Starting phenix.real_space_refine on Sun Aug 24 10:04:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jau_36134/08_2025/8jau_36134.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jau_36134/08_2025/8jau_36134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jau_36134/08_2025/8jau_36134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jau_36134/08_2025/8jau_36134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jau_36134/08_2025/8jau_36134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jau_36134/08_2025/8jau_36134.map" } resolution = 3.22 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= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2476 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 93 5.16 5 C 10893 2.51 5 N 2918 2.21 5 O 3159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17064 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4613 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 6, 'TRANS': 564} Chain: "E" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2214 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 830 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "S" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "B" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4630 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 6, 'TRANS': 566} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "G" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2382 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 272} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 401 SG CYS A 54 49.333 59.267 98.815 1.00 24.05 S ATOM 8881 SG CYS B 54 45.488 59.582 98.089 1.00 35.11 S Time building chain proxies: 3.72, per 1000 atoms: 0.22 Number of scatterers: 17064 At special positions: 0 Unit cell: (107.42, 135.3, 202.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 93 16.00 O 3159 8.00 N 2918 7.00 C 10893 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: 1.47 Conformation dependent library (CDL) restraints added in 750.3 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS A 89 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 89 " pdb="ZN ZN B 601 " - pdb=" SG CYS A 54 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 54 " Number of angles added : 2 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4004 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 5 sheets defined 75.5% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.786A pdb=" N PHE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.782A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.729A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 85 " --> pdb=" O HIS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.906A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.242A pdb=" N LYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 removed outlier: 3.620A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 199 removed outlier: 3.954A pdb=" N GLU A 183 " --> pdb=" O TYR A 179 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 241 through 259 Processing helix chain 'A' and resid 261 through 280 removed outlier: 4.404A pdb=" N GLN A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 303 through 322 removed outlier: 4.013A pdb=" N ALA A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.532A pdb=" N TYR A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 4.102A pdb=" N HIS A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.785A pdb=" N ALA A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.756A pdb=" N LEU A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 removed outlier: 3.610A pdb=" N HIS A 431 " --> pdb=" O GLN A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 463 removed outlier: 3.532A pdb=" N GLU A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 484 Processing helix chain 'A' and resid 487 through 507 removed outlier: 3.624A pdb=" N LYS A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 513 through 528 removed outlier: 3.736A pdb=" N GLY A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 551 Processing helix chain 'A' and resid 555 through 561 Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.578A pdb=" N VAL A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 removed outlier: 4.104A pdb=" N THR E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.630A pdb=" N PHE E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 3.553A pdb=" N LEU E 57 " --> pdb=" O LEU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 138 through 152 removed outlier: 4.038A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.582A pdb=" N MET E 162 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 191 removed outlier: 3.716A pdb=" N PHE E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL E 189 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 207 removed outlier: 3.616A pdb=" N PHE E 207 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 230 removed outlier: 3.596A pdb=" N GLU E 222 " --> pdb=" O TYR E 218 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA E 223 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 254 removed outlier: 3.507A pdb=" N GLU E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP E 245 " --> pdb=" O GLY E 241 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 254 " --> pdb=" O CYS E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 258 through 264 removed outlier: 3.731A pdb=" N VAL E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 271 Processing helix chain 'E' and resid 274 through 280 removed outlier: 3.547A pdb=" N ALA E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 30 removed outlier: 3.537A pdb=" N LEU C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.973A pdb=" N GLY D 50 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE D 52 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 84 removed outlier: 4.338A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 111 removed outlier: 4.638A pdb=" N LEU D 101 " --> pdb=" O PRO D 97 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.796A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.897A pdb=" N GLU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.569A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 72 No H-bonds generated for 'chain 'B' and resid 71 through 72' Processing helix chain 'B' and resid 73 through 74 No H-bonds generated for 'chain 'B' and resid 73 through 74' Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.552A pdb=" N HIS B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 107 removed outlier: 3.730A pdb=" N TYR B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 133 Processing helix chain 'B' and resid 135 through 151 removed outlier: 4.252A pdb=" N LYS B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 175 removed outlier: 3.810A pdb=" N TRP B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 160 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 198 removed outlier: 3.772A pdb=" N GLU B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 236 Processing helix chain 'B' and resid 241 through 259 Processing helix chain 'B' and resid 261 through 280 removed outlier: 3.908A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 301 Processing helix chain 'B' and resid 303 through 322 removed outlier: 3.648A pdb=" N ALA B 309 " --> pdb=" O CYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 Processing helix chain 'B' and resid 351 through 368 removed outlier: 4.319A pdb=" N HIS B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 removed outlier: 4.231A pdb=" N ALA B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 421 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 444 through 463 removed outlier: 4.033A pdb=" N GLN B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 489 through 506 Processing helix chain 'B' and resid 507 through 510 removed outlier: 3.731A pdb=" N TYR B 510 " --> pdb=" O GLY B 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 511 through 528 removed outlier: 4.104A pdb=" N TYR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 550 Processing helix chain 'B' and resid 569 through 577 Processing helix chain 'G' and resid 23 through 36 removed outlier: 3.532A pdb=" N LEU G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 removed outlier: 3.619A pdb=" N GLN G 42 " --> pdb=" O PRO G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'H' and resid 33 through 37 Processing helix chain 'H' and resid 39 through 46 Processing helix chain 'H' and resid 66 through 83 removed outlier: 4.185A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.676A pdb=" N LEU H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.605A pdb=" N THR I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 31 through 47 removed outlier: 3.752A pdb=" N PHE I 39 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 78 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.517A pdb=" N MET I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 112 Processing helix chain 'I' and resid 138 through 151 removed outlier: 4.034A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 171 removed outlier: 3.693A pdb=" N ASP I 170 " --> pdb=" O GLU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 187 removed outlier: 3.781A pdb=" N ILE I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS I 182 " --> pdb=" O GLN I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 195 removed outlier: 4.315A pdb=" N TYR I 194 " --> pdb=" O VAL I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 205 Processing helix chain 'I' and resid 207 through 228 removed outlier: 4.186A pdb=" N GLN I 221 " --> pdb=" O GLU I 217 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER I 224 " --> pdb=" O LYS I 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 254 removed outlier: 3.630A pdb=" N GLU I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU I 240 " --> pdb=" O MET I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 257 No H-bonds generated for 'chain 'I' and resid 255 through 257' Processing helix chain 'I' and resid 258 through 271 removed outlier: 3.571A pdb=" N VAL I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE I 263 " --> pdb=" O TYR I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 289 removed outlier: 3.523A pdb=" N LEU I 278 " --> pdb=" O HIS I 274 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS I 283 " --> pdb=" O HIS I 279 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE I 286 " --> pdb=" O CYS I 282 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG I 287 " --> pdb=" O HIS I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 298 removed outlier: 5.144A pdb=" N ASN I 296 " --> pdb=" O ASN I 292 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET I 297 " --> pdb=" O ASP I 293 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR I 298 " --> pdb=" O MET I 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 18 removed outlier: 6.819A pdb=" N PHE C 4 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL C 75 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N MET C 6 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU C 77 " --> pdb=" O MET C 6 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG C 8 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU C 44 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 51 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 32 removed outlier: 8.068A pdb=" N TYR D 18 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL D 60 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS D 20 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 16 through 19 removed outlier: 3.520A pdb=" N ALA G 73 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL G 75 " --> pdb=" O MET G 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 45 through 46 Processing sheet with id=AA5, first strand: chain 'H' and resid 30 through 32 removed outlier: 7.868A pdb=" N VAL H 60 " --> pdb=" O TYR H 18 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LYS H 20 " --> pdb=" O VAL H 60 " (cutoff:3.500A) 1076 hydrogen bonds defined for protein. 3186 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: 2.50 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5569 1.34 - 1.46: 3486 1.46 - 1.58: 8237 1.58 - 1.69: 0 1.69 - 1.81: 139 Bond restraints: 17431 Sorted by residual: bond pdb=" CB CYS B 105 " pdb=" SG CYS B 105 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" N MET I 26 " pdb=" CA MET I 26 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.42e+00 bond pdb=" CB VAL B 246 " pdb=" CG1 VAL B 246 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB THR A 290 " pdb=" CG2 THR A 290 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.37e+00 bond pdb=" CB THR B 290 " pdb=" CG2 THR B 290 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.27e+00 ... (remaining 17426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 22896 1.37 - 2.73: 506 2.73 - 4.10: 88 4.10 - 5.46: 23 5.46 - 6.83: 4 Bond angle restraints: 23517 Sorted by residual: angle pdb=" C GLU H 54 " pdb=" N ASN H 55 " pdb=" CA ASN H 55 " ideal model delta sigma weight residual 121.54 128.37 -6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N VAL H 69 " pdb=" CA VAL H 69 " pdb=" C VAL H 69 " ideal model delta sigma weight residual 112.96 109.64 3.32 1.00e+00 1.00e+00 1.10e+01 angle pdb=" N GLY B 324 " pdb=" CA GLY B 324 " pdb=" C GLY B 324 " ideal model delta sigma weight residual 110.21 113.05 -2.84 9.10e-01 1.21e+00 9.74e+00 angle pdb=" C SER B 552 " pdb=" N VAL B 553 " pdb=" CA VAL B 553 " ideal model delta sigma weight residual 121.97 127.48 -5.51 1.80e+00 3.09e-01 9.36e+00 angle pdb=" C GLU E 80 " pdb=" N GLU E 81 " pdb=" CA GLU E 81 " ideal model delta sigma weight residual 121.54 127.25 -5.71 1.91e+00 2.74e-01 8.95e+00 ... (remaining 23512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9447 17.93 - 35.85: 869 35.85 - 53.78: 138 53.78 - 71.71: 30 71.71 - 89.63: 23 Dihedral angle restraints: 10507 sinusoidal: 4304 harmonic: 6203 Sorted by residual: dihedral pdb=" CA HIS A 221 " pdb=" C HIS A 221 " pdb=" N TYR A 222 " pdb=" CA TYR A 222 " ideal model delta harmonic sigma weight residual -180.00 -161.20 -18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASN B 303 " pdb=" C ASN B 303 " pdb=" N ILE B 304 " pdb=" CA ILE B 304 " ideal model delta harmonic sigma weight residual -180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP G 48 " pdb=" CB ASP G 48 " pdb=" CG ASP G 48 " pdb=" OD1 ASP G 48 " ideal model delta sinusoidal sigma weight residual -30.00 -89.95 59.95 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 10504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1925 0.043 - 0.086: 552 0.086 - 0.129: 76 0.129 - 0.172: 4 0.172 - 0.215: 1 Chirality restraints: 2558 Sorted by residual: chirality pdb=" CB ILE G 14 " pdb=" CA ILE G 14 " pdb=" CG1 ILE G 14 " pdb=" CG2 ILE G 14 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASN H 55 " pdb=" N ASN H 55 " pdb=" C ASN H 55 " pdb=" CB ASN H 55 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA GLU B 568 " pdb=" N GLU B 568 " pdb=" C GLU B 568 " pdb=" CB GLU B 568 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 2555 not shown) Planarity restraints: 3009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS I 255 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO I 256 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO I 256 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 256 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 37 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO C 38 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 38 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 38 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 49 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO I 50 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " -0.022 5.00e-02 4.00e+02 ... (remaining 3006 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 744 2.73 - 3.27: 17917 3.27 - 3.81: 29430 3.81 - 4.36: 35752 4.36 - 4.90: 61436 Nonbonded interactions: 145279 Sorted by model distance: nonbonded pdb=" OH TYR I 219 " pdb=" OE1 GLU I 246 " model vdw 2.183 3.040 nonbonded pdb=" OG1 THR C 23 " pdb=" OE1 GLU C 26 " model vdw 2.245 3.040 nonbonded pdb=" NH2 ARG B 380 " pdb=" OD1 ASN B 434 " model vdw 2.282 3.120 nonbonded pdb=" ND2 ASN B 482 " pdb=" O GLY B 519 " model vdw 2.282 3.120 nonbonded pdb=" NH1 ARG B 103 " pdb=" OH TYR B 107 " model vdw 2.289 3.120 ... (remaining 145274 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' selection = (chain 'B' and resid 8 through 578) } ncs_group { reference = (chain 'C' and resid 2 through 97) selection = (chain 'G' and resid 2 through 97) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = (chain 'I' and resid 1 through 280) } ncs_group { reference = chain 'F' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 16.790 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.004 0.041 17435 Z= 0.164 Angle : 0.520 6.830 23519 Z= 0.281 Chirality : 0.038 0.215 2558 Planarity : 0.004 0.057 3009 Dihedral : 14.397 89.633 6503 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.17), residues: 2072 helix: -0.10 (0.13), residues: 1456 sheet: -1.44 (1.14), residues: 21 loop : -1.79 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 38 TYR 0.020 0.001 TYR A 294 PHE 0.029 0.002 PHE C 79 TRP 0.009 0.001 TRP B 159 HIS 0.009 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00390 (17431) covalent geometry : angle 0.51978 (23517) hydrogen bonds : bond 0.17340 ( 1076) hydrogen bonds : angle 6.76074 ( 3186) metal coordination : bond 0.00982 ( 4) metal coordination : angle 2.77959 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8132 (m-80) cc_final: 0.7919 (m-80) REVERT: A 445 PHE cc_start: 0.8003 (m-10) cc_final: 0.7747 (m-80) REVERT: E 26 MET cc_start: 0.4846 (ptp) cc_final: 0.4191 (ptp) REVERT: E 82 GLN cc_start: 0.1806 (mm110) cc_final: 0.0675 (tt0) REVERT: E 270 MET cc_start: 0.6431 (tpp) cc_final: 0.6145 (tpp) REVERT: B 9 ILE cc_start: 0.8512 (mp) cc_final: 0.8296 (tp) REVERT: B 451 MET cc_start: 0.7279 (mmt) cc_final: 0.7010 (mmt) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.1348 time to fit residues: 54.8969 Evaluate side-chains 194 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0970 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS A 352 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 193 GLN E 225 ASN E 274 HIS C 42 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 1 GLN B 38 ASN B 153 HIS ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS H 108 ASN I 82 GLN I 116 ASN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.168428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129944 restraints weight = 20531.076| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.94 r_work: 0.3175 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17435 Z= 0.161 Angle : 0.504 5.868 23519 Z= 0.275 Chirality : 0.037 0.146 2558 Planarity : 0.004 0.054 3009 Dihedral : 4.140 29.301 2310 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.54 % Allowed : 6.11 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.18), residues: 2072 helix: 0.43 (0.13), residues: 1504 sheet: -2.25 (0.74), residues: 40 loop : -1.64 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 251 TYR 0.016 0.001 TYR E 253 PHE 0.018 0.001 PHE B 445 TRP 0.008 0.001 TRP B 159 HIS 0.005 0.001 HIS B 279 Details of bonding type rmsd covalent geometry : bond 0.00365 (17431) covalent geometry : angle 0.50319 (23517) hydrogen bonds : bond 0.04728 ( 1076) hydrogen bonds : angle 4.70619 ( 3186) metal coordination : bond 0.01371 ( 4) metal coordination : angle 3.59799 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6334 (tpp) cc_final: 0.6044 (mmt) REVERT: A 359 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.7440 (mmm160) REVERT: A 450 GLU cc_start: 0.8011 (tp30) cc_final: 0.7490 (tp30) REVERT: A 565 GLN cc_start: 0.6141 (mp10) cc_final: 0.5753 (mm110) REVERT: E 270 MET cc_start: 0.5733 (tpp) cc_final: 0.5282 (tpp) REVERT: B 9 ILE cc_start: 0.8352 (mp) cc_final: 0.8095 (tp) REVERT: B 302 ASP cc_start: 0.8226 (t0) cc_final: 0.7735 (t0) REVERT: B 392 ASP cc_start: 0.7047 (t0) cc_final: 0.6645 (t0) REVERT: B 445 PHE cc_start: 0.7872 (m-10) cc_final: 0.7573 (m-10) REVERT: B 451 MET cc_start: 0.7171 (mmt) cc_final: 0.6913 (mmt) REVERT: G 6 MET cc_start: 0.8637 (ttp) cc_final: 0.8433 (ttt) REVERT: H 59 GLU cc_start: 0.8012 (pp20) cc_final: 0.7802 (pp20) outliers start: 10 outliers final: 6 residues processed: 215 average time/residue: 0.1103 time to fit residues: 36.5290 Evaluate side-chains 197 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 566 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 140 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS H 108 ASN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128780 restraints weight = 20659.095| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.96 r_work: 0.3302 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17435 Z= 0.174 Angle : 0.494 6.712 23519 Z= 0.265 Chirality : 0.037 0.141 2558 Planarity : 0.004 0.054 3009 Dihedral : 4.098 31.948 2310 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.35 % Allowed : 8.55 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.18), residues: 2072 helix: 0.65 (0.13), residues: 1495 sheet: -2.15 (0.75), residues: 40 loop : -1.61 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 251 TYR 0.026 0.001 TYR E 253 PHE 0.016 0.001 PHE A 355 TRP 0.008 0.001 TRP B 159 HIS 0.004 0.001 HIS E 182 Details of bonding type rmsd covalent geometry : bond 0.00406 (17431) covalent geometry : angle 0.49162 (23517) hydrogen bonds : bond 0.04140 ( 1076) hydrogen bonds : angle 4.40176 ( 3186) metal coordination : bond 0.01253 ( 4) metal coordination : angle 4.76489 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6408 (tpp) cc_final: 0.6026 (mmt) REVERT: A 160 PHE cc_start: 0.8211 (m-80) cc_final: 0.7827 (m-80) REVERT: A 358 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 359 ARG cc_start: 0.7865 (mtt-85) cc_final: 0.7411 (mmm160) REVERT: A 445 PHE cc_start: 0.8043 (m-10) cc_final: 0.7052 (m-10) REVERT: A 450 GLU cc_start: 0.8006 (tp30) cc_final: 0.7531 (tp30) REVERT: A 565 GLN cc_start: 0.6004 (mp10) cc_final: 0.5713 (mm110) REVERT: E 194 TYR cc_start: 0.6253 (p90) cc_final: 0.5993 (p90) REVERT: E 221 GLN cc_start: 0.8035 (tp40) cc_final: 0.7755 (tp40) REVERT: C 55 LYS cc_start: 0.7769 (pttt) cc_final: 0.7454 (pttm) REVERT: B 9 ILE cc_start: 0.8456 (mp) cc_final: 0.8205 (tp) REVERT: B 387 GLU cc_start: 0.7670 (tt0) cc_final: 0.7457 (tt0) REVERT: B 443 ARG cc_start: 0.7830 (mmt180) cc_final: 0.7578 (mmt180) REVERT: B 445 PHE cc_start: 0.7756 (m-10) cc_final: 0.7358 (m-10) REVERT: B 451 MET cc_start: 0.7214 (mmt) cc_final: 0.6939 (mmt) REVERT: H 59 GLU cc_start: 0.8183 (pp20) cc_final: 0.7907 (pp20) REVERT: I 222 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6801 (tm-30) outliers start: 25 outliers final: 16 residues processed: 220 average time/residue: 0.1263 time to fit residues: 42.0145 Evaluate side-chains 206 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 180 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 35 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 41 optimal weight: 0.0570 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS I 156 GLN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.168725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129437 restraints weight = 20557.709| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.00 r_work: 0.3310 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17435 Z= 0.138 Angle : 0.465 6.568 23519 Z= 0.251 Chirality : 0.036 0.145 2558 Planarity : 0.004 0.052 3009 Dihedral : 4.031 30.566 2310 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.24 % Allowed : 10.28 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.19), residues: 2072 helix: 0.79 (0.13), residues: 1508 sheet: -2.08 (0.76), residues: 40 loop : -1.59 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 251 TYR 0.014 0.001 TYR A 488 PHE 0.013 0.001 PHE E 64 TRP 0.007 0.001 TRP B 159 HIS 0.003 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00315 (17431) covalent geometry : angle 0.46335 (23517) hydrogen bonds : bond 0.03852 ( 1076) hydrogen bonds : angle 4.25039 ( 3186) metal coordination : bond 0.01066 ( 4) metal coordination : angle 4.69360 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6401 (tpp) cc_final: 0.6003 (mmt) REVERT: A 160 PHE cc_start: 0.8186 (m-80) cc_final: 0.7806 (m-80) REVERT: A 445 PHE cc_start: 0.8052 (m-10) cc_final: 0.7019 (m-10) REVERT: A 450 GLU cc_start: 0.8001 (tp30) cc_final: 0.7743 (tp30) REVERT: A 565 GLN cc_start: 0.5955 (mp10) cc_final: 0.5709 (mm110) REVERT: E 148 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.7056 (ttp80) REVERT: D 17 MET cc_start: 0.7236 (ptt) cc_final: 0.6898 (ttp) REVERT: B 9 ILE cc_start: 0.8427 (mp) cc_final: 0.8193 (tp) REVERT: B 443 ARG cc_start: 0.7885 (mmt180) cc_final: 0.7642 (mmt180) REVERT: B 451 MET cc_start: 0.7212 (mmt) cc_final: 0.6950 (mmt) REVERT: H 59 GLU cc_start: 0.8155 (pp20) cc_final: 0.7837 (pp20) REVERT: I 26 MET cc_start: 0.7843 (ptt) cc_final: 0.7525 (ptt) REVERT: I 222 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6755 (tm-30) outliers start: 23 outliers final: 20 residues processed: 208 average time/residue: 0.1198 time to fit residues: 37.8323 Evaluate side-chains 208 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 248 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 164 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 202 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 395 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN G 10 HIS ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.166661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127765 restraints weight = 20456.519| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.96 r_work: 0.3296 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17435 Z= 0.147 Angle : 0.465 6.897 23519 Z= 0.250 Chirality : 0.036 0.140 2558 Planarity : 0.004 0.055 3009 Dihedral : 3.984 28.673 2310 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.73 % Allowed : 11.25 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.19), residues: 2072 helix: 0.87 (0.14), residues: 1504 sheet: -2.04 (0.77), residues: 40 loop : -1.53 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 251 TYR 0.023 0.001 TYR A 488 PHE 0.016 0.001 PHE B 445 TRP 0.007 0.001 TRP B 159 HIS 0.003 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00341 (17431) covalent geometry : angle 0.46285 (23517) hydrogen bonds : bond 0.03795 ( 1076) hydrogen bonds : angle 4.18421 ( 3186) metal coordination : bond 0.01148 ( 4) metal coordination : angle 4.93234 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.624 Fit side-chains REVERT: A 156 MET cc_start: 0.6483 (tpp) cc_final: 0.6064 (mmt) REVERT: A 160 PHE cc_start: 0.8222 (m-80) cc_final: 0.7841 (m-80) REVERT: A 358 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7550 (mm-30) REVERT: A 445 PHE cc_start: 0.8021 (m-10) cc_final: 0.6997 (m-10) REVERT: A 450 GLU cc_start: 0.8028 (tp30) cc_final: 0.7701 (tp30) REVERT: A 565 GLN cc_start: 0.5940 (mp10) cc_final: 0.5666 (mm110) REVERT: E 141 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6823 (mm-30) REVERT: C 55 LYS cc_start: 0.7742 (pttt) cc_final: 0.7467 (pttm) REVERT: D 17 MET cc_start: 0.7334 (ptt) cc_final: 0.6999 (ttp) REVERT: B 9 ILE cc_start: 0.8451 (mp) cc_final: 0.8208 (tp) REVERT: B 392 ASP cc_start: 0.7157 (t0) cc_final: 0.6867 (t0) REVERT: B 446 LYS cc_start: 0.8533 (tptm) cc_final: 0.8243 (tptt) REVERT: B 451 MET cc_start: 0.7194 (mmt) cc_final: 0.6955 (mmt) REVERT: G 6 MET cc_start: 0.8839 (ttp) cc_final: 0.8541 (ttt) REVERT: H 59 GLU cc_start: 0.8179 (pp20) cc_final: 0.7836 (pp20) REVERT: H 64 GLU cc_start: 0.8142 (pt0) cc_final: 0.7867 (pt0) REVERT: I 222 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6755 (tm-30) outliers start: 32 outliers final: 27 residues processed: 221 average time/residue: 0.1286 time to fit residues: 43.1078 Evaluate side-chains 216 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 149 optimal weight: 0.0980 chunk 135 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 279 HIS A 306 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.167204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128474 restraints weight = 20383.113| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.94 r_work: 0.3319 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17435 Z= 0.164 Angle : 0.483 8.453 23519 Z= 0.258 Chirality : 0.037 0.162 2558 Planarity : 0.004 0.051 3009 Dihedral : 3.992 27.694 2310 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.06 % Allowed : 11.90 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.19), residues: 2072 helix: 0.86 (0.14), residues: 1504 sheet: -2.06 (0.77), residues: 40 loop : -1.55 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 251 TYR 0.022 0.001 TYR B 495 PHE 0.019 0.001 PHE C 79 TRP 0.007 0.001 TRP B 159 HIS 0.006 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00385 (17431) covalent geometry : angle 0.48110 (23517) hydrogen bonds : bond 0.03847 ( 1076) hydrogen bonds : angle 4.17046 ( 3186) metal coordination : bond 0.01249 ( 4) metal coordination : angle 5.03317 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6523 (tpp) cc_final: 0.6076 (mmt) REVERT: A 160 PHE cc_start: 0.8272 (m-80) cc_final: 0.7872 (m-80) REVERT: A 359 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7434 (mmm160) REVERT: A 450 GLU cc_start: 0.8029 (tp30) cc_final: 0.7823 (tp30) REVERT: A 565 GLN cc_start: 0.5980 (mp10) cc_final: 0.5714 (mm110) REVERT: B 9 ILE cc_start: 0.8473 (mp) cc_final: 0.8236 (tp) REVERT: B 392 ASP cc_start: 0.7173 (t0) cc_final: 0.6959 (t0) REVERT: B 445 PHE cc_start: 0.7774 (m-10) cc_final: 0.7326 (m-10) REVERT: B 446 LYS cc_start: 0.8534 (tptm) cc_final: 0.8224 (tptt) REVERT: B 451 MET cc_start: 0.7167 (mmt) cc_final: 0.6893 (mmt) REVERT: G 6 MET cc_start: 0.8853 (ttp) cc_final: 0.8591 (ttt) REVERT: H 59 GLU cc_start: 0.8222 (pp20) cc_final: 0.7836 (pp20) REVERT: H 64 GLU cc_start: 0.8140 (pt0) cc_final: 0.7929 (pt0) REVERT: I 195 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8310 (mtpp) REVERT: I 222 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6727 (tm-30) outliers start: 38 outliers final: 29 residues processed: 217 average time/residue: 0.1245 time to fit residues: 41.8040 Evaluate side-chains 220 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 107 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 333 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.167203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128488 restraints weight = 20373.544| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.94 r_work: 0.3318 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17435 Z= 0.160 Angle : 0.481 9.099 23519 Z= 0.256 Chirality : 0.037 0.170 2558 Planarity : 0.004 0.049 3009 Dihedral : 3.988 26.660 2310 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.06 % Allowed : 12.44 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.19), residues: 2072 helix: 0.89 (0.14), residues: 1505 sheet: -2.15 (0.76), residues: 40 loop : -1.56 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 251 TYR 0.028 0.001 TYR E 253 PHE 0.018 0.001 PHE B 445 TRP 0.008 0.001 TRP B 159 HIS 0.004 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00376 (17431) covalent geometry : angle 0.47865 (23517) hydrogen bonds : bond 0.03815 ( 1076) hydrogen bonds : angle 4.14293 ( 3186) metal coordination : bond 0.01226 ( 4) metal coordination : angle 5.05747 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6426 (tpp) cc_final: 0.5987 (mmt) REVERT: A 160 PHE cc_start: 0.8255 (m-80) cc_final: 0.7849 (m-80) REVERT: A 359 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7431 (mmm160) REVERT: A 450 GLU cc_start: 0.8044 (tp30) cc_final: 0.7828 (tp30) REVERT: A 565 GLN cc_start: 0.6023 (mp10) cc_final: 0.5788 (mm110) REVERT: C 55 LYS cc_start: 0.7739 (pttt) cc_final: 0.7269 (pttm) REVERT: B 9 ILE cc_start: 0.8494 (mp) cc_final: 0.8266 (tp) REVERT: B 446 LYS cc_start: 0.8535 (tptm) cc_final: 0.8206 (tptt) REVERT: B 451 MET cc_start: 0.7157 (mmt) cc_final: 0.6888 (mmt) REVERT: G 6 MET cc_start: 0.8811 (ttp) cc_final: 0.8588 (ttt) REVERT: H 59 GLU cc_start: 0.8248 (pp20) cc_final: 0.7841 (pp20) REVERT: I 195 LYS cc_start: 0.8595 (mtpp) cc_final: 0.8290 (mtpp) REVERT: I 222 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6697 (tm-30) outliers start: 38 outliers final: 31 residues processed: 218 average time/residue: 0.1181 time to fit residues: 39.9516 Evaluate side-chains 217 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 201 optimal weight: 0.8980 chunk 182 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 21 optimal weight: 0.0570 chunk 140 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 0.0670 chunk 136 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 425 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.169107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130611 restraints weight = 20447.430| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.94 r_work: 0.3366 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17435 Z= 0.119 Angle : 0.465 10.025 23519 Z= 0.247 Chirality : 0.036 0.161 2558 Planarity : 0.004 0.066 3009 Dihedral : 3.948 24.877 2310 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.73 % Allowed : 13.41 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.19), residues: 2072 helix: 1.00 (0.14), residues: 1510 sheet: -1.99 (0.76), residues: 42 loop : -1.53 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 251 TYR 0.031 0.001 TYR E 253 PHE 0.017 0.001 PHE B 445 TRP 0.008 0.001 TRP B 159 HIS 0.004 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00264 (17431) covalent geometry : angle 0.46292 (23517) hydrogen bonds : bond 0.03656 ( 1076) hydrogen bonds : angle 4.07410 ( 3186) metal coordination : bond 0.00919 ( 4) metal coordination : angle 4.91539 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8369 (m-30) cc_final: 0.8057 (m-30) REVERT: A 156 MET cc_start: 0.6589 (tpp) cc_final: 0.6152 (mmt) REVERT: A 160 PHE cc_start: 0.8257 (m-80) cc_final: 0.7868 (m-80) REVERT: A 425 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8230 (t0) REVERT: A 450 GLU cc_start: 0.7997 (tp30) cc_final: 0.7764 (tp30) REVERT: A 565 GLN cc_start: 0.5987 (mp10) cc_final: 0.5764 (mm110) REVERT: B 445 PHE cc_start: 0.7484 (m-10) cc_final: 0.7234 (m-10) REVERT: B 446 LYS cc_start: 0.8519 (tptm) cc_final: 0.8191 (tptt) REVERT: B 451 MET cc_start: 0.7165 (mmt) cc_final: 0.6910 (mmt) REVERT: G 6 MET cc_start: 0.8782 (ttp) cc_final: 0.8568 (ttt) REVERT: H 59 GLU cc_start: 0.8218 (pp20) cc_final: 0.7833 (pp20) REVERT: H 111 ASP cc_start: 0.8384 (t0) cc_final: 0.8003 (t0) REVERT: I 195 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8277 (mtpp) REVERT: I 222 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6667 (tm-30) REVERT: I 269 ARG cc_start: 0.7561 (mmt-90) cc_final: 0.7361 (mmt-90) outliers start: 32 outliers final: 25 residues processed: 218 average time/residue: 0.1263 time to fit residues: 42.4407 Evaluate side-chains 213 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 0.0070 chunk 151 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129041 restraints weight = 20393.221| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.96 r_work: 0.3293 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17435 Z= 0.139 Angle : 0.485 12.758 23519 Z= 0.256 Chirality : 0.037 0.211 2558 Planarity : 0.004 0.056 3009 Dihedral : 3.958 24.009 2310 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.89 % Allowed : 13.63 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.19), residues: 2072 helix: 1.02 (0.14), residues: 1502 sheet: -2.00 (0.77), residues: 42 loop : -1.52 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 251 TYR 0.034 0.001 TYR E 253 PHE 0.027 0.001 PHE B 445 TRP 0.008 0.001 TRP B 159 HIS 0.005 0.001 HIS C 10 Details of bonding type rmsd covalent geometry : bond 0.00320 (17431) covalent geometry : angle 0.48312 (23517) hydrogen bonds : bond 0.03688 ( 1076) hydrogen bonds : angle 4.07923 ( 3186) metal coordination : bond 0.00996 ( 4) metal coordination : angle 4.91531 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8401 (m-30) cc_final: 0.8094 (m-30) REVERT: A 156 MET cc_start: 0.6516 (tpp) cc_final: 0.6057 (mmt) REVERT: A 160 PHE cc_start: 0.8252 (m-80) cc_final: 0.7862 (m-80) REVERT: A 450 GLU cc_start: 0.8031 (tp30) cc_final: 0.7774 (tp30) REVERT: A 565 GLN cc_start: 0.6055 (mp10) cc_final: 0.5773 (mm110) REVERT: C 8 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8206 (mtp180) REVERT: C 55 LYS cc_start: 0.7635 (pttt) cc_final: 0.7186 (pttm) REVERT: B 445 PHE cc_start: 0.7361 (m-10) cc_final: 0.6909 (m-10) REVERT: B 446 LYS cc_start: 0.8515 (tptm) cc_final: 0.8185 (tptt) REVERT: B 451 MET cc_start: 0.7174 (mmt) cc_final: 0.6920 (mmt) REVERT: G 6 MET cc_start: 0.8778 (ttp) cc_final: 0.8574 (ttt) REVERT: H 59 GLU cc_start: 0.8216 (pp20) cc_final: 0.7831 (pp20) REVERT: H 111 ASP cc_start: 0.8448 (t0) cc_final: 0.8047 (t0) REVERT: I 195 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8275 (mtpp) REVERT: I 222 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6661 (tm-30) REVERT: I 269 ARG cc_start: 0.7558 (mmt-90) cc_final: 0.7354 (mmt-90) outliers start: 35 outliers final: 30 residues processed: 219 average time/residue: 0.1262 time to fit residues: 42.0998 Evaluate side-chains 221 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 10 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 36 optimal weight: 0.0570 chunk 108 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.167606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129199 restraints weight = 20327.983| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.94 r_work: 0.3309 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17435 Z= 0.153 Angle : 0.502 13.162 23519 Z= 0.263 Chirality : 0.037 0.204 2558 Planarity : 0.004 0.054 3009 Dihedral : 3.993 25.980 2310 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.84 % Allowed : 13.74 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.19), residues: 2072 helix: 0.99 (0.14), residues: 1502 sheet: -1.98 (0.77), residues: 42 loop : -1.54 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 251 TYR 0.023 0.001 TYR E 253 PHE 0.025 0.001 PHE B 445 TRP 0.009 0.001 TRP B 159 HIS 0.006 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00359 (17431) covalent geometry : angle 0.50019 (23517) hydrogen bonds : bond 0.03720 ( 1076) hydrogen bonds : angle 4.08732 ( 3186) metal coordination : bond 0.01111 ( 4) metal coordination : angle 4.93942 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8420 (m-30) cc_final: 0.8097 (m-30) REVERT: A 156 MET cc_start: 0.6421 (tpp) cc_final: 0.5965 (mmt) REVERT: A 160 PHE cc_start: 0.8252 (m-80) cc_final: 0.7876 (m-80) REVERT: A 359 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7422 (mmm160) REVERT: A 450 GLU cc_start: 0.8020 (tp30) cc_final: 0.7779 (tp30) REVERT: A 565 GLN cc_start: 0.6079 (mp10) cc_final: 0.5804 (mm110) REVERT: C 8 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8211 (mtp180) REVERT: C 26 GLU cc_start: 0.7941 (mp0) cc_final: 0.7658 (mp0) REVERT: C 55 LYS cc_start: 0.7620 (pttt) cc_final: 0.7202 (pttm) REVERT: B 445 PHE cc_start: 0.7335 (m-10) cc_final: 0.6907 (m-10) REVERT: B 446 LYS cc_start: 0.8514 (tptm) cc_final: 0.8180 (tptt) REVERT: B 451 MET cc_start: 0.7180 (mmt) cc_final: 0.6925 (mmt) REVERT: H 59 GLU cc_start: 0.8258 (pp20) cc_final: 0.7857 (pp20) REVERT: H 111 ASP cc_start: 0.8463 (t0) cc_final: 0.8064 (t0) REVERT: I 195 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8280 (mtpp) REVERT: I 222 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6664 (tm-30) REVERT: I 269 ARG cc_start: 0.7537 (mmt-90) cc_final: 0.7327 (mmt-90) outliers start: 34 outliers final: 32 residues processed: 215 average time/residue: 0.1195 time to fit residues: 39.3355 Evaluate side-chains 224 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 168 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.167243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128076 restraints weight = 20384.691| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.97 r_work: 0.3315 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17435 Z= 0.156 Angle : 0.509 12.775 23519 Z= 0.266 Chirality : 0.037 0.210 2558 Planarity : 0.004 0.052 3009 Dihedral : 3.998 26.846 2310 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.89 % Allowed : 14.06 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.19), residues: 2072 helix: 1.00 (0.14), residues: 1498 sheet: -1.94 (0.78), residues: 42 loop : -1.56 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 251 TYR 0.027 0.001 TYR E 253 PHE 0.024 0.001 PHE C 79 TRP 0.010 0.001 TRP B 159 HIS 0.006 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00368 (17431) covalent geometry : angle 0.50739 (23517) hydrogen bonds : bond 0.03738 ( 1076) hydrogen bonds : angle 4.08167 ( 3186) metal coordination : bond 0.01115 ( 4) metal coordination : angle 4.92465 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4726.09 seconds wall clock time: 81 minutes 41.09 seconds (4901.09 seconds total)