outlier: 3.593A pdb=" N ASP A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 447 removed outlier: 3.747A pdb=" N LYS A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 60 removed outlier: 3.593A pdb=" N VAL D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 83 Processing helix chain 'D' and resid 128 through 134 removed outlier: 4.245A pdb=" N LYS D 132 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY D 134 " --> pdb=" O ALA D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 Processing helix chain 'D' and resid 217 through 228 Processing helix chain 'D' and resid 246 through 255 Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 419 through 426 removed outlier: 3.624A pdb=" N ASN D 424 " --> pdb=" O PRO D 420 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP D 425 " --> pdb=" O LYS D 421 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP D 426 " --> pdb=" O MET D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 447 removed outlier: 3.768A pdb=" N LYS D 430 " --> pdb=" O ASP D 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 removed outlier: 3.594A pdb=" N GLU E 56 " --> pdb=" O ASN E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 83 removed outlier: 3.502A pdb=" N THR E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP E 83 " --> pdb=" O LEU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 100 removed outlier: 4.106A pdb=" N LYS E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU E 96 " --> pdb=" O LYS E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 134 removed outlier: 3.944A pdb=" N LYS E 132 " --> pdb=" O THR E 128 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY E 134 " --> pdb=" O ALA E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 Processing helix chain 'E' and resid 217 through 228 Processing helix chain 'E' and resid 246 through 255 Processing helix chain 'E' and resid 301 through 312 removed outlier: 3.931A pdb=" N VAL E 305 " --> pdb=" O ALA E 301 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA E 306 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 4.409A pdb=" N LYS E 358 " --> pdb=" O THR E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 425 removed outlier: 3.622A pdb=" N ASP E 425 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 446 removed outlier: 3.807A pdb=" N LYS E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.752A pdb=" N VAL B 264 " --> pdb=" O TYR B 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 90 removed outlier: 5.744A pdb=" N LYS B 341 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU B 332 " --> pdb=" O LYS B 341 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR B 343 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET B 330 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA B 345 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 115 Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 144 removed outlier: 5.462A pdb=" N ILE B 141 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 174 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 197 through 198 Processing sheet with id=AA6, first strand: chain 'B' and resid 235 through 238 removed outlier: 6.537A pdb=" N ILE B 235 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU B 293 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 237 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE B 290 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ILE B 318 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 292 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89 removed outlier: 3.702A pdb=" N ALA C 339 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG C 346 " --> pdb=" O LYS C 267 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 264 " --> pdb=" O TYR C 277 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 89 removed outlier: 3.702A pdb=" N ALA C 339 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N THR C 343 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N MET C 330 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA C 345 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 110 through 115 removed outlier: 7.196A pdb=" N THR C 111 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 147 through 148 removed outlier: 6.561A pdb=" N THR C 172 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE C 144 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN C 170 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 196 through 198 removed outlier: 6.799A pdb=" N VAL C 209 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AB4, first strand: chain 'F' and resid 87 through 90 removed outlier: 6.640A pdb=" N ILE F 340 " --> pdb=" O PRO F 333 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE F 342 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU F 331 " --> pdb=" O ILE F 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 112 through 115 Processing sheet with id=AB6, first strand: chain 'F' and resid 140 through 144 removed outlier: 5.699A pdb=" N ILE F 141 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL F 174 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 197 through 200 removed outlier: 6.924A pdb=" N LEU F 207 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASP F 238 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL F 209 " --> pdb=" O ASP F 238 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE F 235 " --> pdb=" O ALA F 291 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU F 293 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU F 237 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE F 290 " --> pdb=" O VAL F 316 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE F 318 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL F 292 " --> pdb=" O ILE F 318 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 276 through 278 removed outlier: 7.126A pdb=" N TYR F 277 " --> pdb=" O LEU F 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.946A pdb=" N TYR A 277 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 87 through 89 removed outlier: 3.680A pdb=" N ILE A 342 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 328 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 110 through 115 removed outlier: 7.199A pdb=" N THR A 111 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 147 through 148 removed outlier: 6.524A pdb=" N THR A 172 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE A 144 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN A 170 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.705A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 200 through 201 removed outlier: 7.397A pdb=" N LYS A 200 " --> pdb=" O VAL A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AC7, first strand: chain 'D' and resid 87 through 90 removed outlier: 7.020A pdb=" N TYR D 277 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.181A pdb=" N ILE D 342 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL D 328 " --> pdb=" O THR D 344 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 110 through 115 removed outlier: 7.004A pdb=" N THR D 111 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 140 through 144 removed outlier: 5.679A pdb=" N ILE D 141 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 174 " --> pdb=" O ILE D 141 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 197 through 198 Processing sheet with id=AD3, first strand: chain 'D' and resid 200 through 201 removed outlier: 7.221A pdb=" N LYS D 200 " --> pdb=" O VAL D 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 293 through 294 Processing sheet with id=AD5, first strand: chain 'E' and resid 87 through 89 removed outlier: 4.184A pdb=" N ARG E 346 " --> pdb=" O LYS E 267 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS E 267 " --> pdb=" O ARG E 346 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL E 264 " --> pdb=" O TYR E 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 87 through 89 removed outlier: 3.734A pdb=" N ILE E 342 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET E 330 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL E 328 " --> pdb=" O THR E 344 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 110 through 115 removed outlier: 7.137A pdb=" N THR E 111 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 147 through 148 removed outlier: 6.658A pdb=" N THR E 172 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE E 144 " --> pdb=" O GLN E 170 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN E 170 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 196 through 198 Processing sheet with id=AE1, first strand: chain 'E' and resid 200 through 201 removed outlier: 7.435A pdb=" N LYS E 200 " --> pdb=" O VAL E 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 293 through 294 612 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.61 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: 2793 1.32 - 1.45: 3539 1.45 - 1.57: 9916 1.57 - 1.69: 0 1.69 - 1.82: 96 Bond restraints: 16344 Sorted by residual: bond pdb=" CA SER D 351 " pdb=" CB SER D 351 " ideal model delta sigma weight residual 1.530 1.483 0.047 1.57e-02 4.06e+03 9.05e+00 bond pdb=" CA SER F 351 " pdb=" CB SER F 351 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.57e-02 4.06e+03 7.78e+00 bond pdb=" C PRO C 350 " pdb=" O PRO C 350 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.30e-02 5.92e+03 7.73e+00 bond pdb=" CA SER B 351 " pdb=" CB SER B 351 " ideal model delta sigma weight residual 1.530 1.484 0.047 1.69e-02 3.50e+03 7.63e+00 bond pdb=" N THR D 354 " pdb=" CA THR D 354 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.21e-02 6.83e+03 7.03e+00 ... (remaining 16339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 21549 1.76 - 3.51: 403 3.51 - 5.27: 61 5.27 - 7.02: 9 7.02 - 8.78: 5 Bond angle restraints: 22027 Sorted by residual: angle pdb=" C GLY E 352 " pdb=" N ARG E 353 " pdb=" CA ARG E 353 " ideal model delta sigma weight residual 121.29 114.47 6.82 1.74e+00 3.30e-01 1.54e+01 angle pdb=" N SER E 351 " pdb=" CA SER E 351 " pdb=" C SER E 351 " ideal model delta sigma weight residual 111.02 106.47 4.55 1.22e+00 6.72e-01 1.39e+01 angle pdb=" N ILE F 355 " pdb=" CA ILE F 355 " pdb=" C ILE F 355 " ideal model delta sigma weight residual 113.00 108.16 4.84 1.30e+00 5.92e-01 1.39e+01 angle pdb=" CA TYR F 348 " pdb=" C TYR F 348 " pdb=" O TYR F 348 " ideal model delta sigma weight residual 121.16 117.07 4.09 1.13e+00 7.83e-01 1.31e+01 angle pdb=" CA ARG C 353 " pdb=" C ARG C 353 " pdb=" O ARG C 353 " ideal model delta sigma weight residual 121.94 117.82 4.12 1.15e+00 7.56e-01 1.28e+01 ... (remaining 22022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 8860 17.85 - 35.71: 991 35.71 - 53.56: 241 53.56 - 71.41: 48 71.41 - 89.27: 17 Dihedral angle restraints: 10157 sinusoidal: 4154 harmonic: 6003 Sorted by residual: dihedral pdb=" CD ARG D 346 " pdb=" NE ARG D 346 " pdb=" CZ ARG D 346 " pdb=" NH1 ARG D 346 " ideal model delta sinusoidal sigma weight residual 0.00 61.87 -61.87 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CD ARG C 353 " pdb=" NE ARG C 353 " pdb=" CZ ARG C 353 " pdb=" NH1 ARG C 353 " ideal model delta sinusoidal sigma weight residual 0.00 -50.28 50.28 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CA ALA C 301 " pdb=" C ALA C 301 " pdb=" N SER C 302 " pdb=" CA SER C 302 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 10154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1931 0.043 - 0.087: 397 0.087 - 0.130: 266 0.130 - 0.174: 3 0.174 - 0.217: 1 Chirality restraints: 2598 Sorted by residual: chirality pdb=" CA ARG C 353 " pdb=" N ARG C 353 " pdb=" C ARG C 353 " pdb=" CB ARG C 353 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE F 355 " pdb=" N ILE F 355 " pdb=" C ILE F 355 " pdb=" CB ILE F 355 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA GLU E 203 " pdb=" N GLU E 203 " pdb=" C GLU E 203 " pdb=" CB GLU E 203 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 2595 not shown) Planarity restraints: 2779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 346 " -0.976 9.50e-02 1.11e+02 4.38e-01 1.16e+02 pdb=" NE ARG D 346 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG D 346 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG D 346 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 346 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 353 " 0.839 9.50e-02 1.11e+02 3.76e-01 8.58e+01 pdb=" NE ARG C 353 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG C 353 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 353 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 353 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 353 " 0.656 9.50e-02 1.11e+02 2.94e-01 5.26e+01 pdb=" NE ARG F 353 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG F 353 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG F 353 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 353 " 0.021 2.00e-02 2.50e+03 ... (remaining 2776 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 7013 2.94 - 3.43: 15651 3.43 - 3.92: 25323 3.92 - 4.41: 28307 4.41 - 4.90: 47906 Nonbonded interactions: 124200 Sorted by model distance: nonbonded pdb=" O ASN A 146 " pdb=" OD1 ASN A 146 " model vdw 2.455 3.040 nonbonded pdb=" O LEU E 349 " pdb=" C PRO E 350 " model vdw 2.487 3.270 nonbonded pdb=" C THR D 354 " pdb=" OG1 THR D 354 " model vdw 2.493 2.616 nonbonded pdb=" OD1 ASP F 311 " pdb=" OG SER F 351 " model vdw 2.508 3.040 nonbonded pdb=" C THR B 354 " pdb=" OG1 THR B 354 " model vdw 2.528 2.616 ... (remaining 124195 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 45 through 95 or resid 109 through 187 or resid 196 throug \ h 447)) selection = chain 'B' selection = (chain 'C' and (resid 45 through 95 or resid 109 through 187 or resid 196 throug \ h 374 or resid 416 through 447)) selection = chain 'D' selection = (chain 'E' and (resid 45 through 95 or resid 109 through 187 or resid 196 throug \ h 447)) selection = chain 'F' } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.770 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.003 0.047 16344 Z= 0.160 Angle : 0.568 8.777 22027 Z= 0.320 Chirality : 0.045 0.217 2598 Planarity : 0.013 0.438 2779 Dihedral : 16.066 89.266 6297 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.00 % Allowed : 19.54 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2056 helix: 0.11 (0.20), residues: 637 sheet: -0.64 (0.28), residues: 374 loop : -0.75 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 115 TYR 0.014 0.001 TYR F 347 PHE 0.011 0.001 PHE D 323 TRP 0.005 0.001 TRP F 439 HIS 0.002 0.000 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00287 (16344) covalent geometry : angle 0.56770 (22027) hydrogen bonds : bond 0.22721 ( 593) hydrogen bonds : angle 8.28211 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: B 161 MET cc_start: -0.0379 (tmm) cc_final: -0.0773 (ptm) REVERT: C 184 PHE cc_start: 0.8010 (m-80) cc_final: 0.7780 (m-80) REVERT: D 152 MET cc_start: 0.1088 (mtp) cc_final: -0.0469 (ptt) REVERT: E 152 MET cc_start: 0.4475 (ptp) cc_final: 0.3997 (ptp) REVERT: E 161 MET cc_start: 0.7145 (mmm) cc_final: 0.6677 (mmm) outliers start: 36 outliers final: 28 residues processed: 144 average time/residue: 0.1294 time to fit residues: 28.2118 Evaluate side-chains 139 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 353 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 0.0670 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 266 GLN F 310 GLN A 146 ASN D 266 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.182165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133942 restraints weight = 23976.235| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.89 r_work: 0.3449 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16344 Z= 0.156 Angle : 0.521 6.116 22027 Z= 0.271 Chirality : 0.046 0.137 2598 Planarity : 0.004 0.054 2779 Dihedral : 5.264 58.658 2255 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.79 % Allowed : 17.93 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2056 helix: 1.07 (0.20), residues: 664 sheet: -0.96 (0.27), residues: 355 loop : -0.84 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 346 TYR 0.019 0.001 TYR F 347 PHE 0.008 0.001 PHE E 184 TRP 0.009 0.002 TRP A 439 HIS 0.002 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00378 (16344) covalent geometry : angle 0.52083 (22027) hydrogen bonds : bond 0.03983 ( 593) hydrogen bonds : angle 5.13170 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 121 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: -0.0523 (tmm) cc_final: -0.0805 (ptm) REVERT: B 347 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.5895 (p90) REVERT: C 184 PHE cc_start: 0.7866 (m-80) cc_final: 0.7648 (m-80) REVERT: F 347 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6743 (p90) REVERT: A 45 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.6679 (p-80) REVERT: A 58 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7889 (pt0) REVERT: D 64 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7962 (ptmm) REVERT: D 152 MET cc_start: 0.1447 (mtp) cc_final: 0.0413 (ptm) REVERT: E 71 MET cc_start: 0.7347 (mmt) cc_final: 0.7025 (mmt) REVERT: E 156 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7249 (p0) outliers start: 68 outliers final: 37 residues processed: 182 average time/residue: 0.1203 time to fit residues: 33.9834 Evaluate side-chains 153 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 TYR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 354 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 158 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 144 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.183163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135414 restraints weight = 24351.119| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.17 r_work: 0.3483 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16344 Z= 0.122 Angle : 0.485 5.383 22027 Z= 0.252 Chirality : 0.045 0.132 2598 Planarity : 0.004 0.050 2779 Dihedral : 4.602 51.805 2228 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.84 % Allowed : 18.49 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 2056 helix: 1.42 (0.20), residues: 667 sheet: -0.95 (0.28), residues: 347 loop : -0.85 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 115 TYR 0.015 0.001 TYR F 347 PHE 0.008 0.001 PHE D 323 TRP 0.007 0.001 TRP A 439 HIS 0.002 0.000 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00294 (16344) covalent geometry : angle 0.48522 (22027) hydrogen bonds : bond 0.03408 ( 593) hydrogen bonds : angle 4.68129 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 117 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8407 (mt) REVERT: B 152 MET cc_start: 0.1860 (mtp) cc_final: 0.1501 (mtp) REVERT: B 161 MET cc_start: -0.0472 (tmm) cc_final: -0.0713 (ptm) REVERT: B 347 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.5997 (p90) REVERT: C 184 PHE cc_start: 0.7889 (m-80) cc_final: 0.7688 (m-80) REVERT: F 79 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8381 (mm) REVERT: F 152 MET cc_start: 0.0463 (OUTLIER) cc_final: -0.0301 (tmm) REVERT: A 45 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6688 (p-80) REVERT: A 329 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8453 (mm-40) REVERT: D 64 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7972 (ptmm) REVERT: D 152 MET cc_start: 0.1523 (mtp) cc_final: 0.0633 (ptm) REVERT: E 156 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7287 (p0) outliers start: 69 outliers final: 44 residues processed: 171 average time/residue: 0.1115 time to fit residues: 30.3436 Evaluate side-chains 162 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 110 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 354 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 58 optimal weight: 0.0370 chunk 25 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.184349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133757 restraints weight = 24164.357| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.30 r_work: 0.3498 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16344 Z= 0.096 Angle : 0.457 6.052 22027 Z= 0.237 Chirality : 0.044 0.128 2598 Planarity : 0.004 0.049 2779 Dihedral : 4.262 48.532 2228 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.62 % Allowed : 19.49 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 2056 helix: 1.70 (0.21), residues: 670 sheet: -0.93 (0.28), residues: 352 loop : -0.82 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 115 TYR 0.011 0.001 TYR C 347 PHE 0.010 0.001 PHE E 184 TRP 0.006 0.001 TRP E 439 HIS 0.002 0.000 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00230 (16344) covalent geometry : angle 0.45696 (22027) hydrogen bonds : bond 0.02810 ( 593) hydrogen bonds : angle 4.35082 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 120 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8318 (mt) REVERT: B 152 MET cc_start: 0.1499 (mtp) cc_final: 0.1111 (mtp) REVERT: B 161 MET cc_start: -0.0506 (tmm) cc_final: -0.0776 (ptm) REVERT: B 323 PHE cc_start: 0.7428 (t80) cc_final: 0.7227 (t80) REVERT: B 347 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.5917 (p90) REVERT: F 79 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8157 (mm) REVERT: F 152 MET cc_start: 0.0685 (OUTLIER) cc_final: -0.0075 (tmm) REVERT: F 347 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.6502 (p90) REVERT: A 45 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6671 (p-80) REVERT: A 329 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8461 (mm-40) REVERT: D 64 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7960 (ptmm) REVERT: D 152 MET cc_start: 0.1399 (mtp) cc_final: 0.0485 (ptm) REVERT: E 161 MET cc_start: 0.6845 (mmm) cc_final: 0.6268 (mmm) outliers start: 65 outliers final: 36 residues processed: 173 average time/residue: 0.1251 time to fit residues: 33.2013 Evaluate side-chains 158 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 TYR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 354 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 117 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 194 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.182338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133210 restraints weight = 24205.802| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.13 r_work: 0.3472 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16344 Z= 0.133 Angle : 0.502 8.152 22027 Z= 0.255 Chirality : 0.045 0.153 2598 Planarity : 0.004 0.049 2779 Dihedral : 4.336 49.454 2223 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.18 % Allowed : 18.82 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.19), residues: 2056 helix: 1.61 (0.21), residues: 670 sheet: -0.99 (0.27), residues: 366 loop : -0.85 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.015 0.001 TYR E 197 PHE 0.009 0.001 PHE D 323 TRP 0.007 0.001 TRP E 439 HIS 0.002 0.000 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00327 (16344) covalent geometry : angle 0.50151 (22027) hydrogen bonds : bond 0.03225 ( 593) hydrogen bonds : angle 4.41663 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 123 time to evaluate : 0.771 Fit side-chains REVERT: B 79 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8414 (mt) REVERT: B 152 MET cc_start: 0.1800 (mtp) cc_final: 0.1464 (mtp) REVERT: B 161 MET cc_start: -0.0420 (tmm) cc_final: -0.0694 (ptm) REVERT: B 347 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5822 (p90) REVERT: C 46 MET cc_start: 0.6014 (tpp) cc_final: 0.5520 (tpt) REVERT: F 79 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8471 (mm) REVERT: F 152 MET cc_start: 0.0829 (OUTLIER) cc_final: 0.0072 (tmm) REVERT: F 347 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6422 (p90) REVERT: A 45 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6657 (p-80) REVERT: A 311 ASP cc_start: 0.7860 (m-30) cc_final: 0.7397 (m-30) REVERT: A 329 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8451 (mm-40) REVERT: D 64 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7740 (ptmm) REVERT: D 79 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8432 (mm) REVERT: D 152 MET cc_start: 0.1420 (OUTLIER) cc_final: 0.0500 (ptm) outliers start: 75 outliers final: 46 residues processed: 181 average time/residue: 0.1171 time to fit residues: 33.4791 Evaluate side-chains 171 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 115 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 TYR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 354 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 56 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 102 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 180 optimal weight: 0.0570 chunk 87 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.181523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134993 restraints weight = 24186.234| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.10 r_work: 0.3465 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16344 Z= 0.145 Angle : 0.517 7.216 22027 Z= 0.263 Chirality : 0.046 0.155 2598 Planarity : 0.004 0.049 2779 Dihedral : 4.425 50.909 2223 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.23 % Allowed : 18.88 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 2056 helix: 1.56 (0.21), residues: 670 sheet: -0.97 (0.28), residues: 352 loop : -0.90 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.016 0.001 TYR C 347 PHE 0.009 0.001 PHE E 184 TRP 0.008 0.002 TRP E 439 HIS 0.002 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00355 (16344) covalent geometry : angle 0.51741 (22027) hydrogen bonds : bond 0.03233 ( 593) hydrogen bonds : angle 4.43333 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 124 time to evaluate : 0.668 Fit side-chains REVERT: B 79 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8447 (mt) REVERT: B 152 MET cc_start: 0.1631 (mtp) cc_final: 0.1247 (mtp) REVERT: B 161 MET cc_start: -0.0282 (tmm) cc_final: -0.0576 (ptm) REVERT: B 347 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.5812 (p90) REVERT: C 46 MET cc_start: 0.6211 (tpp) cc_final: 0.5736 (tpt) REVERT: F 79 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8496 (mm) REVERT: F 152 MET cc_start: 0.0547 (OUTLIER) cc_final: -0.0377 (tmm) REVERT: F 347 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6410 (p90) REVERT: A 45 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6704 (p-80) REVERT: A 311 ASP cc_start: 0.7884 (m-30) cc_final: 0.7422 (m-30) REVERT: A 329 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8471 (mm-40) REVERT: D 64 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7712 (ptmm) REVERT: D 79 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8421 (mm) REVERT: D 152 MET cc_start: 0.1154 (OUTLIER) cc_final: 0.0755 (ptp) REVERT: E 152 MET cc_start: 0.4914 (ptp) cc_final: 0.4714 (ptp) REVERT: E 161 MET cc_start: 0.6903 (mmm) cc_final: 0.6308 (mmm) outliers start: 76 outliers final: 51 residues processed: 185 average time/residue: 0.1247 time to fit residues: 35.6878 Evaluate side-chains 178 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 117 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 TYR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 354 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 54 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 36 optimal weight: 0.3980 chunk 5 optimal weight: 20.0000 chunk 120 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.182627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133980 restraints weight = 24185.647| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.11 r_work: 0.3488 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16344 Z= 0.122 Angle : 0.504 9.309 22027 Z= 0.255 Chirality : 0.045 0.150 2598 Planarity : 0.004 0.050 2779 Dihedral : 4.347 51.716 2223 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.06 % Allowed : 19.65 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 2056 helix: 1.61 (0.21), residues: 671 sheet: -0.96 (0.28), residues: 352 loop : -0.91 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.015 0.001 TYR C 347 PHE 0.011 0.001 PHE D 323 TRP 0.007 0.001 TRP E 439 HIS 0.002 0.000 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00297 (16344) covalent geometry : angle 0.50363 (22027) hydrogen bonds : bond 0.03002 ( 593) hydrogen bonds : angle 4.34571 ( 1701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 118 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8368 (mt) REVERT: B 152 MET cc_start: 0.1521 (mtp) cc_final: 0.1093 (mtp) REVERT: B 161 MET cc_start: -0.0289 (tmm) cc_final: -0.0576 (ptm) REVERT: B 332 LEU cc_start: 0.6551 (pp) cc_final: 0.6186 (pp) REVERT: B 347 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.6034 (p90) REVERT: C 46 MET cc_start: 0.6196 (tpp) cc_final: 0.5667 (tpt) REVERT: F 79 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8383 (mm) REVERT: F 347 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6403 (p90) REVERT: A 45 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.6698 (p-80) REVERT: A 329 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8427 (mm-40) REVERT: D 64 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7737 (ptmm) REVERT: D 79 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8343 (mm) REVERT: D 152 MET cc_start: 0.0797 (OUTLIER) cc_final: 0.0004 (ptm) REVERT: E 161 MET cc_start: 0.6884 (mmm) cc_final: 0.6288 (mmm) outliers start: 73 outliers final: 51 residues processed: 173 average time/residue: 0.1272 time to fit residues: 33.4425 Evaluate side-chains 172 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 112 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 TYR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 354 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.183620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136511 restraints weight = 23942.345| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.77 r_work: 0.3513 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16344 Z= 0.143 Angle : 0.523 8.932 22027 Z= 0.264 Chirality : 0.046 0.151 2598 Planarity : 0.004 0.049 2779 Dihedral : 4.447 53.291 2223 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.06 % Allowed : 19.60 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 2056 helix: 1.54 (0.21), residues: 670 sheet: -0.98 (0.28), residues: 352 loop : -0.91 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 282 TYR 0.016 0.001 TYR C 347 PHE 0.009 0.001 PHE D 323 TRP 0.007 0.001 TRP E 439 HIS 0.002 0.000 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00353 (16344) covalent geometry : angle 0.52300 (22027) hydrogen bonds : bond 0.03215 ( 593) hydrogen bonds : angle 4.41313 ( 1701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 121 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: B 79 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8375 (mt) REVERT: B 152 MET cc_start: 0.1773 (mtp) cc_final: 0.1452 (mtp) REVERT: B 161 MET cc_start: -0.0476 (tmm) cc_final: -0.0700 (ptm) REVERT: B 332 LEU cc_start: 0.6548 (pp) cc_final: 0.6174 (pp) REVERT: B 347 TYR cc_start: 0.6665 (OUTLIER) cc_final: 0.5691 (p90) REVERT: C 46 MET cc_start: 0.6067 (tpp) cc_final: 0.5565 (tpt) REVERT: F 79 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8441 (mm) REVERT: F 347 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6349 (p90) REVERT: A 45 HIS cc_start: 0.7170 (OUTLIER) cc_final: 0.6788 (p-80) REVERT: A 58 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7678 (pt0) REVERT: A 311 ASP cc_start: 0.7821 (m-30) cc_final: 0.7351 (m-30) REVERT: A 329 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8425 (mm-40) REVERT: D 64 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7794 (ptmm) REVERT: D 79 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8310 (mm) REVERT: D 152 MET cc_start: 0.1215 (OUTLIER) cc_final: 0.0660 (ptm) REVERT: E 152 MET cc_start: 0.4826 (ptp) cc_final: 0.4035 (ptp) REVERT: E 161 MET cc_start: 0.6873 (mmm) cc_final: 0.6330 (mmm) outliers start: 73 outliers final: 56 residues processed: 179 average time/residue: 0.1255 time to fit residues: 34.5411 Evaluate side-chains 180 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 114 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 TYR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 354 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 176 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 203 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.184110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137021 restraints weight = 23748.938| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.82 r_work: 0.3514 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16344 Z= 0.122 Angle : 0.515 8.657 22027 Z= 0.260 Chirality : 0.045 0.150 2598 Planarity : 0.004 0.050 2779 Dihedral : 4.379 53.943 2223 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.95 % Allowed : 19.65 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 2056 helix: 1.62 (0.21), residues: 669 sheet: -0.96 (0.28), residues: 352 loop : -0.89 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.015 0.001 TYR C 347 PHE 0.007 0.001 PHE C 184 TRP 0.007 0.001 TRP E 439 HIS 0.002 0.000 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00300 (16344) covalent geometry : angle 0.51480 (22027) hydrogen bonds : bond 0.02966 ( 593) hydrogen bonds : angle 4.33293 ( 1701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 118 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8322 (mt) REVERT: B 152 MET cc_start: 0.1420 (mtp) cc_final: 0.1032 (mtp) REVERT: B 161 MET cc_start: -0.0370 (tmm) cc_final: -0.0659 (ptm) REVERT: B 332 LEU cc_start: 0.6562 (pp) cc_final: 0.6174 (pp) REVERT: B 347 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.5937 (p90) REVERT: C 46 MET cc_start: 0.6099 (tpp) cc_final: 0.5592 (tpt) REVERT: F 79 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8279 (mm) REVERT: F 347 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6291 (p90) REVERT: A 45 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.6782 (p-80) REVERT: A 58 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: A 329 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8425 (mm-40) REVERT: D 64 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7842 (ptmm) REVERT: D 79 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8217 (mm) REVERT: D 152 MET cc_start: 0.0838 (OUTLIER) cc_final: 0.0006 (ptm) REVERT: E 152 MET cc_start: 0.4828 (ptp) cc_final: 0.4036 (ptp) REVERT: E 161 MET cc_start: 0.6857 (mmm) cc_final: 0.6312 (mmm) outliers start: 71 outliers final: 58 residues processed: 173 average time/residue: 0.1131 time to fit residues: 30.6810 Evaluate side-chains 180 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 112 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 TYR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 354 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 45 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.183766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140171 restraints weight = 23840.521| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.81 r_work: 0.3527 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16344 Z= 0.129 Angle : 0.522 8.519 22027 Z= 0.263 Chirality : 0.045 0.151 2598 Planarity : 0.004 0.050 2779 Dihedral : 4.399 55.218 2223 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.79 % Allowed : 19.82 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 2056 helix: 1.60 (0.21), residues: 669 sheet: -0.96 (0.28), residues: 352 loop : -0.89 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.015 0.001 TYR C 347 PHE 0.012 0.001 PHE D 323 TRP 0.007 0.001 TRP E 439 HIS 0.002 0.000 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00317 (16344) covalent geometry : angle 0.52192 (22027) hydrogen bonds : bond 0.03026 ( 593) hydrogen bonds : angle 4.34337 ( 1701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 115 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: B 79 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8280 (mt) REVERT: B 152 MET cc_start: 0.1237 (mtp) cc_final: 0.0869 (mtp) REVERT: B 161 MET cc_start: -0.0248 (tmm) cc_final: -0.0642 (ptm) REVERT: B 332 LEU cc_start: 0.6591 (pp) cc_final: 0.6203 (pp) REVERT: B 347 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.5880 (p90) REVERT: C 46 MET cc_start: 0.6053 (tpp) cc_final: 0.5560 (tpt) REVERT: F 79 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8358 (mm) REVERT: F 347 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.6286 (p90) REVERT: A 45 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6802 (p-80) REVERT: A 58 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7681 (pt0) REVERT: A 95 LYS cc_start: 0.8069 (tptp) cc_final: 0.7745 (ptpt) REVERT: A 311 ASP cc_start: 0.7811 (m-30) cc_final: 0.7340 (m-30) REVERT: A 329 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8431 (mm-40) REVERT: D 64 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7797 (ptmm) REVERT: D 79 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8297 (mm) REVERT: D 152 MET cc_start: 0.0587 (OUTLIER) cc_final: -0.0253 (ptm) REVERT: E 152 MET cc_start: 0.4697 (ptp) cc_final: 0.3931 (ptp) REVERT: E 161 MET cc_start: 0.6859 (mmm) cc_final: 0.6249 (mmm) outliers start: 68 outliers final: 57 residues processed: 168 average time/residue: 0.1156 time to fit residues: 30.6160 Evaluate side-chains 180 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 113 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 TYR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 354 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 205 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 82 optimal weight: 0.3980 chunk 156 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.182990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134161 restraints weight = 24045.280| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.12 r_work: 0.3508 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16344 Z= 0.107 Angle : 0.510 8.599 22027 Z= 0.256 Chirality : 0.045 0.146 2598 Planarity : 0.004 0.050 2779 Dihedral : 4.277 55.288 2223 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.56 % Allowed : 19.99 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 2056 helix: 1.70 (0.21), residues: 668 sheet: -0.93 (0.28), residues: 352 loop : -0.86 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.014 0.001 TYR C 347 PHE 0.008 0.001 PHE C 184 TRP 0.006 0.001 TRP E 439 HIS 0.002 0.000 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00261 (16344) covalent geometry : angle 0.51042 (22027) hydrogen bonds : bond 0.02750 ( 593) hydrogen bonds : angle 4.23038 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3919.44 seconds wall clock time: 68 minutes 12.20 seconds (4092.20 seconds total)