Starting phenix.real_space_refine on Thu Mar 5 13:00:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pdz_13343/03_2026/7pdz_13343.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pdz_13343/03_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_13343/03_2026/7pdz_13343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pdz_13343/03_2026/7pdz_13343.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pdz_13343/03_2026/7pdz_13343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pdz_13343/03_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-5986/lib/python3.9/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 Unresolved non-hydrogen dihedrals: 2 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 2 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 2 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 2 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 2 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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: 5.17, per 1000 atoms: 0.23 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: 2.03 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.01 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: 4.07 Time building geometry restraints manager: 2.60 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: 13371 34.78 - 69.57: 239 69.57 - 104.35: 32 104.35 - 139.13: 5 139.13 - 173.92: 4 Dihedral angle restraints: 13651 sinusoidal: 5548 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 13648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 2582 0.159 - 0.319: 535 0.319 - 0.478: 184 0.478 - 0.638: 91 0.638 - 0.797: 11 Chirality restraints: 3403 Sorted by residual: chirality pdb=" CA HYP T 1 " pdb=" N HYP T 1 " pdb=" C HYP T 1 " pdb=" CB HYP T 1 " both_signs ideal model delta sigma weight residual False 2.72 1.92 0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CG LEU F 117 " pdb=" CB LEU F 117 " pdb=" CD1 LEU F 117 " pdb=" CD2 LEU F 117 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA HYP R 1 " pdb=" N HYP R 1 " pdb=" C HYP R 1 " pdb=" CB HYP R 1 " both_signs ideal model delta sigma weight residual False 2.72 1.97 0.75 2.00e-01 2.50e+01 1.41e+01 ... (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: 3.720 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: 0.070 Set scattering table: 0.060 Process input model: 21.020 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.173 0.797 3403 Planarity : 0.013 0.127 3918 Dihedral : 15.060 173.918 8434 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 covalent geometry : bond 0.02263 (22655) covalent geometry : angle 1.95493 (30719) hydrogen bonds : bond 0.17922 ( 1130) hydrogen bonds : angle 8.30247 ( 2985) Misc. bond : bond 0.32325 ( 7) link_TRANS : bond 0.07017 ( 5) link_TRANS : angle 5.42410 ( 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 : 0.874 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: 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: 0.7410 (tpp) REVERT: E 94 ARG cc_start: 0.8090 (tpt170) cc_final: 0.7825 (tpt170) REVERT: E 187 MET cc_start: 0.8252 (mtp) cc_final: 0.7645 (mpp) REVERT: E 227 THR cc_start: 0.8242 (m) cc_final: 0.7396 (p) REVERT: F 197 HIS cc_start: 0.7446 (t-170) cc_final: 0.6317 (t70) REVERT: I 86 TRP cc_start: 0.8451 (m-10) cc_final: 0.8113 (m-10) REVERT: I 92 ASN cc_start: 0.8926 (m-40) cc_final: 0.8704 (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: 0.7218 (mtm) REVERT: J 292 ASP cc_start: 0.8309 (m-30) cc_final: 0.7685 (t0) REVERT: J 356 TRP cc_start: 0.6575 (m100) cc_final: 0.6000 (m-10) REVERT: K 203 THR cc_start: 0.8500 (p) cc_final: 0.8229 (t) REVERT: L 134 VAL cc_start: 0.9114 (t) cc_final: 0.8235 (t) REVERT: L 242 LEU cc_start: 0.8791 (mt) cc_final: 0.8262 (mt) REVERT: L 371 HIS cc_start: 0.6291 (m-70) cc_final: 0.5961 (m90) REVERT: N 65 LEU cc_start: 0.8238 (mt) cc_final: 0.7998 (mt) REVERT: N 141 SER cc_start: 0.8292 (m) cc_final: 0.8003 (t) REVERT: N 227 MET cc_start: 0.8667 (tpt) cc_final: 0.8441 (tpt) REVERT: O 119 MET cc_start: 0.9034 (mtm) cc_final: 0.8585 (mtp) REVERT: O 357 ILE cc_start: 0.8510 (mt) cc_final: 0.6982 (mt) outliers start: 5 outliers final: 4 residues processed: 618 average time/residue: 0.1701 time to fit residues: 156.1000 Evaluate side-chains 299 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 295 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 20 GLN E 209 HIS E 212 ASN E 270 GLN F 79 HIS F 197 HIS F 203 ASN F 205 GLN F 240 GLN I 41 GLN I 88 HIS ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 HIS K 111 ASN L 246 GLN L 354 GLN N 173 HIS ** O 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.103634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.072124 restraints weight = 69512.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.074423 restraints weight = 36388.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.075826 restraints weight = 23390.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.076889 restraints weight = 17567.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.077490 restraints weight = 14529.097| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22667 Z= 0.174 Angle : 0.785 9.930 30734 Z= 0.403 Chirality : 0.049 0.308 3403 Planarity : 0.005 0.056 3918 Dihedral : 10.469 174.470 3174 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.57 % Allowed : 12.39 % Favored : 85.03 % Cbeta Deviations : 0.00 % 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: -0.53 (0.15), residues: 2736 helix: -0.35 (0.14), residues: 1171 sheet: -0.03 (0.22), residues: 541 loop : -0.27 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 15 TYR 0.023 0.002 TYR K 294 PHE 0.020 0.002 PHE L 352 TRP 0.047 0.003 TRP I 356 HIS 0.007 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00383 (22655) covalent geometry : angle 0.78542 (30719) hydrogen bonds : bond 0.04784 ( 1130) hydrogen bonds : angle 5.83628 ( 2985) Misc. bond : bond 0.00126 ( 7) link_TRANS : bond 0.00207 ( 5) link_TRANS : angle 0.40061 ( 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: 61 poor density : 300 time to evaluate : 0.887 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 174 MET cc_start: 0.8985 (mmp) cc_final: 0.8785 (tmm) REVERT: E 186 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8315 (m) REVERT: E 210 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8849 (tt) REVERT: I 16 MET cc_start: 0.5369 (mmm) cc_final: 0.4857 (mmm) REVERT: I 78 ASN cc_start: 0.8267 (t0) cc_final: 0.8013 (t0) REVERT: I 92 ASN cc_start: 0.9081 (m-40) cc_final: 0.8716 (m-40) REVERT: I 123 MET cc_start: 0.8373 (tpp) cc_final: 0.8163 (tpp) REVERT: I 269 MET cc_start: 0.7582 (mmt) cc_final: 0.7317 (tpp) REVERT: I 280 ASN cc_start: 0.9101 (m-40) cc_final: 0.8867 (m110) REVERT: I 283 MET cc_start: 0.9254 (mmm) cc_final: 0.8991 (mmm) REVERT: J 252 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.8073 (t0) REVERT: J 292 ASP cc_start: 0.8415 (m-30) cc_final: 0.7689 (t0) REVERT: L 105 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8258 (mm) REVERT: L 140 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8265 (mm) REVERT: L 153 MET cc_start: 0.8055 (ttp) cc_final: 0.7738 (tmm) REVERT: L 227 MET cc_start: 0.8204 (ttm) cc_final: 0.7915 (ttm) REVERT: L 371 HIS cc_start: 0.6509 (m-70) cc_final: 0.6309 (m90) REVERT: N 65 LEU cc_start: 0.8065 (mt) cc_final: 0.7695 (mt) REVERT: N 141 SER cc_start: 0.8323 (m) cc_final: 0.8011 (t) REVERT: N 227 MET cc_start: 0.8727 (tpt) cc_final: 0.8420 (tpt) REVERT: O 16 MET cc_start: 0.6852 (mmm) cc_final: 0.6558 (mmm) REVERT: O 227 MET cc_start: 0.8701 (mmm) cc_final: 0.8352 (mmm) REVERT: O 253 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8110 (mp0) outliers start: 61 outliers final: 27 residues processed: 343 average time/residue: 0.1483 time to fit residues: 79.2658 Evaluate side-chains 258 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain F residue 71 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 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 J residue 242 LEU Chi-restraints excluded: chain J residue 252 ASN Chi-restraints excluded: chain K residue 248 ILE 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 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 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 159 VAL 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: 3.9990 chunk 39 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 208 optimal weight: 0.0980 chunk 213 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 206 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 205 GLN I 88 HIS L 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.101979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070067 restraints weight = 70254.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.072309 restraints weight = 37811.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.073618 restraints weight = 24893.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.074632 restraints weight = 18908.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.075230 restraints weight = 15782.078| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22667 Z= 0.171 Angle : 0.703 7.723 30734 Z= 0.353 Chirality : 0.047 0.305 3403 Planarity : 0.005 0.058 3918 Dihedral : 9.619 154.932 3170 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.90 % Allowed : 14.21 % Favored : 83.90 % Cbeta Deviations : 0.00 % 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: -0.10 (0.16), residues: 2736 helix: 0.03 (0.15), residues: 1180 sheet: 0.24 (0.21), residues: 569 loop : -0.13 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 290 TYR 0.022 0.002 TYR F 198 PHE 0.023 0.002 PHE L 352 TRP 0.034 0.002 TRP F 271 HIS 0.006 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00385 (22655) covalent geometry : angle 0.70324 (30719) hydrogen bonds : bond 0.04228 ( 1130) hydrogen bonds : angle 5.49020 ( 2985) Misc. bond : bond 0.00088 ( 7) link_TRANS : bond 0.00273 ( 5) link_TRANS : angle 0.54124 ( 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 289 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.901 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 152 HIS cc_start: 0.8335 (m-70) cc_final: 0.8050 (m-70) REVERT: E 174 MET cc_start: 0.8940 (mmp) cc_final: 0.8698 (tmm) REVERT: F 197 HIS cc_start: 0.6479 (t70) cc_final: 0.4252 (t70) REVERT: F 199 TYR cc_start: 0.9127 (p90) cc_final: 0.8385 (p90) REVERT: I 78 ASN cc_start: 0.8426 (t0) cc_final: 0.8120 (t0) REVERT: I 153 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8522 (tpp) REVERT: I 227 MET cc_start: 0.8688 (tpt) cc_final: 0.8471 (tpt) REVERT: I 269 MET cc_start: 0.7657 (mmt) cc_final: 0.7030 (mpp) REVERT: I 313 MET cc_start: 0.9033 (mmm) cc_final: 0.8773 (mmm) REVERT: J 252 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8058 (t0) REVERT: J 292 ASP cc_start: 0.8531 (m-30) cc_final: 0.7693 (t0) REVERT: J 326 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8010 (mmmt) REVERT: K 189 LEU cc_start: 0.8684 (tp) cc_final: 0.8482 (tp) REVERT: L 105 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8235 (mm) REVERT: L 153 MET cc_start: 0.8071 (ttp) cc_final: 0.7765 (tmm) REVERT: L 355 MET cc_start: 0.7856 (mmt) cc_final: 0.7648 (mmt) REVERT: L 371 HIS cc_start: 0.6871 (m-70) cc_final: 0.6478 (m90) REVERT: N 47 MET cc_start: 0.6315 (ptp) cc_final: 0.5735 (tmm) REVERT: N 123 MET cc_start: 0.9287 (mmm) cc_final: 0.8478 (tpp) REVERT: N 141 SER cc_start: 0.8357 (m) cc_final: 0.8009 (t) REVERT: N 227 MET cc_start: 0.8881 (tpt) cc_final: 0.8486 (tpt) REVERT: N 269 MET cc_start: 0.7786 (mtm) cc_final: 0.7559 (ttp) REVERT: O 16 MET cc_start: 0.6918 (mmm) cc_final: 0.6560 (mmm) REVERT: O 44 MET cc_start: 0.3207 (ptt) cc_final: 0.3003 (ptt) REVERT: O 357 ILE cc_start: 0.8882 (mm) cc_final: 0.8488 (mp) outliers start: 45 outliers final: 26 residues processed: 277 average time/residue: 0.1471 time to fit residues: 64.1707 Evaluate side-chains 251 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 186 THR 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 326 LYS Chi-restraints excluded: chain I residue 356 TRP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 ASN 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 361 GLU 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 257 CYS Chi-restraints excluded: chain T residue 7 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: 40.0000 chunk 109 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 160 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 HIS ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN O 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.109963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.078885 restraints weight = 69132.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.081169 restraints weight = 39064.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.081744 restraints weight = 23980.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082385 restraints weight = 18374.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082361 restraints weight = 15807.531| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 0.061 22667 Z= 0.153 Angle : 0.663 7.588 30734 Z= 0.331 Chirality : 0.046 0.260 3403 Planarity : 0.005 0.091 3918 Dihedral : 8.844 140.184 3170 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.28 % Allowed : 14.42 % Favored : 83.31 % Cbeta Deviations : 0.00 % 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: 0.12 (0.16), residues: 2736 helix: 0.24 (0.15), residues: 1179 sheet: 0.31 (0.22), residues: 570 loop : -0.00 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 372 TYR 0.026 0.002 TYR F 277 PHE 0.021 0.001 PHE L 352 TRP 0.026 0.002 TRP F 271 HIS 0.007 0.001 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00342 (22655) covalent geometry : angle 0.66315 (30719) hydrogen bonds : bond 0.03883 ( 1130) hydrogen bonds : angle 5.28183 ( 2985) Misc. bond : bond 0.00067 ( 7) link_TRANS : bond 0.00241 ( 5) link_TRANS : angle 0.57699 ( 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 287 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 233 time to evaluate : 0.845 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 88 MET cc_start: 0.7778 (mmm) cc_final: 0.7423 (mmm) REVERT: I 47 MET cc_start: 0.5868 (tmm) cc_final: 0.5582 (tmm) REVERT: I 78 ASN cc_start: 0.8418 (t0) cc_final: 0.8090 (t0) REVERT: I 153 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8565 (tpp) REVERT: I 227 MET cc_start: 0.8678 (tpt) cc_final: 0.8456 (tpt) REVERT: I 269 MET cc_start: 0.7767 (mmt) cc_final: 0.7197 (mpp) REVERT: I 313 MET cc_start: 0.8997 (mmm) cc_final: 0.8761 (mmm) REVERT: J 173 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6255 (p-80) REVERT: J 292 ASP cc_start: 0.8452 (m-30) cc_final: 0.7732 (t0) REVERT: J 293 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8455 (mm) REVERT: J 326 LYS cc_start: 0.8310 (mmmt) cc_final: 0.8057 (mmmt) REVERT: K 16 MET cc_start: 0.7829 (mmt) cc_final: 0.7545 (mmt) REVERT: L 105 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8071 (mm) REVERT: L 313 MET cc_start: 0.8774 (tpp) cc_final: 0.8503 (ttm) REVERT: N 47 MET cc_start: 0.6579 (ptp) cc_final: 0.5993 (tmm) REVERT: N 65 LEU cc_start: 0.8163 (mt) cc_final: 0.7949 (mt) REVERT: N 85 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.8006 (tt) REVERT: N 123 MET cc_start: 0.9014 (mmm) cc_final: 0.8500 (tpp) REVERT: N 141 SER cc_start: 0.8370 (m) cc_final: 0.8042 (t) REVERT: N 227 MET cc_start: 0.8857 (tpt) cc_final: 0.8484 (tpt) REVERT: N 313 MET cc_start: 0.9197 (tpp) cc_final: 0.8904 (ttm) REVERT: O 16 MET cc_start: 0.7001 (mmm) cc_final: 0.6705 (mmm) REVERT: O 107 GLU cc_start: 0.7499 (tt0) cc_final: 0.7246 (pt0) REVERT: O 227 MET cc_start: 0.8819 (mmm) cc_final: 0.8522 (mmm) REVERT: O 357 ILE cc_start: 0.8929 (mm) cc_final: 0.8448 (mp) outliers start: 54 outliers final: 31 residues processed: 274 average time/residue: 0.1466 time to fit residues: 63.4659 Evaluate side-chains 257 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 186 THR 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 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 202 THR 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 242 LEU Chi-restraints excluded: chain J residue 252 ASN Chi-restraints excluded: chain J residue 293 LEU 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 60 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 320 LEU 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 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 Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 54 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 205 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 266 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 178 optimal weight: 0.0970 chunk 134 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 HIS E 157 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN L 354 GLN N 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.102137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.070268 restraints weight = 69473.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.072670 restraints weight = 36988.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.074155 restraints weight = 24096.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.075001 restraints weight = 18211.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.075741 restraints weight = 15253.647| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22667 Z= 0.118 Angle : 0.639 10.732 30734 Z= 0.314 Chirality : 0.044 0.214 3403 Planarity : 0.004 0.047 3918 Dihedral : 8.209 141.972 3170 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.94 % Allowed : 15.18 % Favored : 82.88 % Cbeta Deviations : 0.00 % 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: 0.45 (0.16), residues: 2736 helix: 0.54 (0.16), residues: 1156 sheet: 0.39 (0.22), residues: 570 loop : 0.20 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 372 TYR 0.024 0.001 TYR F 277 PHE 0.016 0.001 PHE F 29 TRP 0.026 0.002 TRP F 271 HIS 0.012 0.001 HIS I 275 Details of bonding type rmsd covalent geometry : bond 0.00256 (22655) covalent geometry : angle 0.63952 (30719) hydrogen bonds : bond 0.03580 ( 1130) hydrogen bonds : angle 5.06030 ( 2985) Misc. bond : bond 0.00057 ( 7) link_TRANS : bond 0.00122 ( 5) link_TRANS : angle 0.43536 ( 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 296 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 0.951 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: 0.7738 (mmm) cc_final: 0.7422 (mmm) REVERT: F 199 TYR cc_start: 0.9149 (p90) cc_final: 0.8536 (p90) REVERT: I 78 ASN cc_start: 0.8414 (t0) cc_final: 0.8050 (t0) REVERT: I 153 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8654 (tpp) REVERT: I 227 MET cc_start: 0.8656 (tpt) cc_final: 0.8396 (tpt) REVERT: J 111 ASN cc_start: 0.8226 (m-40) cc_final: 0.7681 (m-40) REVERT: J 292 ASP cc_start: 0.8515 (m-30) cc_final: 0.7801 (t0) REVERT: J 293 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8324 (mm) REVERT: K 16 MET cc_start: 0.7801 (mmt) cc_final: 0.7406 (mmt) REVERT: K 44 MET cc_start: 0.8370 (mtp) cc_final: 0.8003 (mtp) REVERT: K 325 MET cc_start: 0.8879 (mmm) cc_final: 0.8634 (mmm) REVERT: L 44 MET cc_start: 0.7719 (mtp) cc_final: 0.6445 (mtp) REVERT: L 105 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8107 (mm) REVERT: N 47 MET cc_start: 0.5646 (ptp) cc_final: 0.5260 (tmm) REVERT: N 65 LEU cc_start: 0.8195 (mt) cc_final: 0.7969 (mt) REVERT: N 123 MET cc_start: 0.9052 (mmm) cc_final: 0.8516 (tpp) REVERT: N 141 SER cc_start: 0.8264 (m) cc_final: 0.7970 (t) REVERT: N 227 MET cc_start: 0.8840 (tpt) cc_final: 0.8464 (tpt) REVERT: N 313 MET cc_start: 0.9201 (tpp) cc_final: 0.8987 (ttm) REVERT: O 16 MET cc_start: 0.7037 (mmm) cc_final: 0.6725 (mmm) REVERT: O 107 GLU cc_start: 0.7419 (tt0) cc_final: 0.7142 (pt0) REVERT: O 132 MET cc_start: 0.8442 (tmm) cc_final: 0.8087 (ppp) REVERT: O 227 MET cc_start: 0.8854 (mmm) cc_final: 0.8577 (mmm) REVERT: O 357 ILE cc_start: 0.8875 (mm) cc_final: 0.8471 (mp) outliers start: 46 outliers final: 27 residues processed: 284 average time/residue: 0.1428 time to fit residues: 65.0995 Evaluate side-chains 245 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 186 THR 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 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 290 ARG Chi-restraints excluded: chain I residue 356 TRP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 293 LEU 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 142 LEU Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 354 GLN Chi-restraints excluded: chain N residue 201 THR 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 Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 170 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 274 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 273 optimal weight: 0.4980 chunk 260 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 230 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN I 92 ASN I 173 HIS K 115 ASN N 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.101188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.069355 restraints weight = 69896.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.071638 restraints weight = 37464.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.073057 restraints weight = 24642.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.074016 restraints weight = 18743.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.074445 restraints weight = 15636.077| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22667 Z= 0.142 Angle : 0.654 11.829 30734 Z= 0.319 Chirality : 0.045 0.187 3403 Planarity : 0.004 0.046 3918 Dihedral : 7.902 139.001 3170 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.90 % Allowed : 15.81 % Favored : 82.29 % Cbeta Deviations : 0.00 % 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: 0.48 (0.16), residues: 2736 helix: 0.61 (0.16), residues: 1159 sheet: 0.39 (0.22), residues: 570 loop : 0.15 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 225 TYR 0.023 0.001 TYR F 198 PHE 0.015 0.001 PHE F 29 TRP 0.023 0.002 TRP F 271 HIS 0.007 0.001 HIS I 275 Details of bonding type rmsd covalent geometry : bond 0.00314 (22655) covalent geometry : angle 0.65440 (30719) hydrogen bonds : bond 0.03513 ( 1130) hydrogen bonds : angle 5.03653 ( 2985) Misc. bond : bond 0.00054 ( 7) link_TRANS : bond 0.00200 ( 5) link_TRANS : angle 0.53817 ( 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 262 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 0.578 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 88 MET cc_start: 0.7747 (mmm) cc_final: 0.7455 (mmm) REVERT: F 199 TYR cc_start: 0.9200 (p90) cc_final: 0.8611 (p90) REVERT: I 78 ASN cc_start: 0.8419 (t0) cc_final: 0.8021 (t0) REVERT: I 153 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8638 (tpp) REVERT: I 227 MET cc_start: 0.8676 (tpt) cc_final: 0.8413 (tpt) REVERT: J 111 ASN cc_start: 0.8313 (m-40) cc_final: 0.7755 (m-40) REVERT: J 173 HIS cc_start: 0.7012 (OUTLIER) cc_final: 0.6322 (p-80) REVERT: J 293 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8411 (mm) REVERT: K 16 MET cc_start: 0.7963 (mmt) cc_final: 0.7499 (mmt) REVERT: L 105 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8232 (mm) REVERT: N 47 MET cc_start: 0.5742 (ptp) cc_final: 0.5323 (tmm) REVERT: N 123 MET cc_start: 0.9057 (mmm) cc_final: 0.8530 (tpp) REVERT: N 141 SER cc_start: 0.8304 (m) cc_final: 0.8014 (t) REVERT: N 227 MET cc_start: 0.8848 (tpt) cc_final: 0.8476 (tpt) REVERT: O 16 MET cc_start: 0.7148 (mmm) cc_final: 0.6830 (mmm) REVERT: O 44 MET cc_start: 0.1791 (ptt) cc_final: 0.1485 (ptt) REVERT: O 107 GLU cc_start: 0.7337 (tt0) cc_final: 0.7081 (pt0) REVERT: O 132 MET cc_start: 0.8476 (tmm) cc_final: 0.8083 (ppp) REVERT: O 227 MET cc_start: 0.8848 (mmm) cc_final: 0.8599 (mmm) outliers start: 45 outliers final: 33 residues processed: 250 average time/residue: 0.1480 time to fit residues: 58.8856 Evaluate side-chains 243 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 186 THR 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 49 GLN Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 326 LYS 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 J residue 242 LEU Chi-restraints excluded: chain J residue 252 ASN Chi-restraints excluded: chain J residue 293 LEU 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 320 LEU 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 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 Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 144 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 254 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 HIS ** 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 = 0.3902 r_free = 0.3902 target = 0.100256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.068348 restraints weight = 70298.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.070612 restraints weight = 37962.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.072039 restraints weight = 25064.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.072946 restraints weight = 18994.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.073549 restraints weight = 15924.100| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22667 Z= 0.160 Angle : 0.663 10.817 30734 Z= 0.323 Chirality : 0.045 0.190 3403 Planarity : 0.004 0.047 3918 Dihedral : 7.692 136.726 3170 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.85 % Allowed : 15.98 % Favored : 82.17 % Cbeta Deviations : 0.00 % 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 (0.16), residues: 2736 helix: 0.71 (0.16), residues: 1150 sheet: 0.41 (0.21), residues: 580 loop : 0.08 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 215 TYR 0.030 0.001 TYR F 277 PHE 0.014 0.001 PHE F 29 TRP 0.056 0.002 TRP F 271 HIS 0.006 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00358 (22655) covalent geometry : angle 0.66275 (30719) hydrogen bonds : bond 0.03526 ( 1130) hydrogen bonds : angle 5.01107 ( 2985) Misc. bond : bond 0.00070 ( 7) link_TRANS : bond 0.00255 ( 5) link_TRANS : angle 0.58452 ( 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 255 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.832 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: 0.7528 (mmm) cc_final: 0.7222 (mmm) REVERT: E 195 ARG cc_start: 0.8070 (ttp-170) cc_final: 0.7748 (ptt180) REVERT: F 199 TYR cc_start: 0.9156 (p90) cc_final: 0.8619 (p90) REVERT: I 78 ASN cc_start: 0.8623 (t0) cc_final: 0.8199 (t0) REVERT: I 153 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8624 (tpp) REVERT: I 227 MET cc_start: 0.8655 (tpt) cc_final: 0.8389 (tpt) REVERT: I 283 MET cc_start: 0.9050 (mmm) cc_final: 0.8414 (mmm) REVERT: J 47 MET cc_start: 0.7032 (ptt) cc_final: 0.6169 (ptt) REVERT: J 111 ASN cc_start: 0.8437 (m-40) cc_final: 0.7812 (m-40) REVERT: J 173 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.6322 (p-80) REVERT: J 293 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8436 (mm) REVERT: K 16 MET cc_start: 0.8095 (mmt) cc_final: 0.7595 (mmt) REVERT: L 44 MET cc_start: 0.7677 (mtp) cc_final: 0.7430 (mtp) REVERT: L 105 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8096 (mm) REVERT: N 47 MET cc_start: 0.5624 (ptp) cc_final: 0.5286 (tmm) REVERT: N 123 MET cc_start: 0.9063 (mmm) cc_final: 0.8517 (tpp) REVERT: N 141 SER cc_start: 0.8338 (m) cc_final: 0.8051 (t) REVERT: N 227 MET cc_start: 0.8860 (tpt) cc_final: 0.8504 (tpt) REVERT: O 16 MET cc_start: 0.7280 (mmm) cc_final: 0.6920 (mmm) REVERT: O 132 MET cc_start: 0.8482 (tmm) cc_final: 0.8020 (ppp) outliers start: 44 outliers final: 33 residues processed: 246 average time/residue: 0.1514 time to fit residues: 58.7491 Evaluate side-chains 242 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 F residue 173 TRP Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 326 LYS 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 J residue 242 LEU Chi-restraints excluded: chain J residue 252 ASN Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 115 ASN 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 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 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 Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 8 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 265 optimal weight: 0.0980 chunk 266 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 ASN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 HIS 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 = 0.3896 r_free = 0.3896 target = 0.099980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.068030 restraints weight = 70639.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070297 restraints weight = 38150.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071737 restraints weight = 25239.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.072674 restraints weight = 19239.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.073188 restraints weight = 16101.881| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22667 Z= 0.154 Angle : 0.674 12.774 30734 Z= 0.325 Chirality : 0.045 0.196 3403 Planarity : 0.004 0.046 3918 Dihedral : 7.540 136.051 3170 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.90 % Allowed : 16.15 % Favored : 81.96 % Cbeta Deviations : 0.00 % 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: 0.55 (0.16), residues: 2736 helix: 0.72 (0.16), residues: 1150 sheet: 0.44 (0.22), residues: 570 loop : 0.10 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 225 TYR 0.023 0.001 TYR F 277 PHE 0.021 0.001 PHE J 223 TRP 0.044 0.002 TRP F 271 HIS 0.005 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00344 (22655) covalent geometry : angle 0.67401 (30719) hydrogen bonds : bond 0.03475 ( 1130) hydrogen bonds : angle 4.98822 ( 2985) Misc. bond : bond 0.00065 ( 7) link_TRANS : bond 0.00231 ( 5) link_TRANS : angle 0.50497 ( 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 256 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.809 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: 0.7602 (mmm) cc_final: 0.7352 (mmm) REVERT: E 195 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7703 (ptt180) REVERT: F 199 TYR cc_start: 0.9214 (p90) cc_final: 0.8656 (p90) REVERT: I 78 ASN cc_start: 0.8541 (t0) cc_final: 0.8102 (t0) REVERT: I 153 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8648 (tpp) REVERT: I 227 MET cc_start: 0.8612 (tpt) cc_final: 0.8366 (tpt) REVERT: J 111 ASN cc_start: 0.8472 (m-40) cc_final: 0.7845 (m-40) REVERT: J 173 HIS cc_start: 0.6883 (OUTLIER) cc_final: 0.6260 (p-80) REVERT: J 293 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8448 (mm) REVERT: J 356 TRP cc_start: 0.7198 (m100) cc_final: 0.6305 (m100) REVERT: K 16 MET cc_start: 0.8161 (mmt) cc_final: 0.7598 (mmt) REVERT: K 56 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8356 (t0) REVERT: L 44 MET cc_start: 0.7919 (mtp) cc_final: 0.7666 (mtm) REVERT: L 105 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8100 (mm) REVERT: N 47 MET cc_start: 0.5664 (ptp) cc_final: 0.5341 (tmm) REVERT: N 123 MET cc_start: 0.9085 (mmm) cc_final: 0.8504 (tpp) REVERT: N 141 SER cc_start: 0.8330 (m) cc_final: 0.8062 (t) REVERT: N 227 MET cc_start: 0.8850 (tpt) cc_final: 0.8519 (tpt) REVERT: O 16 MET cc_start: 0.7231 (mmm) cc_final: 0.6879 (mmm) REVERT: O 44 MET cc_start: 0.1507 (ptt) cc_final: 0.1269 (ptt) REVERT: O 132 MET cc_start: 0.8597 (tmm) cc_final: 0.8084 (ppp) REVERT: O 227 MET cc_start: 0.8821 (mmm) cc_final: 0.8228 (mmm) outliers start: 45 outliers final: 30 residues processed: 248 average time/residue: 0.1404 time to fit residues: 56.1014 Evaluate side-chains 234 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 F residue 173 TRP Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 326 LYS 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 J residue 242 LEU Chi-restraints excluded: chain J residue 252 ASN 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 56 ASP Chi-restraints excluded: chain K residue 334 GLU 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 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 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 Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 237 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 255 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 144 optimal weight: 0.0870 chunk 212 optimal weight: 0.2980 chunk 268 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.101194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.069303 restraints weight = 70241.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.071566 restraints weight = 37655.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072924 restraints weight = 24529.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.073911 restraints weight = 18636.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.074413 restraints weight = 15597.721| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5600 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= 0.119 Angle : 0.674 12.052 30734 Z= 0.323 Chirality : 0.044 0.260 3403 Planarity : 0.004 0.046 3918 Dihedral : 7.371 135.727 3170 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.73 % Allowed : 16.48 % Favored : 81.79 % Cbeta Deviations : 0.00 % 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: 0.63 (0.16), residues: 2736 helix: 0.79 (0.16), residues: 1156 sheet: 0.48 (0.22), residues: 566 loop : 0.15 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 86 TYR 0.018 0.001 TYR F 198 PHE 0.015 0.001 PHE F 29 TRP 0.033 0.002 TRP F 271 HIS 0.004 0.001 HIS O 161 Details of bonding type rmsd covalent geometry : bond 0.00262 (22655) covalent geometry : angle 0.67453 (30719) hydrogen bonds : bond 0.03358 ( 1130) hydrogen bonds : angle 4.91973 ( 2985) Misc. bond : bond 0.00059 ( 7) link_TRANS : bond 0.00087 ( 5) link_TRANS : angle 0.32660 ( 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 259 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.843 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: E 88 MET cc_start: 0.7650 (mmm) cc_final: 0.7437 (mmm) REVERT: E 195 ARG cc_start: 0.7943 (ttp-170) cc_final: 0.7592 (ptt180) REVERT: F 86 ARG cc_start: 0.8952 (ttp-170) cc_final: 0.8714 (ttp-110) REVERT: F 199 TYR cc_start: 0.9226 (p90) cc_final: 0.8712 (p90) REVERT: I 78 ASN cc_start: 0.8620 (t0) cc_final: 0.8223 (t0) REVERT: I 142 LEU cc_start: 0.9455 (tp) cc_final: 0.9241 (tp) REVERT: I 153 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8645 (tpp) REVERT: I 227 MET cc_start: 0.8643 (tpt) cc_final: 0.8358 (tpt) REVERT: I 283 MET cc_start: 0.8826 (mmp) cc_final: 0.8334 (mmm) REVERT: J 47 MET cc_start: 0.7108 (ptt) cc_final: 0.6236 (ptt) REVERT: J 111 ASN cc_start: 0.8296 (m-40) cc_final: 0.7692 (m-40) REVERT: J 293 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8435 (mm) REVERT: J 356 TRP cc_start: 0.7033 (m100) cc_final: 0.6264 (m100) REVERT: K 16 MET cc_start: 0.7995 (mmt) cc_final: 0.7456 (mmt) REVERT: L 105 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8030 (mm) REVERT: L 227 MET cc_start: 0.8205 (mtp) cc_final: 0.7970 (ttm) REVERT: N 47 MET cc_start: 0.5617 (ptp) cc_final: 0.5266 (tmm) REVERT: N 123 MET cc_start: 0.8954 (mmm) cc_final: 0.8271 (tpp) REVERT: N 141 SER cc_start: 0.8262 (m) cc_final: 0.8051 (t) REVERT: N 227 MET cc_start: 0.8840 (tpt) cc_final: 0.8514 (tpt) REVERT: O 16 MET cc_start: 0.7201 (mmm) cc_final: 0.6850 (mmm) REVERT: O 44 MET cc_start: 0.1412 (ptt) cc_final: 0.1140 (ptt) REVERT: O 227 MET cc_start: 0.8911 (mmm) cc_final: 0.8295 (mmm) REVERT: O 357 ILE cc_start: 0.8892 (mm) cc_final: 0.8523 (mt) outliers start: 41 outliers final: 28 residues processed: 254 average time/residue: 0.1429 time to fit residues: 58.2577 Evaluate side-chains 235 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 173 TRP Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 ASN 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 N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU 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 103 VAL Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 138 optimal weight: 0.3980 chunk 241 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** 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 = 0.3886 r_free = 0.3886 target = 0.099343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.067666 restraints weight = 71193.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.069729 restraints weight = 38271.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.070978 restraints weight = 25209.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.072005 restraints weight = 19322.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072490 restraints weight = 16159.606| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22667 Z= 0.174 Angle : 0.711 13.018 30734 Z= 0.341 Chirality : 0.046 0.241 3403 Planarity : 0.004 0.070 3918 Dihedral : 7.356 133.578 3170 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.43 % Allowed : 17.12 % Favored : 81.45 % Cbeta Deviations : 0.00 % 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 (0.16), residues: 2736 helix: 0.68 (0.16), residues: 1158 sheet: 0.41 (0.22), residues: 566 loop : 0.12 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 177 TYR 0.017 0.002 TYR F 277 PHE 0.015 0.001 PHE F 29 TRP 0.060 0.003 TRP I 356 HIS 0.007 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00393 (22655) covalent geometry : angle 0.71097 (30719) hydrogen bonds : bond 0.03527 ( 1130) hydrogen bonds : angle 5.00713 ( 2985) Misc. bond : bond 0.00077 ( 7) link_TRANS : bond 0.00288 ( 5) link_TRANS : angle 0.51117 ( 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 239 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 195 ARG cc_start: 0.7971 (ttp-170) cc_final: 0.7607 (ptt180) REVERT: F 86 ARG cc_start: 0.9006 (ttp-170) cc_final: 0.8735 (ttp-110) REVERT: F 199 TYR cc_start: 0.9212 (p90) cc_final: 0.8712 (p90) REVERT: I 78 ASN cc_start: 0.8617 (t0) cc_final: 0.8227 (t0) REVERT: I 142 LEU cc_start: 0.9484 (tp) cc_final: 0.9275 (tp) REVERT: I 153 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8661 (tpp) REVERT: I 227 MET cc_start: 0.8612 (tpt) cc_final: 0.8335 (tpt) REVERT: J 47 MET cc_start: 0.7113 (ptt) cc_final: 0.6264 (ptt) REVERT: J 111 ASN cc_start: 0.8433 (m-40) cc_final: 0.7859 (m-40) REVERT: J 293 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8528 (mm) REVERT: J 356 TRP cc_start: 0.7252 (m100) cc_final: 0.6431 (m100) REVERT: K 16 MET cc_start: 0.8303 (mmt) cc_final: 0.7749 (mmt) REVERT: L 95 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7573 (tpm170) REVERT: L 105 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8096 (mm) REVERT: N 123 MET cc_start: 0.8898 (mmm) cc_final: 0.8196 (tpp) REVERT: N 141 SER cc_start: 0.8381 (m) cc_final: 0.7982 (p) REVERT: N 227 MET cc_start: 0.8872 (tpt) cc_final: 0.8560 (tpt) REVERT: O 16 MET cc_start: 0.7317 (mmm) cc_final: 0.7018 (mmm) REVERT: O 44 MET cc_start: 0.1507 (ptt) cc_final: 0.1179 (ptt) REVERT: O 132 MET cc_start: 0.8506 (ppp) cc_final: 0.8219 (ppp) REVERT: O 227 MET cc_start: 0.8890 (mmm) cc_final: 0.8649 (mmm) outliers start: 34 outliers final: 27 residues processed: 234 average time/residue: 0.1441 time to fit residues: 53.8342 Evaluate side-chains 232 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 173 TRP Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 ASN Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain L residue 95 ARG 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 N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU 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 103 VAL Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 170 optimal weight: 0.3980 chunk 134 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 257 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 12 optimal weight: 0.0370 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.100164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.068202 restraints weight = 70235.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.070510 restraints weight = 38011.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.071859 restraints weight = 24957.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.072657 restraints weight = 19042.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073364 restraints weight = 16144.116| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22667 Z= 0.136 Angle : 0.689 12.645 30734 Z= 0.328 Chirality : 0.045 0.237 3403 Planarity : 0.004 0.058 3918 Dihedral : 7.280 132.860 3170 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.39 % Allowed : 17.33 % Favored : 81.28 % Cbeta Deviations : 0.00 % 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: 0.57 (0.16), residues: 2736 helix: 0.74 (0.16), residues: 1164 sheet: 0.40 (0.21), residues: 566 loop : 0.15 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 177 TYR 0.014 0.001 TYR I 143 PHE 0.015 0.001 PHE F 29 TRP 0.080 0.003 TRP O 356 HIS 0.005 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00307 (22655) covalent geometry : angle 0.68899 (30719) hydrogen bonds : bond 0.03364 ( 1130) hydrogen bonds : angle 4.94224 ( 2985) Misc. bond : bond 0.00057 ( 7) link_TRANS : bond 0.00155 ( 5) link_TRANS : angle 0.37455 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4141.80 seconds wall clock time: 72 minutes 18.69 seconds (4338.69 seconds total)