Starting phenix.real_space_refine on Sun May 25 06:13:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ip0_35629/05_2025/8ip0_35629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ip0_35629/05_2025/8ip0_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_35629/05_2025/8ip0_35629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ip0_35629/05_2025/8ip0_35629.map" model { file = "/net/cci-nas-00/data/ceres_data/8ip0_35629/05_2025/8ip0_35629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ip0_35629/05_2025/8ip0_35629.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.30, per 1000 atoms: 0.58 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: 6.36 Conformation dependent library (CDL) restraints added in 3.1 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: 8.64 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: 7.97 Time building geometry restraints manager: 7.42 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: 0.010 Normalize map: mean=0, sd=1: 2.090 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: 0.970 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 59.860 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.210 ------------------------------------------------------------------------------- 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 : 18.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.038 0.001 TRP N 237 HIS 0.009 0.001 HIS B 202 PHE 0.038 0.001 PHE L 22 TYR 0.019 0.001 TYR L 48 ARG 0.005 0.000 ARG H 242 Details of bonding type rmsd hydrogen bonds : bond 0.20482 ( 766) hydrogen bonds : angle 7.13767 ( 2101) covalent geometry : bond 0.00258 (27356) covalent geometry : angle 0.66228 (37514) *********************** 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 : 2.814 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: 0.3619 time to fit residues: 102.2416 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 : 2.692 ------------------------------------------------------------------------------- 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 258 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 128 optimal weight: 0.0000 chunk 79 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 overall best weight: 2.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 196 GLN ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** 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** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.066250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.052416 restraints weight = 174204.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.053739 restraints weight = 96290.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.054591 restraints weight = 65240.840| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1552 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= 0.187 Angle : 0.690 10.140 37514 Z= 0.359 Chirality : 0.042 0.197 4078 Planarity : 0.005 0.060 4495 Dihedral : 17.005 175.730 4768 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.64 % Favored : 88.15 % Rotamer: Outliers : 1.18 % Allowed : 11.34 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 2980 helix: 0.51 (0.18), residues: 892 sheet: -1.77 (0.35), residues: 234 loop : -2.69 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP N 237 HIS 0.009 0.001 HIS B 202 PHE 0.023 0.002 PHE K 76 TYR 0.022 0.002 TYR B 169 ARG 0.008 0.001 ARG N 116 Details of bonding type rmsd hydrogen bonds : bond 0.05346 ( 766) hydrogen bonds : angle 5.23779 ( 2101) covalent geometry : bond 0.00414 (27356) covalent geometry : angle 0.68954 (37514) *********************** 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 163 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 2.741 Fit side-chains revert: symmetry clash REVERT: J 163 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8700 (p0) REVERT: A 98 TYR cc_start: 0.7376 (m-10) cc_final: 0.6949 (m-10) REVERT: D 279 MET cc_start: 0.4927 (ptt) cc_final: 0.4681 (ptp) REVERT: N 49 MET cc_start: 0.8454 (mtm) cc_final: 0.7828 (mtm) REVERT: N 169 TYR cc_start: 0.7625 (t80) cc_final: 0.7165 (t80) REVERT: N 226 TYR cc_start: 0.5991 (p90) cc_final: 0.5624 (p90) REVERT: N 268 MET cc_start: 0.7367 (ppp) cc_final: 0.7130 (ppp) REVERT: H 268 MET cc_start: 0.7996 (tmm) cc_final: 0.7786 (tmm) REVERT: I 119 ILE cc_start: 0.9224 (mm) cc_final: 0.8973 (mp) REVERT: L 72 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7237 (m-80) outliers start: 30 outliers final: 16 residues processed: 153 average time/residue: 0.3379 time to fit residues: 86.1401 Evaluate side-chains 134 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 163 ASN 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 214 VAL Chi-restraints excluded: chain L residue 72 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 78 optimal weight: 0.0570 chunk 171 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 243 optimal weight: 0.9980 chunk 294 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 120 optimal weight: 10.0000 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 163 ASN ** 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** C 272 GLN ** 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** 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 = 0.3810 r_free = 0.3810 target = 0.067817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.054149 restraints weight = 174055.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.055488 restraints weight = 97594.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.056337 restraints weight = 66412.841| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27356 Z= 0.113 Angle : 0.611 10.795 37514 Z= 0.311 Chirality : 0.040 0.170 4078 Planarity : 0.004 0.060 4495 Dihedral : 16.897 173.476 4757 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.23 % Favored : 90.57 % Rotamer: Outliers : 1.41 % Allowed : 15.50 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.15), residues: 2980 helix: 0.46 (0.18), residues: 918 sheet: -1.37 (0.39), residues: 195 loop : -2.73 (0.13), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H 237 HIS 0.007 0.001 HIS B 202 PHE 0.037 0.001 PHE D 92 TYR 0.017 0.001 TYR B 169 ARG 0.003 0.000 ARG O 266 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 766) hydrogen bonds : angle 4.71984 ( 2101) covalent geometry : bond 0.00242 (27356) covalent geometry : angle 0.61129 (37514) *********************** 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 185 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 147 MET cc_start: 0.8851 (tmm) cc_final: 0.8477 (tmm) REVERT: A 98 TYR cc_start: 0.7230 (m-10) cc_final: 0.6731 (m-10) REVERT: B 214 VAL cc_start: 0.9219 (p) cc_final: 0.8966 (p) REVERT: D 279 MET cc_start: 0.4618 (ptt) cc_final: 0.4276 (ptp) REVERT: N 49 MET cc_start: 0.8461 (mtm) cc_final: 0.8072 (mtm) REVERT: N 169 TYR cc_start: 0.7363 (t80) cc_final: 0.6919 (t80) REVERT: N 268 MET cc_start: 0.7589 (ppp) cc_final: 0.7244 (ppp) REVERT: H 119 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8862 (mp) REVERT: H 268 MET cc_start: 0.7890 (tmm) cc_final: 0.7620 (tmm) REVERT: I 119 ILE cc_start: 0.9310 (mm) cc_final: 0.9046 (mp) REVERT: L 72 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7138 (m-80) REVERT: L 95 LYS cc_start: 0.8817 (pptt) cc_final: 0.8298 (mttp) REVERT: M 53 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8089 (mm-30) outliers start: 36 outliers final: 18 residues processed: 175 average time/residue: 0.3152 time to fit residues: 93.8569 Evaluate side-chains 146 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain B residue 90 ASP 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 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 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 L residue 72 PHE 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 297 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 293 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 208 ASN B 65 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** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 HIS ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3743 r_free = 0.3743 target = 0.065448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.051411 restraints weight = 175680.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.052687 restraints weight = 97778.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.053510 restraints weight = 66867.294| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 27356 Z= 0.206 Angle : 0.674 9.788 37514 Z= 0.351 Chirality : 0.041 0.169 4078 Planarity : 0.005 0.063 4495 Dihedral : 17.078 173.739 4757 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.42 % Favored : 87.38 % Rotamer: Outliers : 2.08 % Allowed : 17.61 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 2980 helix: 0.54 (0.18), residues: 889 sheet: -2.06 (0.26), residues: 380 loop : -2.71 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 237 HIS 0.009 0.001 HIS B 202 PHE 0.029 0.002 PHE H 167 TYR 0.021 0.002 TYR C 206 ARG 0.008 0.001 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 766) hydrogen bonds : angle 4.90082 ( 2101) covalent geometry : bond 0.00453 (27356) covalent geometry : angle 0.67394 (37514) *********************** 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: 53 poor density : 124 time to evaluate : 2.932 Fit side-chains revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7338 (m-10) cc_final: 0.6855 (m-10) REVERT: B 217 ARG cc_start: 0.6993 (mtt90) cc_final: 0.6535 (mtt90) REVERT: D 279 MET cc_start: 0.5463 (ptt) cc_final: 0.4668 (ptt) REVERT: N 226 TYR cc_start: 0.5428 (p90) cc_final: 0.5087 (p90) REVERT: H 119 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8958 (mp) REVERT: H 139 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: H 268 MET cc_start: 0.7813 (tmm) cc_final: 0.7570 (ppp) REVERT: I 119 ILE cc_start: 0.9387 (mm) cc_final: 0.9119 (mp) REVERT: M 53 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8077 (mm-30) outliers start: 53 outliers final: 31 residues processed: 169 average time/residue: 0.3445 time to fit residues: 98.2201 Evaluate side-chains 146 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 205 MET 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 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 C residue 188 LEU 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 132 LYS Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 LEU 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 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 139 GLN 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 223 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 62 optimal weight: 0.0370 chunk 190 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 164 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 233 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 159 HIS ** B 275 GLN ** 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.067272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.053437 restraints weight = 171828.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.054748 restraints weight = 95339.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.055606 restraints weight = 64790.890| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27356 Z= 0.114 Angle : 0.627 15.715 37514 Z= 0.316 Chirality : 0.040 0.165 4078 Planarity : 0.004 0.063 4495 Dihedral : 16.976 172.603 4757 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.00 % Favored : 89.77 % Rotamer: Outliers : 2.00 % Allowed : 19.34 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.15), residues: 2980 helix: 0.44 (0.18), residues: 918 sheet: -1.54 (0.39), residues: 194 loop : -2.75 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP N 237 HIS 0.008 0.001 HIS B 202 PHE 0.043 0.001 PHE D 92 TYR 0.019 0.001 TYR D 169 ARG 0.003 0.000 ARG O 266 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 766) hydrogen bonds : angle 4.51728 ( 2101) covalent geometry : bond 0.00242 (27356) covalent geometry : angle 0.62657 (37514) *********************** 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 183 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 2.917 Fit side-chains revert: symmetry clash REVERT: J 202 LEU cc_start: 0.6865 (pt) cc_final: 0.6293 (tp) REVERT: A 98 TYR cc_start: 0.7210 (m-10) cc_final: 0.6440 (m-10) REVERT: B 137 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7859 (t80) REVERT: D 279 MET cc_start: 0.5081 (ptt) cc_final: 0.4747 (ptp) REVERT: N 56 MET cc_start: 0.9221 (tpp) cc_final: 0.8961 (mmm) REVERT: N 226 TYR cc_start: 0.5370 (p90) cc_final: 0.5050 (p90) REVERT: H 119 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8733 (mp) REVERT: H 268 MET cc_start: 0.7822 (tmm) cc_final: 0.7222 (tmm) REVERT: I 119 ILE cc_start: 0.9310 (mm) cc_final: 0.9062 (mp) REVERT: L 13 GLU cc_start: 0.8990 (pp20) cc_final: 0.8765 (pp20) REVERT: M 53 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7935 (mm-30) outliers start: 51 outliers final: 32 residues processed: 171 average time/residue: 0.3283 time to fit residues: 95.3343 Evaluate side-chains 156 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 207 VAL 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 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 C residue 188 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 75 LEU 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 255 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 21 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 270 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 188 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** 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** D 19 ASN D 65 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS ** 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 = 0.3800 r_free = 0.3800 target = 0.067676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.053659 restraints weight = 173351.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.054976 restraints weight = 96946.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.055823 restraints weight = 66130.153| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27356 Z= 0.111 Angle : 0.606 9.191 37514 Z= 0.307 Chirality : 0.039 0.160 4078 Planarity : 0.004 0.064 4495 Dihedral : 16.926 174.208 4757 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.60 % Favored : 89.16 % Rotamer: Outliers : 2.04 % Allowed : 20.20 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.15), residues: 2980 helix: 0.36 (0.18), residues: 939 sheet: -1.35 (0.35), residues: 243 loop : -2.72 (0.13), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP H 237 HIS 0.007 0.001 HIS B 202 PHE 0.027 0.001 PHE O 209 TYR 0.016 0.001 TYR A 14 ARG 0.004 0.000 ARG N 116 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 766) hydrogen bonds : angle 4.42786 ( 2101) covalent geometry : bond 0.00242 (27356) covalent geometry : angle 0.60599 (37514) *********************** 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 184 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7284 (m-10) cc_final: 0.6501 (m-10) REVERT: A 181 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6042 (mt) REVERT: D 279 MET cc_start: 0.5066 (ptt) cc_final: 0.4677 (ptp) REVERT: N 56 MET cc_start: 0.9229 (tpp) cc_final: 0.8990 (mmm) REVERT: N 226 TYR cc_start: 0.5323 (p90) cc_final: 0.5102 (p90) REVERT: O 107 MET cc_start: 0.8437 (mmm) cc_final: 0.8168 (mmm) REVERT: H 119 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8772 (mp) REVERT: H 268 MET cc_start: 0.7740 (tmm) cc_final: 0.7281 (tmm) REVERT: K 41 ASN cc_start: 0.8580 (m110) cc_final: 0.8242 (m110) REVERT: M 53 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7944 (mm-30) outliers start: 52 outliers final: 35 residues processed: 173 average time/residue: 0.3274 time to fit residues: 96.6367 Evaluate side-chains 162 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain J residue 458 HIS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 214 VAL 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 C residue 188 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain N residue 6 LEU 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 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 43 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 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 31 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 226 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 288 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 287 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 219 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 19 ASN ** 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 ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** 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 = 0.3801 r_free = 0.3801 target = 0.067849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.053798 restraints weight = 176884.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.055155 restraints weight = 99648.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.055941 restraints weight = 68205.638| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27356 Z= 0.110 Angle : 0.608 9.321 37514 Z= 0.307 Chirality : 0.039 0.213 4078 Planarity : 0.004 0.064 4495 Dihedral : 16.883 174.903 4757 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.77 % Favored : 90.00 % Rotamer: Outliers : 2.16 % Allowed : 20.99 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.15), residues: 2980 helix: 0.39 (0.18), residues: 940 sheet: -1.31 (0.35), residues: 243 loop : -2.72 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP N 237 HIS 0.007 0.001 HIS B 202 PHE 0.049 0.001 PHE D 92 TYR 0.016 0.001 TYR A 14 ARG 0.003 0.000 ARG N 242 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 766) hydrogen bonds : angle 4.35517 ( 2101) covalent geometry : bond 0.00239 (27356) covalent geometry : angle 0.60796 (37514) *********************** 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 184 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 224 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9044 (mm) REVERT: A 98 TYR cc_start: 0.7361 (m-10) cc_final: 0.6333 (m-10) REVERT: B 79 PHE cc_start: 0.6512 (t80) cc_final: 0.6245 (t80) REVERT: C 49 MET cc_start: 0.8646 (mpp) cc_final: 0.8432 (mpp) REVERT: D 3 ASN cc_start: 0.5296 (OUTLIER) cc_final: 0.5064 (t0) REVERT: D 279 MET cc_start: 0.5060 (ptt) cc_final: 0.4648 (ptp) REVERT: N 56 MET cc_start: 0.9284 (tpp) cc_final: 0.9037 (mmm) REVERT: N 268 MET cc_start: 0.8031 (ptp) cc_final: 0.7823 (ptm) REVERT: H 119 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8746 (mp) REVERT: H 268 MET cc_start: 0.7726 (tmm) cc_final: 0.7215 (tmm) REVERT: K 41 ASN cc_start: 0.8641 (m110) cc_final: 0.8308 (m110) REVERT: M 53 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: M 98 GLN cc_start: 0.2992 (OUTLIER) cc_final: 0.1527 (pp30) outliers start: 55 outliers final: 37 residues processed: 170 average time/residue: 0.3219 time to fit residues: 93.5571 Evaluate side-chains 164 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 458 HIS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 214 VAL 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 3 ASN Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 237 TRP 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 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 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 56 VAL Chi-restraints excluded: chain L residue 72 PHE 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 162 optimal weight: 8.9990 chunk 235 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 19 ASN ** 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** H 19 ASN ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** 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 = 0.3786 r_free = 0.3786 target = 0.067260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.053275 restraints weight = 177479.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.054593 restraints weight = 99948.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.055438 restraints weight = 68652.769| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2462 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= 0.125 Angle : 0.619 10.184 37514 Z= 0.313 Chirality : 0.040 0.224 4078 Planarity : 0.004 0.065 4495 Dihedral : 16.879 175.145 4756 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.50 % Favored : 89.26 % Rotamer: Outliers : 2.16 % Allowed : 21.62 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.15), residues: 2980 helix: 0.43 (0.18), residues: 934 sheet: -1.50 (0.39), residues: 195 loop : -2.77 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP N 237 HIS 0.007 0.001 HIS B 202 PHE 0.048 0.001 PHE M 92 TYR 0.017 0.001 TYR A 14 ARG 0.005 0.000 ARG N 242 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 766) hydrogen bonds : angle 4.37932 ( 2101) covalent geometry : bond 0.00275 (27356) covalent geometry : angle 0.61906 (37514) *********************** 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 180 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 224 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9088 (mm) REVERT: A 98 TYR cc_start: 0.7414 (m-10) cc_final: 0.6489 (m-10) REVERT: B 79 PHE cc_start: 0.6755 (t80) cc_final: 0.6441 (t80) REVERT: D 11 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8469 (pp) REVERT: D 279 MET cc_start: 0.5256 (ptt) cc_final: 0.4738 (ptt) REVERT: N 56 MET cc_start: 0.9249 (tpp) cc_final: 0.8995 (mmm) REVERT: H 119 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8787 (mp) REVERT: H 268 MET cc_start: 0.7742 (tmm) cc_final: 0.6994 (tmm) REVERT: K 41 ASN cc_start: 0.8614 (m110) cc_final: 0.8319 (m110) REVERT: M 53 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7940 (mm-30) outliers start: 55 outliers final: 40 residues processed: 168 average time/residue: 0.3241 time to fit residues: 92.5768 Evaluate side-chains 168 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 458 HIS Chi-restraints excluded: chain J residue 507 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 214 VAL 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 C residue 188 LEU 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 223 VAL Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 237 TRP 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 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 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 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 56 VAL Chi-restraints excluded: chain L residue 72 PHE 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 51 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 161 optimal weight: 6.9990 chunk 230 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 19 ASN ** 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** ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.067572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.053532 restraints weight = 173985.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.054854 restraints weight = 97481.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.055717 restraints weight = 66468.643| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27356 Z= 0.118 Angle : 0.622 10.757 37514 Z= 0.314 Chirality : 0.039 0.178 4078 Planarity : 0.004 0.066 4495 Dihedral : 16.867 175.121 4756 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.20 % Favored : 89.56 % Rotamer: Outliers : 2.00 % Allowed : 21.97 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.15), residues: 2980 helix: 0.43 (0.18), residues: 934 sheet: -1.31 (0.35), residues: 243 loop : -2.73 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP N 237 HIS 0.008 0.001 HIS B 202 PHE 0.054 0.001 PHE D 92 TYR 0.017 0.001 TYR A 14 ARG 0.004 0.000 ARG N 217 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 766) hydrogen bonds : angle 4.38202 ( 2101) covalent geometry : bond 0.00260 (27356) covalent geometry : angle 0.62242 (37514) *********************** 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 176 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 224 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9080 (mm) REVERT: A 98 TYR cc_start: 0.7386 (m-10) cc_final: 0.6385 (m-10) REVERT: B 79 PHE cc_start: 0.6541 (t80) cc_final: 0.6210 (t80) REVERT: D 11 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8498 (pp) REVERT: D 279 MET cc_start: 0.5150 (ptt) cc_final: 0.4678 (ptt) REVERT: N 56 MET cc_start: 0.9180 (tpp) cc_final: 0.8930 (mmm) REVERT: N 226 TYR cc_start: 0.5097 (p90) cc_final: 0.4856 (p90) REVERT: H 119 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8777 (mp) REVERT: H 268 MET cc_start: 0.7734 (tmm) cc_final: 0.7392 (tmm) REVERT: I 279 MET cc_start: 0.5375 (ptp) cc_final: 0.5139 (ptm) REVERT: K 41 ASN cc_start: 0.8602 (m110) cc_final: 0.8290 (m110) REVERT: M 53 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7925 (mm-30) outliers start: 51 outliers final: 44 residues processed: 164 average time/residue: 0.3296 time to fit residues: 91.9058 Evaluate side-chains 169 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 121 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 458 HIS Chi-restraints excluded: chain J residue 507 LEU Chi-restraints excluded: chain J residue 519 PHE Chi-restraints excluded: chain B residue 90 ASP 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 C residue 188 LEU 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 124 MET Chi-restraints excluded: chain D residue 132 LYS 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 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 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 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 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 56 VAL Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain M residue 53 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 235 optimal weight: 0.0670 chunk 51 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 98 optimal weight: 0.2980 chunk 192 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 19 ASN ** 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 ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.068412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.054446 restraints weight = 173542.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.055808 restraints weight = 97431.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.056664 restraints weight = 66209.260| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27356 Z= 0.108 Angle : 0.623 11.386 37514 Z= 0.311 Chirality : 0.039 0.263 4078 Planarity : 0.004 0.067 4495 Dihedral : 16.814 175.895 4756 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.90 % Favored : 89.87 % Rotamer: Outliers : 1.84 % Allowed : 22.28 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.15), residues: 2980 helix: 0.38 (0.18), residues: 941 sheet: -1.13 (0.36), residues: 238 loop : -2.71 (0.13), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP N 237 HIS 0.007 0.001 HIS B 202 PHE 0.025 0.001 PHE M 92 TYR 0.019 0.001 TYR B 169 ARG 0.004 0.000 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 766) hydrogen bonds : angle 4.31107 ( 2101) covalent geometry : bond 0.00236 (27356) covalent geometry : angle 0.62292 (37514) ********************** 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 182 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 202 LEU cc_start: 0.7018 (pt) cc_final: 0.6628 (tt) REVERT: J 224 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9026 (mm) REVERT: A 98 TYR cc_start: 0.7299 (m-10) cc_final: 0.6325 (m-10) REVERT: B 79 PHE cc_start: 0.6578 (t80) cc_final: 0.6240 (t80) REVERT: D 11 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8471 (pp) REVERT: D 279 MET cc_start: 0.5080 (ptt) cc_final: 0.4478 (ptp) REVERT: N 56 MET cc_start: 0.9232 (tpp) cc_final: 0.8974 (mmm) REVERT: N 226 TYR cc_start: 0.5444 (p90) cc_final: 0.5204 (p90) REVERT: H 268 MET cc_start: 0.7692 (tmm) cc_final: 0.7354 (tmm) REVERT: M 53 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7910 (mm-30) outliers start: 47 outliers final: 41 residues processed: 170 average time/residue: 0.3334 time to fit residues: 95.8323 Evaluate side-chains 167 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 458 HIS Chi-restraints excluded: chain J residue 519 PHE Chi-restraints excluded: chain B residue 90 ASP 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 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 132 LYS 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 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 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 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 53 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 283 optimal weight: 0.6980 chunk 113 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 253 optimal weight: 0.6980 chunk 284 optimal weight: 1.9990 chunk 55 optimal weight: 0.0170 chunk 159 optimal weight: 6.9990 chunk 104 optimal weight: 0.0020 chunk 49 optimal weight: 0.2980 overall best weight: 0.3426 ------------------------------------------------------------------------------- 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 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.068982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.055123 restraints weight = 174241.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.056512 restraints weight = 97647.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.057368 restraints weight = 66220.117| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27356 Z= 0.109 Angle : 0.626 11.455 37514 Z= 0.312 Chirality : 0.039 0.268 4078 Planarity : 0.004 0.067 4495 Dihedral : 16.741 176.995 4756 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.66 % Favored : 90.13 % Rotamer: Outliers : 1.80 % Allowed : 22.68 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.15), residues: 2980 helix: 0.43 (0.18), residues: 935 sheet: -1.07 (0.36), residues: 238 loop : -2.68 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP H 237 HIS 0.006 0.001 HIS B 202 PHE 0.053 0.001 PHE D 92 TYR 0.020 0.001 TYR B 169 ARG 0.003 0.000 ARG H 116 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 766) hydrogen bonds : angle 4.28579 ( 2101) covalent geometry : bond 0.00237 (27356) covalent geometry : angle 0.62599 (37514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7840.74 seconds wall clock time: 138 minutes 38.79 seconds (8318.79 seconds total)