Starting phenix.real_space_refine on Sat Jul 4 18:07:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pdz_13343/07_2026/7pdz_13343.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pdz_13343/07_2026/7pdz_13343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pdz_13343/07_2026/7pdz_13343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pdz_13343/07_2026/7pdz_13343.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7pdz_13343/07_2026/7pdz_13343.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pdz_13343/07_2026/7pdz_13343.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pdz_13343/07_2026/7pdz_13343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pdz_13343/07_2026/7pdz_13343.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 6 5.21 5 S 155 5.16 5 C 13971 2.51 5 N 3750 2.21 5 O 4287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22185 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2146 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 262} Chain: "F" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2212 Classifications: {'peptide': 272} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 261} Chain: "I" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "Q" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "S" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "S" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "T" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "T" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.31, per 1000 atoms: 0.19 Number of scatterers: 22185 At special positions: 0 Unit cell: (108.9, 94.38, 254.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 155 16.00 P 16 15.00 Mg 6 11.99 O 4287 8.00 N 3750 7.00 C 13971 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=7, symmetry=0 Links applied TRANS " DTH P 6 " - " ALA P 5 " " DTH Q 6 " - " ALA Q 5 " " DTH R 6 " - " ALA R 5 " " DTH S 6 " - " ALA S 5 " " DTH T 6 " - " ALA T 5 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 886.8 milliseconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH Q 6 " pdb=" CB DTH R 6 " pdb=" CB DTH S 6 " pdb=" CB DTH T 6 " pdb=" CB DTH P 6 " Number of C-beta restraints generated: 5202 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 37 sheets defined 50.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'E' and resid 1 through 16 Processing helix chain 'E' and resid 17 through 19 No H-bonds generated for 'chain 'E' and resid 17 through 19' Processing helix chain 'E' and resid 20 through 32 Processing helix chain 'E' and resid 35 through 43 Processing helix chain 'E' and resid 90 through 113 Processing helix chain 'E' and resid 208 through 245 removed outlier: 3.788A pdb=" N ASN E 212 " --> pdb=" O PRO E 208 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.718A pdb=" N ARG E 268 " --> pdb=" O GLU E 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 24 Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 43 through 62 removed outlier: 3.850A pdb=" N GLY F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS F 52 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN F 56 " --> pdb=" O HIS F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 134 removed outlier: 3.657A pdb=" N TRP F 120 " --> pdb=" O GLY F 116 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS F 124 " --> pdb=" O TRP F 120 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR F 131 " --> pdb=" O ALA F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 220 through 246 Processing helix chain 'F' and resid 249 through 259 Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'I' and resid 44 through 48 Processing helix chain 'I' and resid 55 through 61 Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 removed outlier: 4.086A pdb=" N HIS I 101 " --> pdb=" O PRO I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 126 removed outlier: 4.207A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU I 117 " --> pdb=" O LYS I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 145 removed outlier: 3.520A pdb=" N SER I 141 " --> pdb=" O GLN I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 181 through 196 removed outlier: 4.096A pdb=" N ARG I 196 " --> pdb=" O ILE I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 214 removed outlier: 3.530A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 233 Processing helix chain 'I' and resid 234 through 237 Processing helix chain 'I' and resid 252 through 263 removed outlier: 3.639A pdb=" N ARG I 256 " --> pdb=" O ASN I 252 " (cutoff:3.500A) Proline residue: I 258 - end of helix removed outlier: 4.683A pdb=" N LEU I 261 " --> pdb=" O CYS I 257 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE I 262 " --> pdb=" O PRO I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 268 Processing helix chain 'I' and resid 273 through 283 Processing helix chain 'I' and resid 284 through 285 No H-bonds generated for 'chain 'I' and resid 284 through 285' Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 289 through 295 removed outlier: 3.587A pdb=" N ALA I 295 " --> pdb=" O LYS I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 306 removed outlier: 4.305A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 removed outlier: 3.707A pdb=" N ALA I 319 " --> pdb=" O LYS I 315 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU I 320 " --> pdb=" O GLU I 316 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 347 Processing helix chain 'I' and resid 349 through 356 Processing helix chain 'I' and resid 359 through 366 Processing helix chain 'I' and resid 367 through 369 No H-bonds generated for 'chain 'I' and resid 367 through 369' Processing helix chain 'I' and resid 370 through 375 removed outlier: 4.090A pdb=" N PHE I 375 " --> pdb=" O HIS I 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 48 Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'J' and resid 78 through 92 Processing helix chain 'J' and resid 97 through 101 removed outlier: 3.626A pdb=" N HIS J 101 " --> pdb=" O PRO J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.812A pdb=" N ARG J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 145 removed outlier: 3.827A pdb=" N SER J 145 " --> pdb=" O SER J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 175 Processing helix chain 'J' and resid 181 through 196 removed outlier: 3.670A pdb=" N GLU J 195 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG J 196 " --> pdb=" O ILE J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 222 through 231 Processing helix chain 'J' and resid 233 through 237 removed outlier: 4.048A pdb=" N LEU J 236 " --> pdb=" O SER J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 4.404A pdb=" N PHE J 255 " --> pdb=" O GLY J 251 " (cutoff:3.500A) Proline residue: J 258 - end of helix Processing helix chain 'J' and resid 261 through 262 No H-bonds generated for 'chain 'J' and resid 261 through 262' Processing helix chain 'J' and resid 263 through 268 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 289 through 295 Processing helix chain 'J' and resid 301 through 306 removed outlier: 3.961A pdb=" N TYR J 306 " --> pdb=" O THR J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 321 removed outlier: 3.927A pdb=" N ALA J 319 " --> pdb=" O LYS J 315 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU J 320 " --> pdb=" O GLU J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 348 Processing helix chain 'J' and resid 351 through 355 Processing helix chain 'J' and resid 359 through 366 Processing helix chain 'J' and resid 369 through 374 Processing helix chain 'K' and resid 44 through 48 removed outlier: 4.066A pdb=" N GLY K 48 " --> pdb=" O VAL K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 Processing helix chain 'K' and resid 78 through 92 Processing helix chain 'K' and resid 97 through 101 removed outlier: 3.512A pdb=" N HIS K 101 " --> pdb=" O PRO K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 126 removed outlier: 4.204A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 172 through 175 Processing helix chain 'K' and resid 181 through 195 removed outlier: 3.535A pdb=" N LYS K 191 " --> pdb=" O ASP K 187 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU K 195 " --> pdb=" O LYS K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 216 removed outlier: 3.501A pdb=" N GLU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 233 Processing helix chain 'K' and resid 257 through 262 removed outlier: 3.728A pdb=" N ALA K 260 " --> pdb=" O CYS K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 268 removed outlier: 3.652A pdb=" N GLY K 268 " --> pdb=" O SER K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 285 removed outlier: 3.844A pdb=" N CYS K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 289 through 295 Processing helix chain 'K' and resid 301 through 306 removed outlier: 4.022A pdb=" N TYR K 306 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 334 through 338 removed outlier: 3.645A pdb=" N TYR K 337 " --> pdb=" O GLU K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 341 through 349 Processing helix chain 'K' and resid 350 through 355 removed outlier: 4.109A pdb=" N GLN K 354 " --> pdb=" O THR K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 366 Processing helix chain 'K' and resid 367 through 372 removed outlier: 3.610A pdb=" N ARG K 372 " --> pdb=" O ILE K 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 48 Processing helix chain 'L' and resid 55 through 61 Processing helix chain 'L' and resid 78 through 92 Processing helix chain 'L' and resid 97 through 101 Processing helix chain 'L' and resid 112 through 126 removed outlier: 4.002A pdb=" N ARG L 116 " --> pdb=" O PRO L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 145 Processing helix chain 'L' and resid 172 through 175 Processing helix chain 'L' and resid 181 through 196 removed outlier: 3.710A pdb=" N GLU L 195 " --> pdb=" O LYS L 191 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG L 196 " --> pdb=" O ILE L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 215 Processing helix chain 'L' and resid 222 through 233 Processing helix chain 'L' and resid 252 through 260 Proline residue: L 258 - end of helix Processing helix chain 'L' and resid 261 through 262 No H-bonds generated for 'chain 'L' and resid 261 through 262' Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 273 through 285 removed outlier: 3.556A pdb=" N CYS L 285 " --> pdb=" O SER L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 295 Processing helix chain 'L' and resid 301 through 306 removed outlier: 4.220A pdb=" N TYR L 306 " --> pdb=" O THR L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 321 removed outlier: 4.027A pdb=" N ALA L 319 " --> pdb=" O LYS L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 336 No H-bonds generated for 'chain 'L' and resid 334 through 336' Processing helix chain 'L' and resid 337 through 349 removed outlier: 3.653A pdb=" N LEU L 349 " --> pdb=" O ILE L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 355 Processing helix chain 'L' and resid 359 through 366 removed outlier: 3.648A pdb=" N GLU L 364 " --> pdb=" O GLN L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 372 removed outlier: 3.578A pdb=" N HIS L 371 " --> pdb=" O SER L 368 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG L 372 " --> pdb=" O ILE L 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 48 removed outlier: 3.973A pdb=" N GLY N 48 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 61 Processing helix chain 'N' and resid 78 through 92 Processing helix chain 'N' and resid 97 through 101 removed outlier: 3.579A pdb=" N HIS N 101 " --> pdb=" O PRO N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.925A pdb=" N ARG N 116 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 145 Processing helix chain 'N' and resid 172 through 175 Processing helix chain 'N' and resid 181 through 196 removed outlier: 3.561A pdb=" N LYS N 191 " --> pdb=" O ASP N 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU N 195 " --> pdb=" O LYS N 191 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG N 196 " --> pdb=" O ILE N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 202 through 217 removed outlier: 3.546A pdb=" N CYS N 217 " --> pdb=" O LYS N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 234 removed outlier: 3.679A pdb=" N SER N 232 " --> pdb=" O ALA N 228 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER N 234 " --> pdb=" O ALA N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 260 Proline residue: N 258 - end of helix Processing helix chain 'N' and resid 261 through 262 No H-bonds generated for 'chain 'N' and resid 261 through 262' Processing helix chain 'N' and resid 263 through 268 Processing helix chain 'N' and resid 273 through 284 Processing helix chain 'N' and resid 289 through 296 removed outlier: 3.538A pdb=" N LEU N 293 " --> pdb=" O ILE N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 306 removed outlier: 3.927A pdb=" N TYR N 306 " --> pdb=" O THR N 303 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 321 removed outlier: 3.534A pdb=" N ALA N 319 " --> pdb=" O LYS N 315 " (cutoff:3.500A) Processing helix chain 'N' and resid 334 through 336 No H-bonds generated for 'chain 'N' and resid 334 through 336' Processing helix chain 'N' and resid 337 through 348 Processing helix chain 'N' and resid 349 through 355 Processing helix chain 'N' and resid 359 through 366 Processing helix chain 'N' and resid 367 through 372 removed outlier: 4.034A pdb=" N HIS N 371 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 61 Processing helix chain 'O' and resid 78 through 92 Processing helix chain 'O' and resid 97 through 101 Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.933A pdb=" N ARG O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 144 Processing helix chain 'O' and resid 172 through 175 removed outlier: 3.514A pdb=" N ILE O 175 " --> pdb=" O PRO O 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 172 through 175' Processing helix chain 'O' and resid 181 through 194 removed outlier: 3.772A pdb=" N THR O 194 " --> pdb=" O MET O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 197 No H-bonds generated for 'chain 'O' and resid 195 through 197' Processing helix chain 'O' and resid 202 through 213 Processing helix chain 'O' and resid 222 through 233 Processing helix chain 'O' and resid 234 through 237 Processing helix chain 'O' and resid 251 through 263 removed outlier: 4.346A pdb=" N PHE O 255 " --> pdb=" O GLY O 251 " (cutoff:3.500A) Proline residue: O 258 - end of helix removed outlier: 4.791A pdb=" N LEU O 261 " --> pdb=" O CYS O 257 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE O 262 " --> pdb=" O PRO O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 268 Processing helix chain 'O' and resid 273 through 285 removed outlier: 3.622A pdb=" N CYS O 285 " --> pdb=" O SER O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 289 through 295 removed outlier: 3.863A pdb=" N ALA O 295 " --> pdb=" O LYS O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 301 through 306 removed outlier: 3.829A pdb=" N TYR O 306 " --> pdb=" O THR O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 321 removed outlier: 3.646A pdb=" N ALA O 319 " --> pdb=" O LYS O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 349 Processing helix chain 'O' and resid 350 through 355 Processing helix chain 'O' and resid 359 through 366 removed outlier: 3.671A pdb=" N GLU O 364 " --> pdb=" O GLN O 360 " (cutoff:3.500A) Processing helix chain 'O' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'E' and resid 48 through 52 removed outlier: 4.155A pdb=" N LYS E 48 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS E 57 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 66 through 67 removed outlier: 3.665A pdb=" N SER E 70 " --> pdb=" O ASP E 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 116 through 124 removed outlier: 3.505A pdb=" N PHE E 128 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TRP F 169 " --> pdb=" O GLN F 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN F 164 " --> pdb=" O TRP F 169 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE F 158 " --> pdb=" O SER F 175 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLN F 152 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR F 153 " --> pdb=" O LYS F 146 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS F 146 " --> pdb=" O THR F 153 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE F 140 " --> pdb=" O GLU F 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'F' and resid 86 through 87 removed outlier: 4.734A pdb=" N LYS F 97 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASP F 107 " --> pdb=" O LYS F 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 29 through 32 Processing sheet with id=AA7, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'I' and resid 169 through 170 removed outlier: 6.309A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N MET I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 238 through 241 removed outlier: 3.580A pdb=" N TYR I 240 " --> pdb=" O ILE I 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 29 through 32 Processing sheet with id=AB3, first strand: chain 'J' and resid 35 through 38 Processing sheet with id=AB4, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'J' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'J' and resid 169 through 170 removed outlier: 6.249A pdb=" N THR J 297 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.490A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'K' and resid 169 through 170 removed outlier: 6.157A pdb=" N THR K 297 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.728A pdb=" N PHE L 31 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'L' and resid 169 through 170 Processing sheet with id=AC7, first strand: chain 'L' and resid 169 through 170 Processing sheet with id=AC8, first strand: chain 'L' and resid 238 through 241 Processing sheet with id=AC9, first strand: chain 'N' and resid 18 through 21 removed outlier: 3.531A pdb=" N THR N 106 " --> pdb=" O VAL N 10 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AD2, first strand: chain 'N' and resid 71 through 72 Processing sheet with id=AD3, first strand: chain 'N' and resid 169 through 170 Processing sheet with id=AD4, first strand: chain 'N' and resid 169 through 170 removed outlier: 6.308A pdb=" N THR N 297 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 239 through 241 Processing sheet with id=AD6, first strand: chain 'O' and resid 29 through 32 removed outlier: 3.538A pdb=" N PHE O 31 " --> pdb=" O CYS O 17 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 71 through 72 Processing sheet with id=AD8, first strand: chain 'O' and resid 169 through 170 Processing sheet with id=AD9, first strand: chain 'O' and resid 169 through 170 removed outlier: 6.108A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N SER O 300 " --> pdb=" O ILE O 151 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET O 153 " --> pdb=" O SER O 300 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR O 297 " --> pdb=" O ILE O 330 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 238 through 241 1140 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 6831 1.34 - 1.49: 6863 1.49 - 1.63: 8701 1.63 - 1.78: 54 1.78 - 1.93: 206 Bond restraints: 22655 Sorted by residual: bond pdb=" N HYP P 1 " pdb=" CA HYP P 1 " ideal model delta sigma weight residual 1.466 1.313 0.153 1.50e-02 4.44e+03 1.04e+02 bond pdb=" N HYP S 1 " pdb=" CA HYP S 1 " ideal model delta sigma weight residual 1.466 1.314 0.152 1.50e-02 4.44e+03 1.02e+02 bond pdb=" CA HYP P 1 " pdb=" C HYP P 1 " ideal model delta sigma weight residual 1.525 1.313 0.212 2.10e-02 2.27e+03 1.02e+02 bond pdb=" CA HYP Q 1 " pdb=" C HYP Q 1 " ideal model delta sigma weight residual 1.525 1.315 0.210 2.10e-02 2.27e+03 9.98e+01 bond pdb=" N HYP Q 1 " pdb=" CA HYP Q 1 " ideal model delta sigma weight residual 1.466 1.317 0.149 1.50e-02 4.44e+03 9.92e+01 ... (remaining 22650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 26462 2.63 - 5.25: 3477 5.25 - 7.88: 651 7.88 - 10.50: 108 10.50 - 13.13: 21 Bond angle restraints: 30719 Sorted by residual: angle pdb=" N PRO K 32 " pdb=" CA PRO K 32 " pdb=" C PRO K 32 " ideal model delta sigma weight residual 111.03 98.97 12.06 1.54e+00 4.22e-01 6.14e+01 angle pdb=" CA TYR I 143 " pdb=" CB TYR I 143 " pdb=" CG TYR I 143 " ideal model delta sigma weight residual 113.90 127.03 -13.13 1.80e+00 3.09e-01 5.32e+01 angle pdb=" CA PHE F 54 " pdb=" CB PHE F 54 " pdb=" CG PHE F 54 " ideal model delta sigma weight residual 113.80 121.07 -7.27 1.00e+00 1.00e+00 5.29e+01 angle pdb=" N TRP L 340 " pdb=" CA TRP L 340 " pdb=" C TRP L 340 " ideal model delta sigma weight residual 111.28 103.57 7.71 1.09e+00 8.42e-01 5.00e+01 angle pdb=" CA PHE F 228 " pdb=" CB PHE F 228 " pdb=" CG PHE F 228 " ideal model delta sigma weight residual 113.80 120.74 -6.94 1.00e+00 1.00e+00 4.82e+01 ... (remaining 30714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 13344 34.78 - 69.57: 216 69.57 - 104.35: 32 104.35 - 139.13: 5 139.13 - 173.92: 4 Dihedral angle restraints: 13601 sinusoidal: 5498 harmonic: 8103 Sorted by residual: dihedral pdb=" C5' ADP N 401 " pdb=" O5' ADP N 401 " pdb=" PA ADP N 401 " pdb=" O2A ADP N 401 " ideal model delta sinusoidal sigma weight residual 300.00 126.09 173.92 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP J 401 " pdb=" O5' ADP J 401 " pdb=" PA ADP J 401 " pdb=" O2A ADP J 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.39 -173.39 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP L 401 " pdb=" O5' ADP L 401 " pdb=" PA ADP L 401 " pdb=" O2A ADP L 401 " ideal model delta sinusoidal sigma weight residual -60.00 99.03 -159.02 1 2.00e+01 2.50e-03 4.64e+01 ... (remaining 13598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.934: 3393 0.934 - 1.867: 0 1.867 - 2.801: 0 2.801 - 3.734: 0 3.734 - 4.668: 10 Chirality restraints: 3403 Sorted by residual: chirality pdb=" CA DTH Q 6 " pdb=" N DTH Q 6 " pdb=" C DTH Q 6 " pdb=" CB DTH Q 6 " both_signs ideal model delta sigma weight residual False 2.53 -2.14 4.67 2.00e-01 2.50e+01 5.45e+02 chirality pdb=" CA DTH S 6 " pdb=" N DTH S 6 " pdb=" C DTH S 6 " pdb=" CB DTH S 6 " both_signs ideal model delta sigma weight residual False 2.53 -2.10 4.62 2.00e-01 2.50e+01 5.34e+02 chirality pdb=" CB DTH S 6 " pdb=" CA DTH S 6 " pdb=" OG1 DTH S 6 " pdb=" CG2 DTH S 6 " both_signs ideal model delta sigma weight residual False 2.55 -2.07 4.62 2.00e-01 2.50e+01 5.34e+02 ... (remaining 3400 not shown) Planarity restraints: 3923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 271 " 0.152 2.00e-02 2.50e+03 7.47e-02 1.39e+02 pdb=" CG TRP F 271 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP F 271 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP F 271 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP F 271 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP F 271 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 271 " -0.084 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 271 " 0.102 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 271 " -0.041 2.00e-02 2.50e+03 pdb=" CH2 TRP F 271 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 340 " -0.125 2.00e-02 2.50e+03 6.06e-02 9.20e+01 pdb=" CG TRP J 340 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP J 340 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP J 340 " 0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP J 340 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP J 340 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 340 " 0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 340 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 340 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP J 340 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 240 " 0.111 2.00e-02 2.50e+03 5.62e-02 6.33e+01 pdb=" CG TYR O 240 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR O 240 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR O 240 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR O 240 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR O 240 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR O 240 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR O 240 " 0.062 2.00e-02 2.50e+03 ... (remaining 3920 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 66 2.44 - 3.05: 13778 3.05 - 3.67: 33792 3.67 - 4.28: 50886 4.28 - 4.90: 83747 Nonbonded interactions: 182269 Sorted by model distance: nonbonded pdb=" CD1 TRP R 3 " pdb=" SG CYS R 7 " model vdw 1.820 3.620 nonbonded pdb=" CD1 TRP P 3 " pdb=" SG CYS P 7 " model vdw 1.820 3.620 nonbonded pdb=" CD1 TRP Q 3 " pdb=" SG CYS Q 7 " model vdw 1.824 3.620 nonbonded pdb=" CD1 TRP S 3 " pdb=" SG CYS S 7 " model vdw 1.825 3.620 nonbonded pdb=" CD1 TRP T 3 " pdb=" SG CYS T 7 " model vdw 1.826 3.620 ... (remaining 182264 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 'I' and resid 5 through 375) selection = (chain 'J' and resid 5 through 375) selection = (chain 'K' and resid 5 through 375) selection = (chain 'L' and resid 5 through 375) selection = (chain 'N' and resid 5 through 375) selection = (chain 'O' and resid 5 through 375) } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.070 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.023 0.843 22667 Z= 1.259 Angle : 1.958 13.131 30734 Z= 1.187 Chirality : 0.302 4.668 3403 Planarity : 0.013 0.127 3918 Dihedral : 14.856 173.918 8384 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 0.21 % Allowed : 6.28 % Favored : 93.51 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.14), residues: 2736 helix: -2.05 (0.12), residues: 1150 sheet: 0.08 (0.24), residues: 422 loop : -1.01 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.003 ARG J 196 TYR 0.111 0.016 TYR O 240 PHE 0.084 0.010 PHE L 31 TRP 0.152 0.016 TRP F 271 HIS 0.027 0.004 HIS F 135 Details of bonding type rmsd/Z covalent geometry : bond 0.02263 / 1.12 (22655) covalent geometry : angle 1.95493 / 1.19 (30719) hydrogen bonds : bond 0.17922 / 11.75 ( 1130) hydrogen bonds : angle 8.30247 / 5.75 ( 2985) Misc. bond : bond 0.32325 / 17.00 ( 7) link_TRANS : bond 0.07017 / 3.86 ( 5) link_TRANS : angle 5.42410 / 3.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 613 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 MET cc_start: 0.7817 (mmm) cc_final: 0.7412 (tpp) REVERT: E 94 ARG cc_start: 0.8090 (tpt170) cc_final: 0.7822 (tpt170) REVERT: E 110 LEU cc_start: 0.8124 (mt) cc_final: 0.7916 (mt) REVERT: E 187 MET cc_start: 0.8252 (mtp) cc_final: 0.7646 (mpp) REVERT: E 227 THR cc_start: 0.8242 (m) cc_final: 0.7408 (p) REVERT: F 197 HIS cc_start: 0.7446 (t-170) cc_final: 0.6293 (t70) REVERT: F 266 ARG cc_start: 0.7972 (mmt90) cc_final: 0.7438 (mtp180) REVERT: I 86 TRP cc_start: 0.8451 (m-10) cc_final: 0.8108 (m-10) REVERT: I 92 ASN cc_start: 0.8926 (m-40) cc_final: 0.8688 (m-40) REVERT: I 263 GLN cc_start: 0.8540 (mt0) cc_final: 0.7938 (mp10) REVERT: J 16 MET cc_start: 0.7460 (mtp) cc_final: 0.7233 (mtm) REVERT: J 292 ASP cc_start: 0.8309 (m-30) cc_final: 0.7683 (t0) REVERT: J 356 TRP cc_start: 0.6575 (m100) cc_final: 0.5997 (m-10) REVERT: K 203 THR cc_start: 0.8500 (p) cc_final: 0.8233 (t) REVERT: L 134 VAL cc_start: 0.9114 (t) cc_final: 0.8168 (t) REVERT: L 242 LEU cc_start: 0.8791 (mt) cc_final: 0.8241 (mt) REVERT: L 280 ASN cc_start: 0.8487 (m-40) cc_final: 0.8285 (m-40) REVERT: L 371 HIS cc_start: 0.6291 (m-70) cc_final: 0.5970 (m90) REVERT: N 65 LEU cc_start: 0.8238 (mt) cc_final: 0.8000 (mt) REVERT: N 141 SER cc_start: 0.8292 (m) cc_final: 0.8008 (t) REVERT: N 171 LEU cc_start: 0.8966 (mp) cc_final: 0.8650 (mm) REVERT: N 305 MET cc_start: 0.8636 (mmm) cc_final: 0.8350 (mmm) REVERT: O 119 MET cc_start: 0.9034 (mtm) cc_final: 0.8571 (mtp) outliers start: 5 outliers final: 4 residues processed: 618 average time/residue: 0.1554 time to fit residues: 144.4580 Evaluate side-chains 303 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 299 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 7 CYS Chi-restraints excluded: chain S residue 7 CYS Chi-restraints excluded: chain T residue 7 CYS Chi-restraints excluded: chain P residue 7 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 20 GLN E 45 GLN E 209 HIS E 212 ASN E 270 GLN F 79 HIS ** F 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 GLN I 41 GLN I 88 HIS ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 HIS J 252 ASN K 111 ASN L 246 GLN L 354 GLN ** O 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.103845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.072126 restraints weight = 69698.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.074485 restraints weight = 36467.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.075940 restraints weight = 23398.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.076844 restraints weight = 17581.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.077535 restraints weight = 14678.481| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22667 Z= 0.175 Angle : 0.786 11.456 30734 Z= 0.403 Chirality : 0.049 0.322 3403 Planarity : 0.005 0.061 3918 Dihedral : 9.610 175.373 3124 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.49 % Allowed : 12.61 % Favored : 84.91 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 2736 helix: -0.36 (0.14), residues: 1175 sheet: -0.01 (0.22), residues: 541 loop : -0.23 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 225 TYR 0.023 0.002 TYR K 294 PHE 0.026 0.002 PHE N 31 TRP 0.051 0.003 TRP I 356 HIS 0.007 0.001 HIS K 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (22655) covalent geometry : angle 0.78411 / 0.40 (30719) hydrogen bonds : bond 0.04752 / 3.07 ( 1130) hydrogen bonds : angle 5.80639 / 4.10 ( 2985) Misc. bond : bond 0.00156 / 0.08 ( 7) link_TRANS : bond 0.00640 / 0.35 ( 5) link_TRANS : angle 2.74927 / 1.62 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 302 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.6579 (ppp) cc_final: 0.6257 (ppp) REVERT: E 48 LYS cc_start: 0.9010 (pttm) cc_final: 0.7750 (mmmt) REVERT: E 174 MET cc_start: 0.9044 (mmp) cc_final: 0.8783 (tmm) REVERT: E 186 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8375 (m) REVERT: E 193 LEU cc_start: 0.9366 (mt) cc_final: 0.9032 (tp) REVERT: E 212 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7479 (m-40) REVERT: F 169 TRP cc_start: 0.7655 (p-90) cc_final: 0.7438 (p-90) REVERT: I 16 MET cc_start: 0.5213 (mmm) cc_final: 0.4746 (mmm) REVERT: I 78 ASN cc_start: 0.8155 (t0) cc_final: 0.7913 (t0) REVERT: I 123 MET cc_start: 0.8435 (tpp) cc_final: 0.8223 (tpp) REVERT: I 269 MET cc_start: 0.7530 (mmt) cc_final: 0.6957 (mpp) REVERT: I 280 ASN cc_start: 0.9133 (m-40) cc_final: 0.8865 (m110) REVERT: J 292 ASP cc_start: 0.8492 (m-30) cc_final: 0.7736 (t0) REVERT: L 105 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8227 (mm) REVERT: L 140 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8207 (mm) REVERT: L 153 MET cc_start: 0.8041 (ttp) cc_final: 0.7715 (tmm) REVERT: L 227 MET cc_start: 0.8314 (ttm) cc_final: 0.8104 (ttm) REVERT: N 47 MET cc_start: 0.6749 (ttm) cc_final: 0.6522 (tmm) REVERT: N 65 LEU cc_start: 0.8099 (mt) cc_final: 0.7773 (mt) REVERT: N 141 SER cc_start: 0.8299 (m) cc_final: 0.8003 (t) REVERT: O 16 MET cc_start: 0.6758 (mmm) cc_final: 0.6462 (mmm) REVERT: O 47 MET cc_start: -0.3901 (mmt) cc_final: -0.5236 (ttm) REVERT: O 253 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8109 (mp0) REVERT: O 313 MET cc_start: 0.8946 (mmm) cc_final: 0.8672 (tpt) outliers start: 59 outliers final: 23 residues processed: 344 average time/residue: 0.1429 time to fit residues: 76.7392 Evaluate side-chains 257 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 354 GLN Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 86 TRP Chi-restraints excluded: chain O residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 130 optimal weight: 0.1980 chunk 39 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 212 ASN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS K 353 GLN N 173 HIS O 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.110033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.077610 restraints weight = 69002.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.080138 restraints weight = 37156.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.081723 restraints weight = 24219.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.082767 restraints weight = 18139.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.083511 restraints weight = 15071.253| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22667 Z= 0.183 Angle : 0.705 7.915 30734 Z= 0.354 Chirality : 0.047 0.420 3403 Planarity : 0.005 0.057 3918 Dihedral : 8.703 154.656 3120 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.02 % Allowed : 13.36 % Favored : 84.61 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 2736 helix: -0.00 (0.15), residues: 1184 sheet: 0.08 (0.22), residues: 539 loop : -0.14 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 225 TYR 0.017 0.002 TYR O 294 PHE 0.024 0.002 PHE L 352 TRP 0.057 0.002 TRP F 271 HIS 0.012 0.001 HIS K 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (22655) covalent geometry : angle 0.70432 / 0.35 (30719) hydrogen bonds : bond 0.04273 / 2.75 ( 1130) hydrogen bonds : angle 5.50526 / 3.88 ( 2985) Misc. bond : bond 0.00090 / 0.05 ( 7) link_TRANS : bond 0.00226 / 0.12 ( 5) link_TRANS : angle 1.50371 / 0.87 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.6565 (ppp) cc_final: 0.6285 (ppp) REVERT: E 152 HIS cc_start: 0.8275 (m-70) cc_final: 0.8066 (m-70) REVERT: E 212 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.7132 (m110) REVERT: F 197 HIS cc_start: 0.6364 (t70) cc_final: 0.4299 (t70) REVERT: F 199 TYR cc_start: 0.9042 (p90) cc_final: 0.8310 (p90) REVERT: I 16 MET cc_start: 0.5169 (mmm) cc_final: 0.4735 (mmm) REVERT: I 78 ASN cc_start: 0.8404 (t0) cc_final: 0.8096 (t0) REVERT: I 153 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8459 (tpp) REVERT: I 227 MET cc_start: 0.8596 (tpt) cc_final: 0.8388 (tpt) REVERT: I 269 MET cc_start: 0.7549 (mmt) cc_final: 0.6947 (mpp) REVERT: I 313 MET cc_start: 0.9032 (mmm) cc_final: 0.8764 (mmm) REVERT: J 173 HIS cc_start: 0.6973 (OUTLIER) cc_final: 0.6341 (p-80) REVERT: J 292 ASP cc_start: 0.8534 (m-30) cc_final: 0.7703 (t0) REVERT: J 326 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8144 (mmmt) REVERT: K 16 MET cc_start: 0.7674 (mmt) cc_final: 0.7377 (mmt) REVERT: K 184 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8149 (t70) REVERT: L 47 MET cc_start: 0.5753 (ptt) cc_final: 0.5237 (ptt) REVERT: L 105 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8208 (mm) REVERT: L 153 MET cc_start: 0.8003 (ttp) cc_final: 0.7704 (tmm) REVERT: N 141 SER cc_start: 0.8372 (m) cc_final: 0.8023 (t) REVERT: N 227 MET cc_start: 0.8932 (tpt) cc_final: 0.8659 (tpt) REVERT: N 269 MET cc_start: 0.7845 (mtm) cc_final: 0.7638 (ttp) REVERT: O 16 MET cc_start: 0.6853 (mmm) cc_final: 0.6500 (mmm) REVERT: O 227 MET cc_start: 0.8791 (mmm) cc_final: 0.8413 (mmm) REVERT: O 269 MET cc_start: 0.7208 (mtt) cc_final: 0.6962 (ttm) outliers start: 48 outliers final: 25 residues processed: 280 average time/residue: 0.1362 time to fit residues: 60.6025 Evaluate side-chains 254 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 356 TRP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 173 HIS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 30.0000 chunk 109 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 206 optimal weight: 0.0050 chunk 256 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 212 ASN ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN L 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.101415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070625 restraints weight = 70223.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.072893 restraints weight = 37256.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.074388 restraints weight = 24251.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.075289 restraints weight = 18168.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.075814 restraints weight = 15007.705| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22667 Z= 0.137 Angle : 0.652 8.106 30734 Z= 0.324 Chirality : 0.046 0.395 3403 Planarity : 0.004 0.049 3918 Dihedral : 7.999 146.865 3120 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.02 % Allowed : 14.29 % Favored : 83.68 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2736 helix: 0.24 (0.15), residues: 1178 sheet: 0.19 (0.22), residues: 540 loop : 0.00 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 225 TYR 0.019 0.001 TYR E 232 PHE 0.018 0.001 PHE L 352 TRP 0.040 0.002 TRP F 271 HIS 0.006 0.001 HIS F 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (22655) covalent geometry : angle 0.65123 / 0.32 (30719) hydrogen bonds : bond 0.03811 / 2.48 ( 1130) hydrogen bonds : angle 5.25656 / 3.70 ( 2985) Misc. bond : bond 0.00058 / 0.03 ( 7) link_TRANS : bond 0.00203 / 0.10 ( 5) link_TRANS : angle 1.36983 / 0.73 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.6725 (ppp) cc_final: 0.6473 (ppp) REVERT: E 88 MET cc_start: 0.7671 (mmm) cc_final: 0.7308 (mmm) REVERT: E 212 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7070 (m110) REVERT: I 16 MET cc_start: 0.5087 (mmm) cc_final: 0.4729 (mmm) REVERT: I 47 MET cc_start: 0.5800 (tmm) cc_final: 0.5534 (tmm) REVERT: I 78 ASN cc_start: 0.8388 (t0) cc_final: 0.8042 (t0) REVERT: I 92 ASN cc_start: 0.9003 (m-40) cc_final: 0.8704 (m-40) REVERT: I 123 MET cc_start: 0.8362 (tpp) cc_final: 0.8129 (tpp) REVERT: I 145 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7732 (p) REVERT: I 153 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8539 (tpp) REVERT: I 227 MET cc_start: 0.8640 (tpt) cc_final: 0.8394 (tpt) REVERT: I 269 MET cc_start: 0.7648 (mmt) cc_final: 0.7174 (mpp) REVERT: J 292 ASP cc_start: 0.8417 (m-30) cc_final: 0.7683 (t0) REVERT: J 326 LYS cc_start: 0.8302 (mmmt) cc_final: 0.8045 (mmmt) REVERT: K 16 MET cc_start: 0.7701 (mmt) cc_final: 0.7460 (mmt) REVERT: L 44 MET cc_start: 0.7683 (mtt) cc_final: 0.7463 (mtp) REVERT: L 47 MET cc_start: 0.5785 (ptt) cc_final: 0.5271 (ptt) REVERT: L 105 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8063 (mm) REVERT: L 313 MET cc_start: 0.8786 (tpp) cc_final: 0.8463 (ttm) REVERT: L 355 MET cc_start: 0.7832 (mmt) cc_final: 0.7456 (mmt) REVERT: N 65 LEU cc_start: 0.8133 (mt) cc_final: 0.7915 (mt) REVERT: N 123 MET cc_start: 0.9020 (mmm) cc_final: 0.8486 (tpp) REVERT: N 141 SER cc_start: 0.8338 (m) cc_final: 0.8023 (t) REVERT: N 227 MET cc_start: 0.8919 (tpt) cc_final: 0.8613 (tpt) REVERT: N 313 MET cc_start: 0.9211 (tpp) cc_final: 0.8970 (tpp) REVERT: O 16 MET cc_start: 0.6922 (mmm) cc_final: 0.6590 (mmm) REVERT: O 227 MET cc_start: 0.8761 (mmm) cc_final: 0.8450 (mmm) outliers start: 48 outliers final: 25 residues processed: 279 average time/residue: 0.1415 time to fit residues: 62.7986 Evaluate side-chains 249 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 356 TRP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 250 ILE Chi-restraints excluded: chain O residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 54 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 205 optimal weight: 0.6980 chunk 101 optimal weight: 0.0030 chunk 266 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 182 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 152 HIS E 157 GLN E 212 ASN F 61 GLN ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.101324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.070628 restraints weight = 70138.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.072896 restraints weight = 36995.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.074421 restraints weight = 23983.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.075325 restraints weight = 17826.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.075941 restraints weight = 14710.734| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22667 Z= 0.127 Angle : 0.645 7.620 30734 Z= 0.317 Chirality : 0.046 0.394 3403 Planarity : 0.004 0.047 3918 Dihedral : 7.456 147.587 3120 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.85 % Allowed : 14.71 % Favored : 83.43 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 2736 helix: 0.36 (0.15), residues: 1184 sheet: 0.37 (0.22), residues: 572 loop : 0.07 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 116 TYR 0.016 0.001 TYR E 232 PHE 0.016 0.001 PHE F 29 TRP 0.050 0.002 TRP F 169 HIS 0.005 0.001 HIS O 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (22655) covalent geometry : angle 0.64448 / 0.32 (30719) hydrogen bonds : bond 0.03613 / 2.34 ( 1130) hydrogen bonds : angle 5.10867 / 3.59 ( 2985) Misc. bond : bond 0.00056 / 0.03 ( 7) link_TRANS : bond 0.00162 / 0.08 ( 5) link_TRANS : angle 1.35547 / 0.72 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.6711 (ppp) cc_final: 0.6492 (ppp) REVERT: E 88 MET cc_start: 0.7605 (mmm) cc_final: 0.7299 (mmm) REVERT: F 199 TYR cc_start: 0.9068 (p90) cc_final: 0.8281 (p90) REVERT: I 16 MET cc_start: 0.5043 (mmm) cc_final: 0.4720 (mmm) REVERT: I 78 ASN cc_start: 0.8415 (t0) cc_final: 0.8041 (t0) REVERT: I 92 ASN cc_start: 0.9043 (m-40) cc_final: 0.8719 (m-40) REVERT: I 145 SER cc_start: 0.7961 (OUTLIER) cc_final: 0.7670 (p) REVERT: I 153 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8591 (tpp) REVERT: I 227 MET cc_start: 0.8649 (tpt) cc_final: 0.8372 (tpt) REVERT: I 269 MET cc_start: 0.7774 (mmt) cc_final: 0.7329 (mpp) REVERT: I 283 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8454 (mtt) REVERT: I 290 ARG cc_start: 0.8259 (tpp80) cc_final: 0.7888 (mmt90) REVERT: J 111 ASN cc_start: 0.8255 (m-40) cc_final: 0.7701 (m-40) REVERT: J 292 ASP cc_start: 0.8485 (m-30) cc_final: 0.7800 (t0) REVERT: J 326 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8139 (mmmt) REVERT: J 355 MET cc_start: 0.8073 (mmt) cc_final: 0.7820 (mmm) REVERT: K 16 MET cc_start: 0.7779 (mmt) cc_final: 0.7508 (mmt) REVERT: K 44 MET cc_start: 0.8395 (mtp) cc_final: 0.7994 (mtp) REVERT: K 325 MET cc_start: 0.8958 (mmm) cc_final: 0.8742 (mmm) REVERT: L 47 MET cc_start: 0.5904 (ptt) cc_final: 0.5478 (ptt) REVERT: L 105 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8105 (mm) REVERT: N 65 LEU cc_start: 0.8218 (mt) cc_final: 0.7985 (mt) REVERT: N 123 MET cc_start: 0.9008 (mmm) cc_final: 0.8466 (tpp) REVERT: N 141 SER cc_start: 0.8284 (m) cc_final: 0.7993 (t) REVERT: N 227 MET cc_start: 0.8882 (tpt) cc_final: 0.8638 (tpt) REVERT: N 313 MET cc_start: 0.9207 (tpp) cc_final: 0.8988 (ttm) REVERT: O 16 MET cc_start: 0.6990 (mmm) cc_final: 0.6687 (mmm) REVERT: O 227 MET cc_start: 0.8855 (mmm) cc_final: 0.8613 (mmm) outliers start: 44 outliers final: 29 residues processed: 267 average time/residue: 0.1366 time to fit residues: 58.2115 Evaluate side-chains 249 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 356 TRP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 250 ILE Chi-restraints excluded: chain O residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 170 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 chunk 260 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 265 optimal weight: 0.0670 chunk 142 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.099618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.068010 restraints weight = 70515.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.070209 restraints weight = 38345.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071534 restraints weight = 25255.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.072326 restraints weight = 19233.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.072964 restraints weight = 16216.301| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22667 Z= 0.187 Angle : 0.678 9.406 30734 Z= 0.332 Chirality : 0.046 0.403 3403 Planarity : 0.004 0.048 3918 Dihedral : 7.152 145.434 3120 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.02 % Allowed : 15.39 % Favored : 82.59 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2736 helix: 0.54 (0.15), residues: 1155 sheet: 0.14 (0.22), residues: 542 loop : 0.12 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 116 TYR 0.024 0.002 TYR F 277 PHE 0.016 0.001 PHE J 223 TRP 0.068 0.002 TRP F 271 HIS 0.007 0.001 HIS K 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (22655) covalent geometry : angle 0.67710 / 0.33 (30719) hydrogen bonds : bond 0.03694 / 2.37 ( 1130) hydrogen bonds : angle 5.12351 / 3.60 ( 2985) Misc. bond : bond 0.00082 / 0.04 ( 7) link_TRANS : bond 0.00118 / 0.07 ( 5) link_TRANS : angle 1.25714 / 0.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 MET cc_start: 0.7475 (mmm) cc_final: 0.7185 (mmm) REVERT: E 195 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7904 (ttp-170) REVERT: F 199 TYR cc_start: 0.9220 (p90) cc_final: 0.8484 (p90) REVERT: I 16 MET cc_start: 0.5081 (mmm) cc_final: 0.4787 (mmm) REVERT: I 78 ASN cc_start: 0.8704 (t0) cc_final: 0.8289 (t0) REVERT: I 92 ASN cc_start: 0.9052 (m-40) cc_final: 0.8710 (m-40) REVERT: I 145 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7721 (p) REVERT: I 153 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8621 (tpp) REVERT: I 227 MET cc_start: 0.8656 (tpt) cc_final: 0.8393 (tpt) REVERT: I 283 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8471 (mtt) REVERT: I 290 ARG cc_start: 0.8382 (tpp80) cc_final: 0.7870 (mmt90) REVERT: J 47 MET cc_start: 0.7045 (ptt) cc_final: 0.6192 (ptt) REVERT: J 111 ASN cc_start: 0.8449 (m-40) cc_final: 0.7900 (m-40) REVERT: J 173 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6334 (p-80) REVERT: J 355 MET cc_start: 0.7953 (mmt) cc_final: 0.7749 (mmm) REVERT: K 16 MET cc_start: 0.8028 (mmt) cc_final: 0.7775 (mmt) REVERT: K 44 MET cc_start: 0.8402 (mtp) cc_final: 0.7981 (mtp) REVERT: L 47 MET cc_start: 0.5995 (ptt) cc_final: 0.5640 (ptt) REVERT: L 105 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8150 (mm) REVERT: N 141 SER cc_start: 0.8393 (m) cc_final: 0.8099 (t) REVERT: N 227 MET cc_start: 0.8928 (tpt) cc_final: 0.8659 (tpt) REVERT: O 16 MET cc_start: 0.7302 (mmm) cc_final: 0.6932 (mmm) REVERT: O 44 MET cc_start: 0.1596 (ptt) cc_final: 0.1269 (ptt) outliers start: 48 outliers final: 35 residues processed: 248 average time/residue: 0.1400 time to fit residues: 55.8415 Evaluate side-chains 241 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 356 TRP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 173 HIS Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 16 MET Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 361 GLU Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 250 ILE Chi-restraints excluded: chain O residue 257 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 144 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 254 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 183 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 ASN ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.100658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.069007 restraints weight = 69796.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.071291 restraints weight = 37383.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.072649 restraints weight = 24418.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073447 restraints weight = 18476.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.074079 restraints weight = 15558.232| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22667 Z= 0.134 Angle : 0.651 10.771 30734 Z= 0.316 Chirality : 0.045 0.399 3403 Planarity : 0.004 0.046 3918 Dihedral : 7.015 148.076 3120 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.02 % Allowed : 15.98 % Favored : 82.00 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2736 helix: 0.66 (0.16), residues: 1160 sheet: 0.34 (0.21), residues: 579 loop : 0.15 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 86 TYR 0.025 0.001 TYR F 277 PHE 0.013 0.001 PHE F 29 TRP 0.066 0.002 TRP F 169 HIS 0.004 0.001 HIS K 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (22655) covalent geometry : angle 0.65081 / 0.32 (30719) hydrogen bonds : bond 0.03426 / 2.21 ( 1130) hydrogen bonds : angle 4.99436 / 3.51 ( 2985) Misc. bond : bond 0.00053 / 0.03 ( 7) link_TRANS : bond 0.00117 / 0.06 ( 5) link_TRANS : angle 1.33936 / 0.70 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 MET cc_start: 0.7381 (mmm) cc_final: 0.7105 (mmm) REVERT: E 195 ARG cc_start: 0.8121 (ttp-170) cc_final: 0.7766 (ptt180) REVERT: F 199 TYR cc_start: 0.9238 (p90) cc_final: 0.8515 (p90) REVERT: I 16 MET cc_start: 0.5031 (mmm) cc_final: 0.4718 (mmm) REVERT: I 78 ASN cc_start: 0.8651 (t0) cc_final: 0.8238 (t0) REVERT: I 92 ASN cc_start: 0.9046 (m-40) cc_final: 0.8711 (m-40) REVERT: I 145 SER cc_start: 0.8055 (OUTLIER) cc_final: 0.7660 (p) REVERT: I 153 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8605 (tpp) REVERT: I 227 MET cc_start: 0.8598 (tpt) cc_final: 0.8321 (tpt) REVERT: J 111 ASN cc_start: 0.8424 (m-40) cc_final: 0.7805 (m-40) REVERT: J 293 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8421 (mm) REVERT: K 16 MET cc_start: 0.7907 (mmt) cc_final: 0.7662 (mmt) REVERT: K 44 MET cc_start: 0.8317 (mtp) cc_final: 0.7909 (mtp) REVERT: L 105 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8069 (mm) REVERT: N 123 MET cc_start: 0.8909 (mmm) cc_final: 0.8295 (tpp) REVERT: N 141 SER cc_start: 0.8348 (m) cc_final: 0.8031 (t) REVERT: N 227 MET cc_start: 0.8899 (tpt) cc_final: 0.8651 (tpt) REVERT: O 16 MET cc_start: 0.7192 (mmm) cc_final: 0.6861 (mmm) REVERT: O 44 MET cc_start: 0.1585 (ptt) cc_final: 0.1220 (ptt) REVERT: O 132 MET cc_start: 0.8455 (ttp) cc_final: 0.8146 (tmm) REVERT: O 227 MET cc_start: 0.8867 (mmm) cc_final: 0.8647 (mmm) outliers start: 48 outliers final: 29 residues processed: 252 average time/residue: 0.1413 time to fit residues: 56.9205 Evaluate side-chains 238 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 8 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 239 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 265 optimal weight: 0.3980 chunk 266 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 92 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN K 353 GLN ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.098401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.066275 restraints weight = 71502.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.068510 restraints weight = 39379.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.069860 restraints weight = 26132.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.070632 restraints weight = 19984.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.071289 restraints weight = 16943.661| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22667 Z= 0.226 Angle : 0.725 11.573 30734 Z= 0.353 Chirality : 0.047 0.401 3403 Planarity : 0.004 0.048 3918 Dihedral : 7.055 146.224 3120 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.94 % Allowed : 16.44 % Favored : 81.62 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.16), residues: 2736 helix: 0.50 (0.15), residues: 1162 sheet: 0.13 (0.22), residues: 537 loop : 0.03 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 86 TYR 0.017 0.002 TYR F 277 PHE 0.015 0.002 PHE L 200 TRP 0.081 0.003 TRP F 169 HIS 0.009 0.001 HIS K 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 (22655) covalent geometry : angle 0.72479 / 0.35 (30719) hydrogen bonds : bond 0.03758 / 2.42 ( 1130) hydrogen bonds : angle 5.17681 / 3.65 ( 2985) Misc. bond : bond 0.00089 / 0.05 ( 7) link_TRANS : bond 0.00191 / 0.12 ( 5) link_TRANS : angle 1.20582 / 0.62 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 MET cc_start: 0.7499 (mmm) cc_final: 0.7282 (mmm) REVERT: F 199 TYR cc_start: 0.9247 (p90) cc_final: 0.8593 (p90) REVERT: I 16 MET cc_start: 0.5011 (mmm) cc_final: 0.4703 (mmm) REVERT: I 78 ASN cc_start: 0.8667 (t0) cc_final: 0.8278 (t0) REVERT: I 153 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8659 (tpp) REVERT: I 205 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7052 (mt-10) REVERT: I 227 MET cc_start: 0.8659 (tpt) cc_final: 0.8386 (tpt) REVERT: J 47 MET cc_start: 0.7238 (ptt) cc_final: 0.6392 (ptt) REVERT: J 111 ASN cc_start: 0.8411 (m-40) cc_final: 0.7861 (m-40) REVERT: J 173 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6370 (p-80) REVERT: J 293 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8388 (mm) REVERT: K 16 MET cc_start: 0.8262 (mmt) cc_final: 0.8012 (mmp) REVERT: K 44 MET cc_start: 0.8488 (mtp) cc_final: 0.8078 (mtp) REVERT: K 184 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8017 (t70) REVERT: L 105 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8135 (mm) REVERT: L 294 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8265 (m-10) REVERT: N 123 MET cc_start: 0.9012 (mmm) cc_final: 0.8404 (tpp) REVERT: N 227 MET cc_start: 0.8919 (tpt) cc_final: 0.8674 (tpt) REVERT: O 16 MET cc_start: 0.7299 (mmm) cc_final: 0.6999 (mmm) REVERT: O 227 MET cc_start: 0.8941 (mmm) cc_final: 0.8678 (mmm) outliers start: 46 outliers final: 32 residues processed: 240 average time/residue: 0.1320 time to fit residues: 50.3556 Evaluate side-chains 230 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 173 HIS Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 16 MET Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 294 TYR Chi-restraints excluded: chain L residue 370 VAL Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 282 ILE Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 237 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 255 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 257 optimal weight: 0.1980 chunk 144 optimal weight: 0.9980 chunk 212 optimal weight: 0.5980 chunk 268 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 223 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.100627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.068970 restraints weight = 70254.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071189 restraints weight = 37872.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072535 restraints weight = 24924.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073499 restraints weight = 18834.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.073740 restraints weight = 15716.443| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22667 Z= 0.126 Angle : 0.670 12.515 30734 Z= 0.323 Chirality : 0.045 0.396 3403 Planarity : 0.004 0.046 3918 Dihedral : 6.946 149.982 3120 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.60 % Allowed : 16.86 % Favored : 81.53 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2736 helix: 0.66 (0.15), residues: 1172 sheet: 0.35 (0.21), residues: 564 loop : 0.06 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 86 TYR 0.022 0.001 TYR F 277 PHE 0.015 0.001 PHE I 279 TRP 0.056 0.002 TRP I 356 HIS 0.005 0.001 HIS F 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (22655) covalent geometry : angle 0.66989 / 0.32 (30719) hydrogen bonds : bond 0.03371 / 2.18 ( 1130) hydrogen bonds : angle 4.99224 / 3.52 ( 2985) Misc. bond : bond 0.00052 / 0.03 ( 7) link_TRANS : bond 0.00154 / 0.08 ( 5) link_TRANS : angle 1.34259 / 0.70 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 MET cc_start: 0.7426 (mmm) cc_final: 0.7219 (mmm) REVERT: E 195 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7676 (ptt180) REVERT: F 199 TYR cc_start: 0.9207 (p90) cc_final: 0.8479 (p90) REVERT: I 16 MET cc_start: 0.4992 (mmm) cc_final: 0.4750 (mmm) REVERT: I 78 ASN cc_start: 0.8602 (t0) cc_final: 0.8198 (t0) REVERT: I 145 SER cc_start: 0.8057 (OUTLIER) cc_final: 0.7728 (p) REVERT: I 153 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8670 (tpp) REVERT: I 227 MET cc_start: 0.8667 (tpt) cc_final: 0.8393 (tpt) REVERT: J 111 ASN cc_start: 0.8441 (m-40) cc_final: 0.7797 (m-40) REVERT: J 293 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8444 (mm) REVERT: J 356 TRP cc_start: 0.7181 (m100) cc_final: 0.6315 (m100) REVERT: K 16 MET cc_start: 0.7804 (mmt) cc_final: 0.7408 (mmt) REVERT: L 105 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7988 (mm) REVERT: N 141 SER cc_start: 0.8291 (m) cc_final: 0.8029 (t) REVERT: N 227 MET cc_start: 0.8884 (tpt) cc_final: 0.8668 (tpt) REVERT: N 269 MET cc_start: 0.7728 (mtm) cc_final: 0.7524 (mtp) REVERT: O 16 MET cc_start: 0.7269 (mmm) cc_final: 0.6920 (mmm) REVERT: O 44 MET cc_start: 0.1492 (ptt) cc_final: 0.1182 (ptt) REVERT: O 227 MET cc_start: 0.8882 (mmm) cc_final: 0.8649 (mmm) outliers start: 38 outliers final: 24 residues processed: 237 average time/residue: 0.1399 time to fit residues: 52.9178 Evaluate side-chains 227 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 138 optimal weight: 0.1980 chunk 241 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 229 optimal weight: 0.6980 chunk 7 optimal weight: 30.0000 chunk 235 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 225 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 223 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.100043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.068306 restraints weight = 70818.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070501 restraints weight = 38232.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.071725 restraints weight = 25143.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.072750 restraints weight = 19220.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.073245 restraints weight = 15953.335| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22667 Z= 0.143 Angle : 0.691 12.547 30734 Z= 0.332 Chirality : 0.046 0.393 3403 Planarity : 0.004 0.075 3918 Dihedral : 6.872 148.167 3120 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.18 % Allowed : 17.83 % Favored : 80.99 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.16), residues: 2736 helix: 0.61 (0.15), residues: 1176 sheet: 0.37 (0.22), residues: 554 loop : 0.08 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 14 TYR 0.016 0.001 TYR N 198 PHE 0.015 0.001 PHE I 279 TRP 0.054 0.002 TRP I 356 HIS 0.005 0.001 HIS K 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (22655) covalent geometry : angle 0.69095 / 0.33 (30719) hydrogen bonds : bond 0.03454 / 2.24 ( 1130) hydrogen bonds : angle 4.95402 / 3.49 ( 2985) Misc. bond : bond 0.00055 / 0.03 ( 7) link_TRANS : bond 0.00132 / 0.07 ( 5) link_TRANS : angle 1.29635 / 0.68 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.7153 (ppp) cc_final: 0.6705 (ppp) REVERT: E 195 ARG cc_start: 0.8033 (ttp-170) cc_final: 0.7650 (ptt180) REVERT: F 199 TYR cc_start: 0.9067 (p90) cc_final: 0.8421 (p90) REVERT: I 16 MET cc_start: 0.4987 (mmm) cc_final: 0.4730 (mmm) REVERT: I 78 ASN cc_start: 0.8619 (t0) cc_final: 0.8221 (t0) REVERT: I 153 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8627 (tpp) REVERT: I 227 MET cc_start: 0.8678 (tpt) cc_final: 0.8388 (tpt) REVERT: J 111 ASN cc_start: 0.8449 (m-40) cc_final: 0.7819 (m-40) REVERT: J 293 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8485 (mm) REVERT: J 356 TRP cc_start: 0.7154 (m100) cc_final: 0.6354 (m100) REVERT: K 16 MET cc_start: 0.7938 (mmt) cc_final: 0.7486 (mmt) REVERT: L 105 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7985 (mm) REVERT: L 355 MET cc_start: 0.7801 (mmt) cc_final: 0.7207 (mmt) REVERT: L 372 ARG cc_start: 0.6644 (ptm-80) cc_final: 0.5864 (ptm160) REVERT: N 141 SER cc_start: 0.8327 (m) cc_final: 0.8075 (t) REVERT: N 227 MET cc_start: 0.8910 (tpt) cc_final: 0.8689 (tpt) REVERT: N 269 MET cc_start: 0.7722 (mtm) cc_final: 0.7517 (mtp) REVERT: O 16 MET cc_start: 0.7253 (mmm) cc_final: 0.6876 (mmm) REVERT: O 227 MET cc_start: 0.8904 (mmm) cc_final: 0.8665 (mmm) outliers start: 28 outliers final: 21 residues processed: 226 average time/residue: 0.1558 time to fit residues: 56.3243 Evaluate side-chains 220 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 370 VAL Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 170 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 138 optimal weight: 0.3980 chunk 42 optimal weight: 0.0470 chunk 0 optimal weight: 40.0000 chunk 257 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN O 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.100002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.068276 restraints weight = 70452.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.070538 restraints weight = 38215.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.071741 restraints weight = 25135.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.072729 restraints weight = 19262.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073233 restraints weight = 16091.326| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22667 Z= 0.145 Angle : 0.695 14.984 30734 Z= 0.331 Chirality : 0.046 0.480 3403 Planarity : 0.004 0.063 3918 Dihedral : 6.789 146.649 3120 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.14 % Allowed : 17.92 % Favored : 80.94 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2736 helix: 0.65 (0.15), residues: 1177 sheet: 0.37 (0.22), residues: 553 loop : 0.09 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 14 TYR 0.016 0.001 TYR F 277 PHE 0.015 0.001 PHE I 279 TRP 0.053 0.002 TRP I 356 HIS 0.005 0.001 HIS K 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (22655) covalent geometry : angle 0.69502 / 0.33 (30719) hydrogen bonds : bond 0.03387 / 2.19 ( 1130) hydrogen bonds : angle 4.92286 / 3.47 ( 2985) Misc. bond : bond 0.00053 / 0.03 ( 7) link_TRANS : bond 0.00127 / 0.06 ( 5) link_TRANS : angle 1.30159 / 0.68 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3855.39 seconds wall clock time: 67 minutes 39.29 seconds (4059.29 seconds total)