Starting phenix.real_space_refine on Fri Feb 6 15:44:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ip0_35629/02_2026/8ip0_35629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ip0_35629/02_2026/8ip0_35629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ip0_35629/02_2026/8ip0_35629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ip0_35629/02_2026/8ip0_35629.map" model { file = "/net/cci-nas-00/data/ceres_data/8ip0_35629/02_2026/8ip0_35629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ip0_35629/02_2026/8ip0_35629.cif" } resolution = 3.6 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= 0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 110 5.49 5 S 74 5.16 5 C 16551 2.51 5 N 4555 2.21 5 O 5236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26526 Number of models: 1 Model: "" Number of chains: 16 Chain: "J" Number of atoms: 3801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3801 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 15, 'TRANS': 451} Chain breaks: 7 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1695 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 192} Chain breaks: 1 Chain: "B" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "C" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "D" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "N" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "O" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1911 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 13, 'TRANS': 227} Chain breaks: 4 Chain: "E" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "F" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 8, 'rna3p_pyr': 18} Link IDs: {'rna2p': 18, 'rna3p': 25} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 850 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "P" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "H" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "I" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "K" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 918 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 802 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain breaks: 1 Chain: "M" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 918 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Time building chain proxies: 6.52, per 1000 atoms: 0.25 Number of scatterers: 26526 At special positions: 0 Unit cell: (108.24, 120.12, 223.08, 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) S 74 16.00 P 110 15.00 O 5236 8.00 N 4555 7.00 C 16551 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5756 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 33 sheets defined 36.4% alpha, 9.2% beta 11 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'J' and resid 20 through 39 removed outlier: 3.589A pdb=" N ARG J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 27 " --> pdb=" O HIS J 23 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA J 28 " --> pdb=" O ARG J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 51 Processing helix chain 'J' and resid 69 through 81 Processing helix chain 'J' and resid 128 through 133 Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 138 through 151 Processing helix chain 'J' and resid 158 through 166 removed outlier: 3.680A pdb=" N ASN J 164 " --> pdb=" O ASN J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 189 removed outlier: 4.047A pdb=" N SER J 182 " --> pdb=" O LYS J 178 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN J 189 " --> pdb=" O LYS J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 224 Processing helix chain 'J' and resid 226 through 231 removed outlier: 4.428A pdb=" N VAL J 230 " --> pdb=" O PHE J 226 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA J 231 " --> pdb=" O TRP J 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 226 through 231' Processing helix chain 'J' and resid 259 through 271 removed outlier: 4.390A pdb=" N ASP J 265 " --> pdb=" O GLU J 261 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE J 266 " --> pdb=" O ASP J 262 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU J 267 " --> pdb=" O PHE J 263 " (cutoff:3.500A) Proline residue: J 268 - end of helix Processing helix chain 'J' and resid 272 through 274 No H-bonds generated for 'chain 'J' and resid 272 through 274' Processing helix chain 'J' and resid 290 through 309 removed outlier: 4.212A pdb=" N GLY J 294 " --> pdb=" O VAL J 290 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA J 295 " --> pdb=" O PRO J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 357 removed outlier: 3.756A pdb=" N TYR J 352 " --> pdb=" O SER J 348 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN J 353 " --> pdb=" O VAL J 349 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN J 357 " --> pdb=" O ASN J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 373 removed outlier: 3.738A pdb=" N LEU J 369 " --> pdb=" O ARG J 365 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 387 Processing helix chain 'J' and resid 391 through 398 removed outlier: 3.609A pdb=" N LEU J 396 " --> pdb=" O GLY J 392 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU J 397 " --> pdb=" O PHE J 393 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER J 398 " --> pdb=" O GLY J 394 " (cutoff:3.500A) Processing helix chain 'J' and resid 400 through 404 removed outlier: 3.737A pdb=" N ARG J 403 " --> pdb=" O ILE J 400 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP J 404 " --> pdb=" O PRO J 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 400 through 404' Processing helix chain 'J' and resid 415 through 423 removed outlier: 4.141A pdb=" N LEU J 419 " --> pdb=" O ASP J 415 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE J 420 " --> pdb=" O ALA J 416 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN J 422 " --> pdb=" O GLN J 418 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS J 423 " --> pdb=" O LEU J 419 " (cutoff:3.500A) Processing helix chain 'J' and resid 439 through 458 removed outlier: 3.529A pdb=" N TYR J 443 " --> pdb=" O ALA J 439 " (cutoff:3.500A) Processing helix chain 'J' and resid 470 through 489 removed outlier: 3.506A pdb=" N GLU J 474 " --> pdb=" O LYS J 470 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL J 482 " --> pdb=" O LYS J 478 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU J 485 " --> pdb=" O LYS J 481 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 507 Processing helix chain 'J' and resid 514 through 524 removed outlier: 4.214A pdb=" N ALA J 520 " --> pdb=" O PHE J 516 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN J 521 " --> pdb=" O VAL J 517 " (cutoff:3.500A) Processing helix chain 'J' and resid 525 through 532 Processing helix chain 'J' and resid 535 through 540 Processing helix chain 'A' and resid 40 through 52 Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.786A pdb=" N THR A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'B' and resid 45 through 60 removed outlier: 3.925A pdb=" N MET B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 4.040A pdb=" N PHE B 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 237 through 249 removed outlier: 3.637A pdb=" N SER B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N THR B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ALA B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.547A pdb=" N VAL B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 60 removed outlier: 4.029A pdb=" N MET C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 180 through 192 removed outlier: 4.070A pdb=" N TRP C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LYS C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 188 " --> pdb=" O TRP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 4.020A pdb=" N GLU C 234 " --> pdb=" O PHE C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.680A pdb=" N THR C 244 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 267 removed outlier: 3.677A pdb=" N LYS C 267 " --> pdb=" O GLU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 278 Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'D' and resid 47 through 57 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.845A pdb=" N LYS D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 192 removed outlier: 4.115A pdb=" N TRP D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 245 Processing helix chain 'D' and resid 262 through 267 removed outlier: 3.779A pdb=" N LYS D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 276 removed outlier: 3.794A pdb=" N ALA D 274 " --> pdb=" O GLN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 300 removed outlier: 3.508A pdb=" N LEU D 290 " --> pdb=" O ASN D 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 57 removed outlier: 3.747A pdb=" N MET N 49 " --> pdb=" O SER N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 61 Processing helix chain 'N' and resid 89 through 94 Processing helix chain 'N' and resid 105 through 110 removed outlier: 3.926A pdb=" N LYS N 109 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 195 removed outlier: 4.266A pdb=" N TRP N 184 " --> pdb=" O ALA N 180 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA N 193 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU N 194 " --> pdb=" O GLN N 190 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU N 195 " --> pdb=" O ALA N 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 245 Processing helix chain 'N' and resid 261 through 267 removed outlier: 3.910A pdb=" N VAL N 265 " --> pdb=" O GLY N 261 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS N 267 " --> pdb=" O GLU N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 276 Processing helix chain 'N' and resid 286 through 300 removed outlier: 3.637A pdb=" N LEU N 290 " --> pdb=" O ASN N 286 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY N 300 " --> pdb=" O ASP N 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 removed outlier: 4.162A pdb=" N ARG O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 94 removed outlier: 3.808A pdb=" N ASP O 91 " --> pdb=" O LYS O 87 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE O 92 " --> pdb=" O PHE O 88 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE O 94 " --> pdb=" O ASP O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 106 Processing helix chain 'O' and resid 175 through 180 Processing helix chain 'O' and resid 181 through 192 removed outlier: 4.661A pdb=" N ALA O 187 " --> pdb=" O GLU O 183 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU O 189 " --> pdb=" O VAL O 185 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN O 190 " --> pdb=" O LYS O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 271 through 279 removed outlier: 3.733A pdb=" N GLN O 275 " --> pdb=" O GLU O 271 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU O 276 " --> pdb=" O GLN O 272 " (cutoff:3.500A) Processing helix chain 'O' and resid 289 through 299 removed outlier: 3.896A pdb=" N ASP O 293 " --> pdb=" O LYS O 289 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA O 295 " --> pdb=" O PHE O 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.726A pdb=" N MET H 49 " --> pdb=" O SER H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 61 Processing helix chain 'H' and resid 89 through 94 Processing helix chain 'H' and resid 105 through 110 removed outlier: 3.943A pdb=" N LYS H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 195 removed outlier: 3.979A pdb=" N TRP H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU H 194 " --> pdb=" O GLN H 190 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU H 195 " --> pdb=" O ALA H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 245 Processing helix chain 'H' and resid 261 through 267 removed outlier: 3.941A pdb=" N VAL H 265 " --> pdb=" O GLY H 261 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS H 267 " --> pdb=" O GLU H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 276 Processing helix chain 'H' and resid 286 through 300 removed outlier: 3.583A pdb=" N LEU H 290 " --> pdb=" O ASN H 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 57 removed outlier: 3.955A pdb=" N MET I 49 " --> pdb=" O SER I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 94 Processing helix chain 'I' and resid 105 through 110 removed outlier: 4.139A pdb=" N LYS I 109 " --> pdb=" O LYS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 195 removed outlier: 4.082A pdb=" N TRP I 184 " --> pdb=" O ALA I 180 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 245 Processing helix chain 'I' and resid 261 through 267 removed outlier: 3.731A pdb=" N VAL I 265 " --> pdb=" O GLY I 261 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS I 267 " --> pdb=" O GLU I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 276 Processing helix chain 'I' and resid 286 through 300 removed outlier: 3.640A pdb=" N GLY I 300 " --> pdb=" O ASP I 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 31 Processing helix chain 'K' and resid 34 through 39 removed outlier: 4.056A pdb=" N CYS K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 68 removed outlier: 4.393A pdb=" N GLU K 68 " --> pdb=" O ARG K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 81 Processing helix chain 'K' and resid 88 through 99 removed outlier: 4.062A pdb=" N PHE K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU K 96 " --> pdb=" O PHE K 92 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE K 97 " --> pdb=" O ALA K 93 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN K 98 " --> pdb=" O GLN K 94 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP K 99 " --> pdb=" O LYS K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 112 removed outlier: 4.259A pdb=" N SER K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU K 109 " --> pdb=" O SER K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 31 removed outlier: 3.562A pdb=" N HIS L 31 " --> pdb=" O LEU L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 65 removed outlier: 3.856A pdb=" N LYS L 54 " --> pdb=" O ASP L 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL L 56 " --> pdb=" O LYS L 52 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN L 57 " --> pdb=" O GLU L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 81 removed outlier: 4.293A pdb=" N TYR L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE L 76 " --> pdb=" O PHE L 72 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU L 80 " --> pdb=" O PHE L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 99 removed outlier: 3.711A pdb=" N PHE L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU L 96 " --> pdb=" O PHE L 92 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE L 97 " --> pdb=" O ALA L 93 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLN L 98 " --> pdb=" O GLN L 94 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP L 99 " --> pdb=" O LYS L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 106 Processing helix chain 'L' and resid 109 through 113 Processing helix chain 'M' and resid 10 through 31 Processing helix chain 'M' and resid 35 through 40 Processing helix chain 'M' and resid 41 through 64 removed outlier: 4.391A pdb=" N GLU M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 81 removed outlier: 3.946A pdb=" N PHE M 72 " --> pdb=" O GLU M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 84 No H-bonds generated for 'chain 'M' and resid 82 through 84' Processing helix chain 'M' and resid 85 through 99 removed outlier: 3.638A pdb=" N PHE M 89 " --> pdb=" O ARG M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 113 removed outlier: 3.795A pdb=" N THR M 107 " --> pdb=" O ILE M 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 9 through 14 Processing sheet with id=AA2, first strand: chain 'J' and resid 83 through 89 removed outlier: 3.543A pdb=" N TYR J 119 " --> pdb=" O ARG J 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 245 through 247 removed outlier: 3.500A pdb=" N ASN J 246 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ILE J 288 " --> pdb=" O VAL J 233 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N CYS J 235 " --> pdb=" O ILE J 288 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 245 through 247 removed outlier: 3.500A pdb=" N ASN J 246 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY J 321 " --> pdb=" O ASP J 256 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER J 338 " --> pdb=" O HIS J 326 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU J 328 " --> pdb=" O LEU J 336 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU J 336 " --> pdb=" O GLU J 328 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN J 330 " --> pdb=" O ILE J 334 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE J 334 " --> pdb=" O GLN J 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 278 through 279 Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.656A pdb=" N GLU A 172 " --> pdb=" O LYS A 18 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 18 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 174 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 16 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA8, first strand: chain 'A' and resid 88 through 91 Processing sheet with id=AA9, first strand: chain 'B' and resid 9 through 10 removed outlier: 3.652A pdb=" N VAL B 126 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 125 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 44 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.722A pdb=" N LEU B 69 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA B 76 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 136 through 138 Processing sheet with id=AB3, first strand: chain 'C' and resid 6 through 10 removed outlier: 6.365A pdb=" N ALA C 42 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.579A pdb=" N ALA C 172 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG C 121 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 121 through 122 removed outlier: 3.808A pdb=" N PHE D 7 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU D 11 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER D 213 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 15 through 17 removed outlier: 4.179A pdb=" N ALA D 15 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR D 165 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 34 through 36 removed outlier: 6.319A pdb=" N ILE D 34 " --> pdb=" O TYR D 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 68 through 69 removed outlier: 3.733A pdb=" N LEU D 69 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA D 76 " --> pdb=" O LEU D 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 138 through 140 Processing sheet with id=AC1, first strand: chain 'N' and resid 168 through 172 removed outlier: 3.939A pdb=" N PHE N 7 " --> pdb=" O ARG N 217 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU N 11 " --> pdb=" O SER N 213 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N SER N 213 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP N 259 " --> pdb=" O ALA N 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 15 through 17 removed outlier: 4.232A pdb=" N ALA N 15 " --> pdb=" O THR N 165 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR N 165 " --> pdb=" O ALA N 15 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 34 through 36 removed outlier: 6.644A pdb=" N ILE N 34 " --> pdb=" O TYR N 41 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 67 through 69 removed outlier: 3.879A pdb=" N ALA N 76 " --> pdb=" O LEU N 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 138 through 140 Processing sheet with id=AC6, first strand: chain 'H' and resid 121 through 122 removed outlier: 3.905A pdb=" N PHE H 7 " --> pdb=" O ARG H 217 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU H 11 " --> pdb=" O SER H 213 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N SER H 213 " --> pdb=" O LEU H 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 15 through 17 removed outlier: 4.068A pdb=" N ALA H 15 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR H 165 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 34 through 36 removed outlier: 6.570A pdb=" N ILE H 34 " --> pdb=" O TYR H 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 67 through 69 removed outlier: 3.819A pdb=" N ALA H 76 " --> pdb=" O LEU H 69 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 138 through 140 Processing sheet with id=AD2, first strand: chain 'I' and resid 121 through 122 removed outlier: 6.905A pdb=" N PHE I 7 " --> pdb=" O ALA I 216 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ALA I 216 " --> pdb=" O PHE I 7 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR I 9 " --> pdb=" O VAL I 214 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL I 214 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU I 11 " --> pdb=" O ARG I 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 15 through 17 removed outlier: 4.213A pdb=" N ALA I 15 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR I 165 " --> pdb=" O ALA I 15 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AD5, first strand: chain 'I' and resid 67 through 69 removed outlier: 3.902A pdb=" N ALA I 76 " --> pdb=" O LEU I 69 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 138 through 140 751 hydrogen bonds defined for protein. 2061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 3.11 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: 8091 1.34 - 1.46: 5296 1.46 - 1.58: 13627 1.58 - 1.70: 216 1.70 - 1.82: 126 Bond restraints: 27356 Sorted by residual: bond pdb=" N VAL J 155 " pdb=" CA VAL J 155 " ideal model delta sigma weight residual 1.467 1.443 0.024 1.09e-02 8.42e+03 4.96e+00 bond pdb=" C1' DC G 55 " pdb=" N1 DC G 55 " ideal model delta sigma weight residual 1.490 1.552 -0.062 3.00e-02 1.11e+03 4.23e+00 bond pdb=" CA ILE M 103 " pdb=" C ILE M 103 " ideal model delta sigma weight residual 1.523 1.503 0.020 1.27e-02 6.20e+03 2.48e+00 bond pdb=" CA ILE D 44 " pdb=" C ILE D 44 " ideal model delta sigma weight residual 1.522 1.540 -0.018 1.19e-02 7.06e+03 2.24e+00 bond pdb=" CA LYS A 105 " pdb=" C LYS A 105 " ideal model delta sigma weight residual 1.524 1.538 -0.014 9.50e-03 1.11e+04 2.17e+00 ... (remaining 27351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 37055 2.57 - 5.14: 401 5.14 - 7.70: 47 7.70 - 10.27: 9 10.27 - 12.84: 2 Bond angle restraints: 37514 Sorted by residual: angle pdb=" N SER J 150 " pdb=" CA SER J 150 " pdb=" C SER J 150 " ideal model delta sigma weight residual 111.36 121.56 -10.20 1.09e+00 8.42e-01 8.76e+01 angle pdb=" N THR M 100 " pdb=" CA THR M 100 " pdb=" C THR M 100 " ideal model delta sigma weight residual 111.07 119.84 -8.77 1.07e+00 8.73e-01 6.72e+01 angle pdb=" N ILE J 151 " pdb=" CA ILE J 151 " pdb=" C ILE J 151 " ideal model delta sigma weight residual 111.56 116.73 -5.17 8.60e-01 1.35e+00 3.62e+01 angle pdb=" N CYS J 166 " pdb=" CA CYS J 166 " pdb=" C CYS J 166 " ideal model delta sigma weight residual 110.23 118.57 -8.34 1.45e+00 4.76e-01 3.31e+01 angle pdb=" N PHE J 162 " pdb=" CA PHE J 162 " pdb=" C PHE J 162 " ideal model delta sigma weight residual 111.36 117.33 -5.97 1.09e+00 8.42e-01 3.00e+01 ... (remaining 37509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 15763 34.92 - 69.83: 583 69.83 - 104.75: 44 104.75 - 139.67: 2 139.67 - 174.58: 5 Dihedral angle restraints: 16397 sinusoidal: 7499 harmonic: 8898 Sorted by residual: dihedral pdb=" O4' C F 14 " pdb=" C1' C F 14 " pdb=" N1 C F 14 " pdb=" C2 C F 14 " ideal model delta sinusoidal sigma weight residual 200.00 52.10 147.90 1 1.50e+01 4.44e-03 7.88e+01 dihedral pdb=" O4' U F 38 " pdb=" C1' U F 38 " pdb=" N1 U F 38 " pdb=" C2 U F 38 " ideal model delta sinusoidal sigma weight residual 200.00 56.23 143.77 1 1.50e+01 4.44e-03 7.71e+01 dihedral pdb=" CA LEU J 342 " pdb=" C LEU J 342 " pdb=" N GLN J 343 " pdb=" CA GLN J 343 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 16394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3666 0.065 - 0.130: 380 0.130 - 0.195: 24 0.195 - 0.260: 5 0.260 - 0.325: 3 Chirality restraints: 4078 Sorted by residual: chirality pdb=" CA SER J 150 " pdb=" N SER J 150 " pdb=" C SER J 150 " pdb=" CB SER J 150 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA LYS A 105 " pdb=" N LYS A 105 " pdb=" C LYS A 105 " pdb=" CB LYS A 105 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA THR M 100 " pdb=" N THR M 100 " pdb=" C THR M 100 " pdb=" CB THR M 100 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4075 not shown) Planarity restraints: 4495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO J 156 " 0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C PRO J 156 " -0.078 2.00e-02 2.50e+03 pdb=" O PRO J 156 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA J 157 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP M 99 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C ASP M 99 " 0.066 2.00e-02 2.50e+03 pdb=" O ASP M 99 " -0.025 2.00e-02 2.50e+03 pdb=" N THR M 100 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 88 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C PHE B 88 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE B 88 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA B 89 " -0.019 2.00e-02 2.50e+03 ... (remaining 4492 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 127 2.42 - 3.04: 16354 3.04 - 3.66: 42028 3.66 - 4.28: 56553 4.28 - 4.90: 90761 Nonbonded interactions: 205823 Sorted by model distance: nonbonded pdb=" O ALA J 157 " pdb=" CD PRO J 161 " model vdw 1.795 3.440 nonbonded pdb=" O2 DC E -1 " pdb=" N2 DG G 58 " model vdw 1.870 2.496 nonbonded pdb=" OG SER J 197 " pdb=" OP1 DG G 58 " model vdw 1.918 3.040 nonbonded pdb=" CG LYS J 153 " pdb=" CG2 THR J 158 " model vdw 1.981 3.860 nonbonded pdb=" CZ3 TRP J 149 " pdb=" CD2 PHE J 162 " model vdw 2.010 3.640 ... (remaining 205818 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'N' } ncs_group { reference = (chain 'K' and (resid 10 through 31 or resid 42 through 115)) selection = chain 'L' selection = (chain 'M' and (resid 10 through 31 or resid 42 through 115)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.900 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27356 Z= 0.131 Angle : 0.662 12.838 37514 Z= 0.360 Chirality : 0.041 0.325 4078 Planarity : 0.004 0.069 4495 Dihedral : 17.611 174.581 10641 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.13 % Favored : 90.67 % Rotamer: Outliers : 0.43 % Allowed : 0.86 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.15), residues: 2980 helix: 0.76 (0.19), residues: 843 sheet: -1.49 (0.37), residues: 209 loop : -2.56 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 242 TYR 0.019 0.001 TYR L 48 PHE 0.038 0.001 PHE L 22 TRP 0.038 0.001 TRP N 237 HIS 0.009 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00258 (27356) covalent geometry : angle 0.66228 (37514) hydrogen bonds : bond 0.20482 ( 766) hydrogen bonds : angle 7.13767 ( 2101) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 217 ARG cc_start: 0.6623 (mtt90) cc_final: 0.6149 (mtt90) REVERT: D 279 MET cc_start: 0.4350 (ptt) cc_final: 0.4123 (ptp) REVERT: N 49 MET cc_start: 0.8492 (mtm) cc_final: 0.8157 (mtm) REVERT: N 169 TYR cc_start: 0.7354 (t80) cc_final: 0.7046 (t80) REVERT: N 268 MET cc_start: 0.7173 (ppp) cc_final: 0.6909 (ppp) REVERT: K 76 PHE cc_start: 0.8480 (m-80) cc_final: 0.8237 (m-10) REVERT: L 64 ARG cc_start: 0.0767 (OUTLIER) cc_final: 0.0455 (tpm170) outliers start: 11 outliers final: 4 residues processed: 174 average time/residue: 0.1778 time to fit residues: 50.7729 Evaluate side-chains 130 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 205 MET Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain L residue 64 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 163 ASN J 196 GLN ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.066350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.052562 restraints weight = 174366.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.053872 restraints weight = 96198.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.054709 restraints weight = 65147.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.055244 restraints weight = 50324.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.055553 restraints weight = 42583.870| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27356 Z= 0.184 Angle : 0.673 10.432 37514 Z= 0.350 Chirality : 0.042 0.200 4078 Planarity : 0.004 0.060 4495 Dihedral : 16.981 175.108 4768 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.58 % Favored : 88.22 % Rotamer: Outliers : 1.10 % Allowed : 11.34 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.15), residues: 2980 helix: 0.55 (0.18), residues: 882 sheet: -1.65 (0.35), residues: 229 loop : -2.67 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 159 TYR 0.020 0.002 TYR B 169 PHE 0.021 0.002 PHE K 76 TRP 0.033 0.002 TRP N 237 HIS 0.008 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00406 (27356) covalent geometry : angle 0.67299 (37514) hydrogen bonds : bond 0.05688 ( 766) hydrogen bonds : angle 5.28461 ( 2101) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7343 (m-10) cc_final: 0.6948 (m-10) REVERT: D 279 MET cc_start: 0.4974 (ptt) cc_final: 0.4718 (ptp) REVERT: N 49 MET cc_start: 0.8492 (mtm) cc_final: 0.8020 (mtm) REVERT: N 169 TYR cc_start: 0.7634 (t80) cc_final: 0.7161 (t80) REVERT: N 226 TYR cc_start: 0.6059 (p90) cc_final: 0.5701 (p90) REVERT: N 268 MET cc_start: 0.7279 (ppp) cc_final: 0.6997 (ppp) REVERT: L 95 LYS cc_start: 0.8722 (pptt) cc_final: 0.8304 (mttm) outliers start: 28 outliers final: 16 residues processed: 152 average time/residue: 0.1651 time to fit residues: 42.2502 Evaluate side-chains 132 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain O residue 178 CYS Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 265 VAL Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 43 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 299 optimal weight: 6.9990 chunk 271 optimal weight: 0.7980 chunk 268 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 61 optimal weight: 0.0000 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN ** L 70 GLN ** 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 = 0.3780 r_free = 0.3780 target = 0.066691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.052803 restraints weight = 174044.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.054144 restraints weight = 96875.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.054966 restraints weight = 65483.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.055432 restraints weight = 50827.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.055814 restraints weight = 43592.065| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27356 Z= 0.137 Angle : 0.626 10.758 37514 Z= 0.322 Chirality : 0.040 0.168 4078 Planarity : 0.004 0.062 4495 Dihedral : 16.937 172.791 4757 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.23 % Favored : 89.56 % Rotamer: Outliers : 1.45 % Allowed : 15.69 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.15), residues: 2980 helix: 0.64 (0.18), residues: 887 sheet: -1.55 (0.38), residues: 202 loop : -2.70 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 266 TYR 0.019 0.001 TYR A 14 PHE 0.038 0.001 PHE D 92 TRP 0.041 0.001 TRP H 237 HIS 0.008 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00300 (27356) covalent geometry : angle 0.62577 (37514) hydrogen bonds : bond 0.04407 ( 766) hydrogen bonds : angle 4.82654 ( 2101) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 147 MET cc_start: 0.9046 (tmm) cc_final: 0.8572 (tmm) REVERT: A 98 TYR cc_start: 0.7354 (m-10) cc_final: 0.6778 (m-10) REVERT: D 279 MET cc_start: 0.4958 (ptt) cc_final: 0.4719 (ptp) REVERT: N 49 MET cc_start: 0.8428 (mtm) cc_final: 0.7988 (mtm) REVERT: N 169 TYR cc_start: 0.7577 (t80) cc_final: 0.7131 (t80) REVERT: N 226 TYR cc_start: 0.5972 (p90) cc_final: 0.5711 (p90) REVERT: N 268 MET cc_start: 0.7375 (ppp) cc_final: 0.7027 (ppp) REVERT: H 119 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8879 (mp) REVERT: H 268 MET cc_start: 0.7973 (tmm) cc_final: 0.7698 (tmm) REVERT: I 119 ILE cc_start: 0.9270 (mm) cc_final: 0.9010 (mp) REVERT: L 95 LYS cc_start: 0.8831 (pptt) cc_final: 0.8563 (pptt) REVERT: M 53 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7976 (mm-30) outliers start: 37 outliers final: 22 residues processed: 165 average time/residue: 0.1559 time to fit residues: 44.1128 Evaluate side-chains 142 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 275 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain O residue 103 ASP Chi-restraints excluded: chain O residue 178 CYS Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain M residue 53 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 184 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 260 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.066788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.052915 restraints weight = 173035.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.054229 restraints weight = 96638.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.055061 restraints weight = 65611.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.055553 restraints weight = 50808.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.055913 restraints weight = 43299.348| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27356 Z= 0.124 Angle : 0.612 11.080 37514 Z= 0.314 Chirality : 0.040 0.168 4078 Planarity : 0.004 0.062 4495 Dihedral : 16.983 173.622 4757 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.84 % Favored : 88.96 % Rotamer: Outliers : 2.00 % Allowed : 17.18 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.15), residues: 2980 helix: 0.47 (0.18), residues: 914 sheet: -1.48 (0.40), residues: 191 loop : -2.74 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 242 TYR 0.019 0.001 TYR B 169 PHE 0.020 0.001 PHE O 94 TRP 0.040 0.001 TRP H 237 HIS 0.008 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00272 (27356) covalent geometry : angle 0.61168 (37514) hydrogen bonds : bond 0.04027 ( 766) hydrogen bonds : angle 4.64237 ( 2101) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7080 (m-10) cc_final: 0.6600 (m-10) REVERT: D 279 MET cc_start: 0.5161 (ptt) cc_final: 0.4848 (ptp) REVERT: N 49 MET cc_start: 0.8450 (mtm) cc_final: 0.8007 (mtm) REVERT: N 56 MET cc_start: 0.9229 (tpp) cc_final: 0.8995 (mmm) REVERT: N 169 TYR cc_start: 0.7564 (t80) cc_final: 0.7066 (t80) REVERT: N 268 MET cc_start: 0.7652 (ppp) cc_final: 0.7307 (ppp) REVERT: H 119 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8752 (mp) REVERT: I 119 ILE cc_start: 0.9292 (mm) cc_final: 0.9036 (mp) REVERT: L 95 LYS cc_start: 0.8523 (pptt) cc_final: 0.8233 (pptt) REVERT: M 53 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8088 (mm-30) outliers start: 51 outliers final: 28 residues processed: 169 average time/residue: 0.1377 time to fit residues: 40.0895 Evaluate side-chains 151 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 205 MET Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 291 PHE Chi-restraints excluded: chain O residue 103 ASP Chi-restraints excluded: chain O residue 178 CYS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain M residue 53 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 95 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 158 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 288 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 GLN ** 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 = 0.3779 r_free = 0.3779 target = 0.066891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.052887 restraints weight = 174002.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.054184 restraints weight = 97141.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.055023 restraints weight = 66522.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.055566 restraints weight = 51699.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.055912 restraints weight = 43736.847| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27356 Z= 0.131 Angle : 0.623 14.647 37514 Z= 0.317 Chirality : 0.040 0.162 4078 Planarity : 0.004 0.064 4495 Dihedral : 16.980 174.005 4757 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.54 % Favored : 89.23 % Rotamer: Outliers : 2.16 % Allowed : 18.63 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.15), residues: 2980 helix: 0.39 (0.18), residues: 927 sheet: -1.61 (0.36), residues: 239 loop : -2.72 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 217 TYR 0.018 0.001 TYR A 14 PHE 0.045 0.001 PHE D 92 TRP 0.045 0.001 TRP N 237 HIS 0.008 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00288 (27356) covalent geometry : angle 0.62300 (37514) hydrogen bonds : bond 0.03960 ( 766) hydrogen bonds : angle 4.54808 ( 2101) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 202 LEU cc_start: 0.6899 (pt) cc_final: 0.6345 (tp) REVERT: A 98 TYR cc_start: 0.7271 (m-10) cc_final: 0.6522 (m-10) REVERT: D 279 MET cc_start: 0.5291 (ptt) cc_final: 0.4926 (ptp) REVERT: N 56 MET cc_start: 0.9237 (tpp) cc_final: 0.9017 (mmm) REVERT: N 169 TYR cc_start: 0.7634 (t80) cc_final: 0.7287 (t80) REVERT: N 226 TYR cc_start: 0.5444 (p90) cc_final: 0.5214 (p90) REVERT: H 119 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8734 (mp) REVERT: H 268 MET cc_start: 0.8129 (tmm) cc_final: 0.7769 (tmm) REVERT: I 119 ILE cc_start: 0.9298 (mm) cc_final: 0.9045 (mp) REVERT: L 22 PHE cc_start: 0.8377 (m-80) cc_final: 0.8169 (m-80) REVERT: L 95 LYS cc_start: 0.8524 (pptt) cc_final: 0.8216 (pptt) REVERT: M 53 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7934 (mm-30) outliers start: 55 outliers final: 38 residues processed: 172 average time/residue: 0.1432 time to fit residues: 42.2966 Evaluate side-chains 161 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 291 PHE Chi-restraints excluded: chain O residue 103 ASP Chi-restraints excluded: chain O residue 178 CYS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 159 HIS Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain M residue 53 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 241 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 277 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 220 optimal weight: 0.0970 chunk 148 optimal weight: 0.9980 chunk 227 optimal weight: 0.0020 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.067278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.053307 restraints weight = 173701.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.054621 restraints weight = 97403.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.055456 restraints weight = 66243.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.055957 restraints weight = 51477.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.056341 restraints weight = 43877.330| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27356 Z= 0.118 Angle : 0.614 11.279 37514 Z= 0.312 Chirality : 0.039 0.172 4078 Planarity : 0.004 0.064 4495 Dihedral : 16.947 171.993 4757 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.47 % Favored : 89.30 % Rotamer: Outliers : 2.55 % Allowed : 19.34 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.15), residues: 2980 helix: 0.42 (0.18), residues: 922 sheet: -1.52 (0.39), residues: 194 loop : -2.76 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.017 0.001 TYR A 14 PHE 0.040 0.001 PHE O 209 TRP 0.043 0.001 TRP H 237 HIS 0.008 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00260 (27356) covalent geometry : angle 0.61421 (37514) hydrogen bonds : bond 0.03794 ( 766) hydrogen bonds : angle 4.46635 ( 2101) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 130 time to evaluate : 0.958 Fit side-chains REVERT: J 202 LEU cc_start: 0.7216 (pt) cc_final: 0.6699 (tp) REVERT: A 98 TYR cc_start: 0.7318 (m-10) cc_final: 0.6576 (m-10) REVERT: A 181 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5985 (mt) REVERT: D 279 MET cc_start: 0.5184 (ptt) cc_final: 0.4831 (ptp) REVERT: N 56 MET cc_start: 0.9179 (tpp) cc_final: 0.8947 (mmm) REVERT: N 226 TYR cc_start: 0.5513 (p90) cc_final: 0.5305 (p90) REVERT: O 107 MET cc_start: 0.8457 (mmm) cc_final: 0.8206 (mmm) REVERT: H 119 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8729 (mp) REVERT: H 268 MET cc_start: 0.7961 (tmm) cc_final: 0.7399 (tmm) REVERT: I 119 ILE cc_start: 0.9292 (mm) cc_final: 0.9052 (mp) REVERT: K 55 VAL cc_start: 0.8760 (t) cc_final: 0.8448 (p) REVERT: L 22 PHE cc_start: 0.8383 (m-80) cc_final: 0.8141 (m-80) REVERT: L 95 LYS cc_start: 0.8479 (pptt) cc_final: 0.8207 (pptt) REVERT: M 53 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8042 (mm-30) outliers start: 65 outliers final: 45 residues processed: 179 average time/residue: 0.1429 time to fit residues: 44.0941 Evaluate side-chains 170 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 458 HIS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 291 PHE Chi-restraints excluded: chain O residue 103 ASP Chi-restraints excluded: chain O residue 178 CYS Chi-restraints excluded: chain O residue 212 ARG Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 159 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain M residue 53 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 191 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 50 ASN A 147 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.065378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.051419 restraints weight = 174215.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.052683 restraints weight = 96951.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.053480 restraints weight = 66250.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.054000 restraints weight = 51720.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.054352 restraints weight = 44002.301| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27356 Z= 0.181 Angle : 0.668 9.478 37514 Z= 0.345 Chirality : 0.041 0.205 4078 Planarity : 0.004 0.067 4495 Dihedral : 17.035 173.548 4756 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.25 % Favored : 87.52 % Rotamer: Outliers : 2.55 % Allowed : 20.28 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.15), residues: 2980 helix: 0.49 (0.18), residues: 907 sheet: -1.54 (0.33), residues: 265 loop : -2.74 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 217 TYR 0.019 0.001 TYR A 14 PHE 0.048 0.002 PHE D 92 TRP 0.054 0.002 TRP N 237 HIS 0.009 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00398 (27356) covalent geometry : angle 0.66785 (37514) hydrogen bonds : bond 0.04236 ( 766) hydrogen bonds : angle 4.65761 ( 2101) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 124 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 202 LEU cc_start: 0.7138 (pt) cc_final: 0.6605 (tp) REVERT: J 224 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9136 (mm) REVERT: A 98 TYR cc_start: 0.7485 (m-10) cc_final: 0.6487 (m-10) REVERT: B 206 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8392 (p90) REVERT: D 279 MET cc_start: 0.5427 (ptt) cc_final: 0.4967 (ptp) REVERT: N 56 MET cc_start: 0.9208 (tpp) cc_final: 0.8968 (mmm) REVERT: N 226 TYR cc_start: 0.5255 (p90) cc_final: 0.4990 (p90) REVERT: H 268 MET cc_start: 0.7902 (tmm) cc_final: 0.7551 (ppp) REVERT: I 119 ILE cc_start: 0.9316 (mm) cc_final: 0.9058 (mp) REVERT: K 55 VAL cc_start: 0.8804 (t) cc_final: 0.8571 (p) REVERT: M 53 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: M 98 GLN cc_start: 0.2816 (OUTLIER) cc_final: 0.1259 (pp30) outliers start: 65 outliers final: 47 residues processed: 176 average time/residue: 0.1527 time to fit residues: 46.4730 Evaluate side-chains 168 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 117 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 458 HIS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 291 PHE Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 103 ASP Chi-restraints excluded: chain O residue 178 CYS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 159 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain M residue 98 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 97 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 65 ASN H 202 HIS ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** 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 = 0.3726 r_free = 0.3726 target = 0.064626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.050586 restraints weight = 174497.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.051859 restraints weight = 97393.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.052675 restraints weight = 66724.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.053167 restraints weight = 51879.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.053539 restraints weight = 44296.695| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27356 Z= 0.210 Angle : 0.702 10.485 37514 Z= 0.362 Chirality : 0.042 0.187 4078 Planarity : 0.005 0.069 4495 Dihedral : 17.133 172.742 4756 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.48 % Favored : 87.28 % Rotamer: Outliers : 3.06 % Allowed : 20.48 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.15), residues: 2980 helix: 0.48 (0.18), residues: 900 sheet: -1.91 (0.28), residues: 347 loop : -2.77 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 217 TYR 0.019 0.002 TYR B 138 PHE 0.039 0.002 PHE O 209 TRP 0.051 0.002 TRP H 237 HIS 0.010 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00461 (27356) covalent geometry : angle 0.70208 (37514) hydrogen bonds : bond 0.04418 ( 766) hydrogen bonds : angle 4.79608 ( 2101) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 122 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8350 (p90) REVERT: D 11 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8579 (pp) REVERT: D 279 MET cc_start: 0.5744 (ptt) cc_final: 0.5183 (ptt) REVERT: N 7 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7192 (p90) REVERT: N 56 MET cc_start: 0.9197 (tpp) cc_final: 0.8932 (mmm) REVERT: N 124 MET cc_start: 0.8673 (pmm) cc_final: 0.8115 (pmm) REVERT: N 226 TYR cc_start: 0.5234 (p90) cc_final: 0.4966 (p90) REVERT: H 268 MET cc_start: 0.7868 (tmm) cc_final: 0.7501 (ppp) REVERT: I 119 ILE cc_start: 0.9382 (mm) cc_final: 0.9119 (mp) REVERT: L 22 PHE cc_start: 0.8386 (m-80) cc_final: 0.8157 (m-80) REVERT: L 95 LYS cc_start: 0.8975 (pptt) cc_final: 0.8749 (pptt) REVERT: M 53 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7991 (mm-30) outliers start: 78 outliers final: 55 residues processed: 184 average time/residue: 0.1496 time to fit residues: 46.5737 Evaluate side-chains 175 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain J residue 458 HIS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 291 PHE Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 103 ASP Chi-restraints excluded: chain O residue 178 CYS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain O residue 265 VAL Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 159 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 53 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 198 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 299 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 189 optimal weight: 0.0670 chunk 238 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.6924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.065780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.051787 restraints weight = 173801.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.053107 restraints weight = 96567.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.053926 restraints weight = 65276.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.054465 restraints weight = 50702.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.054803 restraints weight = 42897.141| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27356 Z= 0.137 Angle : 0.665 11.032 37514 Z= 0.337 Chirality : 0.041 0.189 4078 Planarity : 0.004 0.069 4495 Dihedral : 17.085 172.772 4756 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.68 % Favored : 88.09 % Rotamer: Outliers : 2.86 % Allowed : 21.11 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.15), residues: 2980 helix: 0.33 (0.18), residues: 923 sheet: -1.86 (0.28), residues: 343 loop : -2.76 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG N 116 TYR 0.018 0.001 TYR B 138 PHE 0.051 0.002 PHE D 92 TRP 0.079 0.002 TRP N 237 HIS 0.010 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00304 (27356) covalent geometry : angle 0.66454 (37514) hydrogen bonds : bond 0.04034 ( 766) hydrogen bonds : angle 4.59260 ( 2101) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 121 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 224 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8960 (mm) REVERT: A 98 TYR cc_start: 0.7461 (m-10) cc_final: 0.6532 (m-10) REVERT: A 147 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: B 79 PHE cc_start: 0.6695 (t80) cc_final: 0.6365 (t80) REVERT: D 11 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8522 (pp) REVERT: D 97 MET cc_start: 0.8203 (ppp) cc_final: 0.7736 (ppp) REVERT: D 279 MET cc_start: 0.5345 (ptt) cc_final: 0.4815 (ptt) REVERT: N 56 MET cc_start: 0.9151 (tpp) cc_final: 0.8930 (mmm) REVERT: N 124 MET cc_start: 0.8641 (pmm) cc_final: 0.8183 (pmm) REVERT: N 226 TYR cc_start: 0.5243 (p90) cc_final: 0.5017 (p90) REVERT: H 268 MET cc_start: 0.7809 (tmm) cc_final: 0.7147 (tmm) REVERT: I 119 ILE cc_start: 0.9334 (mm) cc_final: 0.9087 (mp) REVERT: L 22 PHE cc_start: 0.8306 (m-80) cc_final: 0.8047 (m-80) REVERT: M 53 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7960 (mm-30) outliers start: 73 outliers final: 56 residues processed: 178 average time/residue: 0.1403 time to fit residues: 42.9411 Evaluate side-chains 176 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 116 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 458 HIS Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 291 PHE Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 103 ASP Chi-restraints excluded: chain O residue 178 CYS Chi-restraints excluded: chain O residue 212 ARG Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain O residue 265 VAL Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 159 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain L residue 81 TYR Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain M residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 193 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.065186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.051148 restraints weight = 173904.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.052455 restraints weight = 96282.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.053267 restraints weight = 65632.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.053742 restraints weight = 51012.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.054118 restraints weight = 43773.300| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27356 Z= 0.167 Angle : 0.688 11.407 37514 Z= 0.350 Chirality : 0.042 0.218 4078 Planarity : 0.004 0.070 4495 Dihedral : 17.103 173.390 4756 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.52 % Favored : 87.25 % Rotamer: Outliers : 2.47 % Allowed : 21.69 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.15), residues: 2980 helix: 0.40 (0.18), residues: 906 sheet: -1.89 (0.28), residues: 343 loop : -2.75 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG N 116 TYR 0.020 0.001 TYR D 169 PHE 0.035 0.002 PHE O 209 TRP 0.075 0.002 TRP N 237 HIS 0.010 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00369 (27356) covalent geometry : angle 0.68770 (37514) hydrogen bonds : bond 0.04179 ( 766) hydrogen bonds : angle 4.70203 ( 2101) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 118 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 224 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9016 (mm) REVERT: B 79 PHE cc_start: 0.6779 (t80) cc_final: 0.6428 (t80) REVERT: D 11 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8535 (pp) REVERT: D 97 MET cc_start: 0.8158 (ppp) cc_final: 0.7677 (ppp) REVERT: D 279 MET cc_start: 0.5552 (ptt) cc_final: 0.5046 (ptt) REVERT: N 7 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7154 (p90) REVERT: N 56 MET cc_start: 0.9153 (tpp) cc_final: 0.8891 (mmm) REVERT: N 124 MET cc_start: 0.8625 (pmm) cc_final: 0.8345 (pmm) REVERT: H 268 MET cc_start: 0.7702 (tmm) cc_final: 0.7017 (tmm) REVERT: I 119 ILE cc_start: 0.9358 (mm) cc_final: 0.9104 (mp) REVERT: L 13 GLU cc_start: 0.9011 (pp20) cc_final: 0.8724 (pp20) REVERT: L 22 PHE cc_start: 0.8525 (m-80) cc_final: 0.8174 (m-80) REVERT: M 53 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7956 (mm-30) outliers start: 63 outliers final: 53 residues processed: 167 average time/residue: 0.1463 time to fit residues: 41.9475 Evaluate side-chains 172 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 115 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 458 HIS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 291 PHE Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 103 ASP Chi-restraints excluded: chain O residue 178 CYS Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 223 VAL Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain O residue 265 VAL Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 159 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain L residue 81 TYR Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain M residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 218 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 125 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.065374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.051406 restraints weight = 173260.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.052722 restraints weight = 96018.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.053499 restraints weight = 65159.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.054041 restraints weight = 50859.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.054365 restraints weight = 43224.048| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27356 Z= 0.155 Angle : 0.679 11.758 37514 Z= 0.345 Chirality : 0.042 0.244 4078 Planarity : 0.004 0.070 4495 Dihedral : 17.127 173.267 4756 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.98 % Favored : 87.79 % Rotamer: Outliers : 2.63 % Allowed : 21.58 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.15), residues: 2980 helix: 0.22 (0.18), residues: 932 sheet: -1.88 (0.28), residues: 353 loop : -2.78 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG N 116 TYR 0.019 0.001 TYR B 138 PHE 0.060 0.002 PHE D 92 TRP 0.071 0.002 TRP H 237 HIS 0.010 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00344 (27356) covalent geometry : angle 0.67919 (37514) hydrogen bonds : bond 0.04032 ( 766) hydrogen bonds : angle 4.65478 ( 2101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4451.23 seconds wall clock time: 77 minutes 54.40 seconds (4674.40 seconds total)