Starting phenix.real_space_refine on Mon Apr 6 23:15:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y52_72506/04_2026/9y52_72506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y52_72506/04_2026/9y52_72506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y52_72506/04_2026/9y52_72506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y52_72506/04_2026/9y52_72506.map" model { file = "/net/cci-nas-00/data/ceres_data/9y52_72506/04_2026/9y52_72506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y52_72506/04_2026/9y52_72506.cif" } resolution = 3.46 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= 0.004 sd= 0.020 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 10 5.49 5 Mg 5 5.21 5 S 127 5.16 5 C 14189 2.51 5 N 3742 2.21 5 O 4314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22387 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "B" Number of atoms: 2878 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 366, 2871 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 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 Conformer: "B" Number of residues, atoms: 366, 2871 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 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 bond proxies already assigned to first conformer: 2924 Chain: "C" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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: "D" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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: "E" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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: "W" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1358 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "a" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "b" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "c" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "d" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "e" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "A" 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: "B" 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: "C" 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: "D" 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: "E" 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} Time building chain proxies: 5.89, per 1000 atoms: 0.26 Number of scatterers: 22387 At special positions: 0 Unit cell: (115.02, 126.36, 232.2, 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 127 16.00 P 10 15.00 Mg 5 11.99 O 4314 8.00 N 3742 7.00 C 14189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5288 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 37 sheets defined 49.3% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 38 through 41 removed outlier: 3.553A pdb=" N GLN A 41 " --> pdb=" O PRO A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 38 through 41' Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.747A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.814A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.804A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.845A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.633A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.535A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.666A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.511A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 289 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.852A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.510A pdb=" N MET A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 306' Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.529A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.790A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.616A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 61' Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.845A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.772A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.583A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.903A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.720A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.608A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.643A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 257' Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.568A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.501A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 263 through 267' Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.818A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.517A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 305' Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 356 removed outlier: 3.556A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 57 through 61 removed outlier: 3.676A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 61' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.738A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.876A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.749A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.795A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.781A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 255' Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.780A pdb=" N THR C 260 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.602A pdb=" N PHE C 266 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.880A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.556A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 356 removed outlier: 3.661A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.687A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS D 61 " --> pdb=" O ALA D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 61' Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.800A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.955A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.668A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.849A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.722A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 255' Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.835A pdb=" N THR D 260 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.502A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 349 through 356 removed outlier: 3.626A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.513A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 61 removed outlier: 3.735A pdb=" N SER E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS E 61 " --> pdb=" O ALA E 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 57 through 61' Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.567A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.720A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 195 removed outlier: 3.928A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.716A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.781A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 255 removed outlier: 3.724A pdb=" N ARG E 254 " --> pdb=" O GLY E 251 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE E 255 " --> pdb=" O ASN E 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 251 through 255' Processing helix chain 'E' and resid 257 through 262 removed outlier: 3.724A pdb=" N THR E 260 " --> pdb=" O CYS E 257 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 removed outlier: 3.555A pdb=" N PHE E 266 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 263 through 267' Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.892A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.520A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.713A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'W' and resid 41 through 52 Processing helix chain 'W' and resid 53 through 66 removed outlier: 3.611A pdb=" N GLU W 57 " --> pdb=" O GLY W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 93 removed outlier: 3.715A pdb=" N LYS W 71 " --> pdb=" O GLY W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 105 Processing helix chain 'W' and resid 105 through 122 removed outlier: 3.604A pdb=" N ASN W 122 " --> pdb=" O PHE W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 136 Processing helix chain 'W' and resid 137 through 146 removed outlier: 3.536A pdb=" N TRP W 143 " --> pdb=" O ALA W 140 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL W 144 " --> pdb=" O LEU W 141 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET W 146 " --> pdb=" O TRP W 143 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 172 removed outlier: 3.979A pdb=" N TYR W 164 " --> pdb=" O ALA W 160 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG W 167 " --> pdb=" O PHE W 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 176 through 201 removed outlier: 4.135A pdb=" N VAL W 180 " --> pdb=" O ASP W 176 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP W 190 " --> pdb=" O TYR W 186 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 20 removed outlier: 3.838A pdb=" N ILE a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL a 20 " --> pdb=" O ASN a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 31 Processing helix chain 'a' and resid 58 through 60 No H-bonds generated for 'chain 'a' and resid 58 through 60' Processing helix chain 'a' and resid 66 through 74 Processing helix chain 'a' and resid 110 through 120 Processing helix chain 'a' and resid 120 through 128 removed outlier: 4.165A pdb=" N ILE a 124 " --> pdb=" O SER a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 143 removed outlier: 3.524A pdb=" N ASP a 142 " --> pdb=" O GLY a 139 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE a 143 " --> pdb=" O LEU a 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 139 through 143' Processing helix chain 'a' and resid 145 through 153 removed outlier: 4.198A pdb=" N LEU a 149 " --> pdb=" O ASP a 145 " (cutoff:3.500A) Processing helix chain 'a' and resid 154 through 156 No H-bonds generated for 'chain 'a' and resid 154 through 156' Processing helix chain 'b' and resid 8 through 20 removed outlier: 3.843A pdb=" N ILE b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL b 20 " --> pdb=" O ASN b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 31 Processing helix chain 'b' and resid 58 through 60 No H-bonds generated for 'chain 'b' and resid 58 through 60' Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 110 through 120 Processing helix chain 'b' and resid 120 through 128 removed outlier: 4.217A pdb=" N ILE b 124 " --> pdb=" O SER b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 143 removed outlier: 3.638A pdb=" N ASP b 142 " --> pdb=" O GLY b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 153 Processing helix chain 'b' and resid 154 through 156 No H-bonds generated for 'chain 'b' and resid 154 through 156' Processing helix chain 'c' and resid 8 through 20 removed outlier: 3.885A pdb=" N ILE c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL c 20 " --> pdb=" O ASN c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 31 Processing helix chain 'c' and resid 58 through 60 No H-bonds generated for 'chain 'c' and resid 58 through 60' Processing helix chain 'c' and resid 66 through 73 Processing helix chain 'c' and resid 110 through 120 Processing helix chain 'c' and resid 120 through 128 removed outlier: 4.144A pdb=" N ILE c 124 " --> pdb=" O SER c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 removed outlier: 3.587A pdb=" N ASP c 142 " --> pdb=" O GLY c 139 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE c 143 " --> pdb=" O LEU c 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 139 through 143' Processing helix chain 'c' and resid 146 through 153 Processing helix chain 'c' and resid 154 through 156 No H-bonds generated for 'chain 'c' and resid 154 through 156' Processing helix chain 'd' and resid 8 through 20 removed outlier: 3.882A pdb=" N ILE d 12 " --> pdb=" O ASN d 8 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL d 20 " --> pdb=" O ASN d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 31 Processing helix chain 'd' and resid 58 through 60 No H-bonds generated for 'chain 'd' and resid 58 through 60' Processing helix chain 'd' and resid 66 through 74 Processing helix chain 'd' and resid 110 through 120 Processing helix chain 'd' and resid 120 through 128 removed outlier: 4.123A pdb=" N ILE d 124 " --> pdb=" O SER d 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 143 removed outlier: 3.661A pdb=" N ASP d 142 " --> pdb=" O GLY d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 153 Processing helix chain 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing helix chain 'e' and resid 8 through 20 removed outlier: 3.820A pdb=" N ILE e 12 " --> pdb=" O ASN e 8 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL e 20 " --> pdb=" O ASN e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 25 through 31 Processing helix chain 'e' and resid 58 through 60 No H-bonds generated for 'chain 'e' and resid 58 through 60' Processing helix chain 'e' and resid 66 through 74 Processing helix chain 'e' and resid 110 through 120 Processing helix chain 'e' and resid 120 through 128 removed outlier: 4.111A pdb=" N ILE e 124 " --> pdb=" O SER e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 139 through 143 removed outlier: 3.699A pdb=" N ASP e 142 " --> pdb=" O GLY e 139 " (cutoff:3.500A) Processing helix chain 'e' and resid 146 through 153 Processing helix chain 'e' and resid 154 through 156 No H-bonds generated for 'chain 'e' and resid 154 through 156' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.530A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.546A pdb=" N TYR A 53 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 7.463A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.580A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 7.392A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.665A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 170 removed outlier: 7.443A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'D' and resid 8 through 12 removed outlier: 3.511A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'D' and resid 103 through 107 Processing sheet with id=AC2, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.504A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 removed outlier: 7.506A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.529A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 170 removed outlier: 7.507A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD1, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.476A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL a 49 " --> pdb=" O LEU a 40 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU a 40 " --> pdb=" O VAL a 49 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N GLU a 51 " --> pdb=" O PHE a 38 " (cutoff:3.500A) removed outlier: 10.625A pdb=" N PHE a 38 " --> pdb=" O GLU a 51 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LYS a 53 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL a 36 " --> pdb=" O LYS a 53 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE a 55 " --> pdb=" O LYS a 34 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS a 133 " --> pdb=" O LEU a 99 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.476A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL a 49 " --> pdb=" O LEU a 40 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU a 40 " --> pdb=" O VAL a 49 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N GLU a 51 " --> pdb=" O PHE a 38 " (cutoff:3.500A) removed outlier: 10.625A pdb=" N PHE a 38 " --> pdb=" O GLU a 51 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LYS a 53 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL a 36 " --> pdb=" O LYS a 53 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE a 55 " --> pdb=" O LYS a 34 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.640A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL b 49 " --> pdb=" O LEU b 40 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU b 40 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N GLU b 51 " --> pdb=" O PHE b 38 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N PHE b 38 " --> pdb=" O GLU b 51 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LYS b 53 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL b 36 " --> pdb=" O LYS b 53 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE b 55 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N HIS b 133 " --> pdb=" O LEU b 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.640A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL b 49 " --> pdb=" O LEU b 40 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU b 40 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N GLU b 51 " --> pdb=" O PHE b 38 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N PHE b 38 " --> pdb=" O GLU b 51 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LYS b 53 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL b 36 " --> pdb=" O LYS b 53 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE b 55 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.537A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS c 133 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.537A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR c 88 " --> pdb=" O LEU c 161 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU c 161 " --> pdb=" O THR c 88 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU c 90 " --> pdb=" O VAL c 159 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.558A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL d 49 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU d 40 " --> pdb=" O VAL d 49 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N GLU d 51 " --> pdb=" O PHE d 38 " (cutoff:3.500A) removed outlier: 10.745A pdb=" N PHE d 38 " --> pdb=" O GLU d 51 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LYS d 53 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL d 36 " --> pdb=" O LYS d 53 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE d 55 " --> pdb=" O LYS d 34 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS d 133 " --> pdb=" O LEU d 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.558A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL d 49 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU d 40 " --> pdb=" O VAL d 49 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N GLU d 51 " --> pdb=" O PHE d 38 " (cutoff:3.500A) removed outlier: 10.745A pdb=" N PHE d 38 " --> pdb=" O GLU d 51 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LYS d 53 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL d 36 " --> pdb=" O LYS d 53 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE d 55 " --> pdb=" O LYS d 34 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.537A pdb=" N THR e 6 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N VAL e 49 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU e 37 " --> pdb=" O GLU e 50 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA e 52 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N ALA e 35 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N GLN e 54 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N LYS e 33 " --> pdb=" O GLN e 54 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS e 34 " --> pdb=" O ASP e 86 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS e 133 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.537A pdb=" N THR e 6 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N VAL e 49 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU e 37 " --> pdb=" O GLU e 50 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA e 52 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N ALA e 35 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N GLN e 54 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N LYS e 33 " --> pdb=" O GLN e 54 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS e 34 " --> pdb=" O ASP e 86 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 2877 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7147 1.34 - 1.46: 4353 1.46 - 1.58: 11100 1.58 - 1.69: 15 1.69 - 1.81: 218 Bond restraints: 22833 Sorted by residual: bond pdb=" CA THR e 63 " pdb=" CB THR e 63 " ideal model delta sigma weight residual 1.532 1.573 -0.041 1.51e-02 4.39e+03 7.23e+00 bond pdb=" CA THR d 63 " pdb=" CB THR d 63 " ideal model delta sigma weight residual 1.532 1.572 -0.040 1.51e-02 4.39e+03 7.03e+00 bond pdb=" CA THR b 63 " pdb=" CB THR b 63 " ideal model delta sigma weight residual 1.532 1.571 -0.039 1.51e-02 4.39e+03 6.70e+00 bond pdb=" N THR c 63 " pdb=" CA THR c 63 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.15e-02 7.56e+03 6.39e+00 bond pdb=" CA THR a 63 " pdb=" CB THR a 63 " ideal model delta sigma weight residual 1.532 1.569 -0.037 1.51e-02 4.39e+03 6.11e+00 ... (remaining 22828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 29991 2.24 - 4.47: 773 4.47 - 6.71: 111 6.71 - 8.94: 18 8.94 - 11.18: 7 Bond angle restraints: 30900 Sorted by residual: angle pdb=" C ASP a 62 " pdb=" N THR a 63 " pdb=" CA THR a 63 " ideal model delta sigma weight residual 122.61 133.79 -11.18 1.56e+00 4.11e-01 5.13e+01 angle pdb=" C ASP d 62 " pdb=" N THR d 63 " pdb=" CA THR d 63 " ideal model delta sigma weight residual 122.61 133.53 -10.92 1.56e+00 4.11e-01 4.90e+01 angle pdb=" C ASP e 62 " pdb=" N THR e 63 " pdb=" CA THR e 63 " ideal model delta sigma weight residual 122.61 133.38 -10.77 1.56e+00 4.11e-01 4.76e+01 angle pdb=" C ASP b 62 " pdb=" N THR b 63 " pdb=" CA THR b 63 " ideal model delta sigma weight residual 122.61 132.84 -10.23 1.56e+00 4.11e-01 4.30e+01 angle pdb=" C HIS B 40 " pdb=" N GLN B 41 " pdb=" CA GLN B 41 " ideal model delta sigma weight residual 121.54 131.59 -10.05 1.91e+00 2.74e-01 2.77e+01 ... (remaining 30895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 12718 17.35 - 34.70: 880 34.70 - 52.05: 201 52.05 - 69.40: 36 69.40 - 86.75: 37 Dihedral angle restraints: 13872 sinusoidal: 5659 harmonic: 8213 Sorted by residual: dihedral pdb=" CA GLN A 49 " pdb=" C GLN A 49 " pdb=" N LYS A 50 " pdb=" CA LYS A 50 " ideal model delta harmonic sigma weight residual 180.00 154.67 25.33 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ARG d 81 " pdb=" C ARG d 81 " pdb=" N TYR d 82 " pdb=" CA TYR d 82 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PRO W 148 " pdb=" C PRO W 148 " pdb=" N LYS W 149 " pdb=" CA LYS W 149 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 13869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2997 0.080 - 0.159: 434 0.159 - 0.239: 24 0.239 - 0.318: 6 0.318 - 0.398: 1 Chirality restraints: 3462 Sorted by residual: chirality pdb=" CB VAL A 43 " pdb=" CA VAL A 43 " pdb=" CG1 VAL A 43 " pdb=" CG2 VAL A 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE E 151 " pdb=" CA ILE E 151 " pdb=" CG1 ILE E 151 " pdb=" CG2 ILE E 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 3459 not shown) Planarity restraints: 3924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA W 41 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO W 42 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO W 42 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO W 42 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 37 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO A 38 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 37 " 0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO B 38 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " 0.035 5.00e-02 4.00e+02 ... (remaining 3921 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 45 2.66 - 3.22: 18573 3.22 - 3.78: 33363 3.78 - 4.34: 47415 4.34 - 4.90: 77029 Nonbonded interactions: 176425 Sorted by model distance: nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.099 2.170 nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.107 2.170 nonbonded pdb=" O3B ADP A 400 " pdb="MG MG A 401 " model vdw 2.107 2.170 nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.112 2.170 nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.122 2.170 ... (remaining 176420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 39 or resid 50 through 172 or resid 174 through \ 401)) selection = (chain 'B' and (resid 4 through 39 or resid 50 through 172 or resid 174 through \ 401)) selection = (chain 'C' and (resid 4 through 172 or resid 174 through 401)) selection = (chain 'D' and (resid 4 through 172 or resid 174 through 401)) selection = (chain 'E' and (resid 4 through 172 or resid 174 through 401)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.500 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22833 Z= 0.213 Angle : 0.856 11.177 30900 Z= 0.465 Chirality : 0.054 0.398 3462 Planarity : 0.008 0.074 3924 Dihedral : 13.643 86.752 8584 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.14), residues: 2782 helix: -2.53 (0.11), residues: 1145 sheet: -0.65 (0.22), residues: 543 loop : -0.67 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 312 TYR 0.020 0.002 TYR B 294 PHE 0.042 0.003 PHE E 90 TRP 0.027 0.002 TRP B 86 HIS 0.010 0.002 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00427 (22833) covalent geometry : angle 0.85559 (30900) hydrogen bonds : bond 0.19585 ( 1006) hydrogen bonds : angle 7.91518 ( 2877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8834 (tpt) cc_final: 0.8574 (tpp) REVERT: A 227 MET cc_start: 0.8763 (mmm) cc_final: 0.8524 (mmm) REVERT: A 236 LEU cc_start: 0.9329 (mt) cc_final: 0.9076 (tt) REVERT: A 292 ASP cc_start: 0.9111 (m-30) cc_final: 0.8860 (t0) REVERT: A 355 MET cc_start: 0.9044 (mmt) cc_final: 0.8756 (mmm) REVERT: C 82 MET cc_start: 0.8729 (tpt) cc_final: 0.8423 (mmm) REVERT: C 121 GLN cc_start: 0.9372 (tt0) cc_final: 0.8838 (tm-30) REVERT: C 176 MET cc_start: 0.8970 (mmm) cc_final: 0.8760 (mtt) REVERT: C 227 MET cc_start: 0.9123 (mmm) cc_final: 0.8908 (mmm) REVERT: C 283 MET cc_start: 0.9068 (mmm) cc_final: 0.8792 (mpp) REVERT: C 355 MET cc_start: 0.9343 (mmt) cc_final: 0.9107 (mmm) REVERT: D 354 GLN cc_start: 0.8783 (pm20) cc_final: 0.8425 (pm20) REVERT: E 176 MET cc_start: 0.8467 (mmm) cc_final: 0.8106 (mtt) REVERT: E 246 GLN cc_start: 0.8522 (mt0) cc_final: 0.8148 (mt0) REVERT: E 355 MET cc_start: 0.9279 (mmt) cc_final: 0.8913 (mpp) REVERT: W 93 CYS cc_start: 0.7754 (m) cc_final: 0.7516 (p) REVERT: W 118 PHE cc_start: 0.9259 (t80) cc_final: 0.8918 (t80) REVERT: a 115 MET cc_start: 0.9131 (tpt) cc_final: 0.8667 (tpp) REVERT: b 78 ASN cc_start: 0.9081 (m-40) cc_final: 0.8606 (p0) REVERT: b 115 MET cc_start: 0.9240 (tpt) cc_final: 0.8606 (tpp) REVERT: c 46 GLN cc_start: 0.8948 (mt0) cc_final: 0.8707 (mt0) REVERT: c 166 LEU cc_start: 0.8886 (tt) cc_final: 0.8683 (tt) REVERT: d 54 GLN cc_start: 0.8910 (mt0) cc_final: 0.8422 (mp10) REVERT: d 68 TYR cc_start: 0.8802 (t80) cc_final: 0.8567 (t80) REVERT: d 85 TYR cc_start: 0.8171 (t80) cc_final: 0.7967 (t80) REVERT: d 115 MET cc_start: 0.9052 (tpt) cc_final: 0.8674 (tpp) REVERT: e 16 ASN cc_start: 0.9537 (m-40) cc_final: 0.8949 (p0) REVERT: e 21 ARG cc_start: 0.8647 (mpt-90) cc_final: 0.8262 (mpt180) REVERT: e 46 GLN cc_start: 0.9547 (mt0) cc_final: 0.9014 (tt0) REVERT: e 54 GLN cc_start: 0.8891 (mt0) cc_final: 0.8088 (mp10) REVERT: e 115 MET cc_start: 0.9022 (tpt) cc_final: 0.8466 (tpp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1654 time to fit residues: 52.0693 Evaluate side-chains 147 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS C 87 HIS C 128 ASN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN E 87 HIS E 128 ASN W 111 GLN W 166 ASN W 179 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.033210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.025500 restraints weight = 198705.063| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 4.67 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22833 Z= 0.181 Angle : 0.586 7.076 30900 Z= 0.301 Chirality : 0.043 0.164 3462 Planarity : 0.005 0.070 3924 Dihedral : 5.235 49.352 3114 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 0.25 % Allowed : 3.00 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 2782 helix: -0.32 (0.14), residues: 1164 sheet: -0.52 (0.21), residues: 575 loop : -0.06 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 45 TYR 0.014 0.001 TYR B 294 PHE 0.019 0.001 PHE D 90 TRP 0.015 0.001 TRP W 207 HIS 0.006 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00391 (22833) covalent geometry : angle 0.58552 (30900) hydrogen bonds : bond 0.03821 ( 1006) hydrogen bonds : angle 5.18730 ( 2877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.967 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: A 82 MET cc_start: 0.8939 (tpt) cc_final: 0.8716 (tpp) REVERT: A 227 MET cc_start: 0.8830 (mmm) cc_final: 0.8607 (mmm) REVERT: A 236 LEU cc_start: 0.9388 (mt) cc_final: 0.9125 (tt) REVERT: A 292 ASP cc_start: 0.9106 (m-30) cc_final: 0.8880 (t0) REVERT: C 121 GLN cc_start: 0.9425 (tt0) cc_final: 0.8927 (tm-30) REVERT: C 132 MET cc_start: 0.8259 (ppp) cc_final: 0.7935 (tmm) REVERT: C 283 MET cc_start: 0.9058 (mmm) cc_final: 0.8708 (mmm) REVERT: C 355 MET cc_start: 0.9318 (mmt) cc_final: 0.8894 (mpp) REVERT: E 176 MET cc_start: 0.8129 (mmm) cc_final: 0.7344 (mtt) REVERT: E 283 MET cc_start: 0.9218 (mmt) cc_final: 0.8684 (mpp) REVERT: E 355 MET cc_start: 0.9341 (mmt) cc_final: 0.8984 (mpp) REVERT: W 93 CYS cc_start: 0.7648 (m) cc_final: 0.7238 (p) REVERT: W 118 PHE cc_start: 0.9406 (t80) cc_final: 0.8983 (t80) REVERT: W 122 ASN cc_start: 0.8185 (t0) cc_final: 0.7834 (t0) REVERT: W 153 TYR cc_start: 0.8710 (t80) cc_final: 0.8463 (t80) REVERT: W 157 MET cc_start: 0.9132 (mmp) cc_final: 0.8806 (mmp) REVERT: a 115 MET cc_start: 0.9209 (tpt) cc_final: 0.8729 (tpp) REVERT: b 115 MET cc_start: 0.9344 (tpt) cc_final: 0.8809 (tpp) REVERT: c 1 MET cc_start: 0.8857 (ttm) cc_final: 0.8596 (ttm) REVERT: c 46 GLN cc_start: 0.9010 (mt0) cc_final: 0.8757 (mt0) REVERT: c 115 MET cc_start: 0.9117 (tpp) cc_final: 0.8161 (tpp) REVERT: d 54 GLN cc_start: 0.8985 (mt0) cc_final: 0.8520 (mp10) REVERT: d 85 TYR cc_start: 0.8172 (t80) cc_final: 0.7950 (t80) REVERT: d 115 MET cc_start: 0.9021 (tpt) cc_final: 0.8806 (tpp) REVERT: e 16 ASN cc_start: 0.9498 (m-40) cc_final: 0.8924 (p0) REVERT: e 21 ARG cc_start: 0.8715 (mpt-90) cc_final: 0.8261 (mpt180) REVERT: e 46 GLN cc_start: 0.9563 (mt0) cc_final: 0.9143 (mt0) REVERT: e 54 GLN cc_start: 0.8964 (mt0) cc_final: 0.8126 (mp10) REVERT: e 115 MET cc_start: 0.9018 (tpt) cc_final: 0.8485 (tpp) outliers start: 6 outliers final: 5 residues processed: 153 average time/residue: 0.1505 time to fit residues: 37.4777 Evaluate side-chains 146 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain W residue 158 ASN Chi-restraints excluded: chain c residue 78 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 183 optimal weight: 0.0970 chunk 161 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 273 optimal weight: 0.9980 chunk 275 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 overall best weight: 2.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 162 ASN b 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.033242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.025396 restraints weight = 237921.557| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 5.13 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22833 Z= 0.144 Angle : 0.531 11.492 30900 Z= 0.266 Chirality : 0.042 0.139 3462 Planarity : 0.004 0.046 3924 Dihedral : 4.930 47.931 3114 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.41 % Allowed : 3.99 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.16), residues: 2782 helix: 0.74 (0.16), residues: 1162 sheet: -0.35 (0.22), residues: 565 loop : 0.28 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 45 TYR 0.010 0.001 TYR B 294 PHE 0.013 0.001 PHE B 90 TRP 0.011 0.001 TRP B 340 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00312 (22833) covalent geometry : angle 0.53065 (30900) hydrogen bonds : bond 0.03117 ( 1006) hydrogen bonds : angle 4.62072 ( 2877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.842 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: A 82 MET cc_start: 0.8939 (tpt) cc_final: 0.8686 (tpp) REVERT: A 227 MET cc_start: 0.8824 (mmm) cc_final: 0.8620 (mmm) REVERT: A 236 LEU cc_start: 0.9389 (mt) cc_final: 0.9115 (tt) REVERT: A 292 ASP cc_start: 0.9127 (m-30) cc_final: 0.8913 (t0) REVERT: C 121 GLN cc_start: 0.9434 (tt0) cc_final: 0.8925 (tm-30) REVERT: C 132 MET cc_start: 0.8395 (ppp) cc_final: 0.7999 (tmm) REVERT: C 355 MET cc_start: 0.9328 (mmt) cc_final: 0.8900 (mpp) REVERT: E 176 MET cc_start: 0.8132 (mmm) cc_final: 0.7234 (mtt) REVERT: E 355 MET cc_start: 0.9343 (mmt) cc_final: 0.8985 (mpp) REVERT: W 93 CYS cc_start: 0.7687 (m) cc_final: 0.7273 (p) REVERT: W 118 PHE cc_start: 0.9419 (t80) cc_final: 0.9015 (t80) REVERT: W 122 ASN cc_start: 0.8207 (t0) cc_final: 0.7834 (t0) REVERT: W 153 TYR cc_start: 0.8834 (t80) cc_final: 0.8411 (t80) REVERT: W 157 MET cc_start: 0.9076 (mmp) cc_final: 0.8788 (mmp) REVERT: a 115 MET cc_start: 0.9221 (tpt) cc_final: 0.8933 (tpt) REVERT: b 115 MET cc_start: 0.9407 (tpt) cc_final: 0.8807 (tpp) REVERT: c 1 MET cc_start: 0.8886 (ttm) cc_final: 0.8654 (ttm) REVERT: c 46 GLN cc_start: 0.9006 (mt0) cc_final: 0.8786 (mt0) REVERT: c 115 MET cc_start: 0.9074 (tpp) cc_final: 0.8140 (tpp) REVERT: d 54 GLN cc_start: 0.8986 (mt0) cc_final: 0.8553 (mp10) REVERT: d 85 TYR cc_start: 0.8069 (t80) cc_final: 0.7852 (t80) REVERT: d 115 MET cc_start: 0.9071 (tpt) cc_final: 0.8768 (tpp) REVERT: e 16 ASN cc_start: 0.9486 (m-40) cc_final: 0.9200 (m110) REVERT: e 21 ARG cc_start: 0.8740 (mpt-90) cc_final: 0.8283 (mpt180) REVERT: e 46 GLN cc_start: 0.9573 (mt0) cc_final: 0.9145 (mt0) REVERT: e 54 GLN cc_start: 0.9014 (mt0) cc_final: 0.8211 (mp10) REVERT: e 115 MET cc_start: 0.9059 (tpt) cc_final: 0.8539 (tpp) outliers start: 10 outliers final: 5 residues processed: 148 average time/residue: 0.1500 time to fit residues: 36.2906 Evaluate side-chains 142 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain W residue 158 ASN Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain d residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 232 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 111 optimal weight: 0.0870 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 88 optimal weight: 0.0670 chunk 235 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 overall best weight: 1.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.033455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.025913 restraints weight = 181934.605| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 4.44 r_work: 0.2556 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22833 Z= 0.103 Angle : 0.495 9.690 30900 Z= 0.244 Chirality : 0.041 0.139 3462 Planarity : 0.004 0.048 3924 Dihedral : 4.749 46.159 3114 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.45 % Allowed : 4.69 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2782 helix: 1.16 (0.16), residues: 1157 sheet: -0.26 (0.22), residues: 565 loop : 0.53 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 45 TYR 0.009 0.001 TYR d 68 PHE 0.011 0.001 PHE B 90 TRP 0.010 0.001 TRP B 340 HIS 0.003 0.000 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00227 (22833) covalent geometry : angle 0.49512 (30900) hydrogen bonds : bond 0.02780 ( 1006) hydrogen bonds : angle 4.35015 ( 2877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8921 (tpt) cc_final: 0.8668 (tpp) REVERT: A 227 MET cc_start: 0.8855 (mmm) cc_final: 0.8649 (mmm) REVERT: A 236 LEU cc_start: 0.9368 (mt) cc_final: 0.9050 (tt) REVERT: A 292 ASP cc_start: 0.9280 (m-30) cc_final: 0.8926 (t0) REVERT: A 325 MET cc_start: 0.8889 (mmm) cc_final: 0.8667 (mmm) REVERT: C 121 GLN cc_start: 0.9510 (tt0) cc_final: 0.8998 (tm-30) REVERT: C 132 MET cc_start: 0.8861 (ppp) cc_final: 0.8538 (ppp) REVERT: C 355 MET cc_start: 0.9445 (mmt) cc_final: 0.9053 (mpp) REVERT: E 176 MET cc_start: 0.8492 (mmm) cc_final: 0.7616 (mtt) REVERT: E 283 MET cc_start: 0.9223 (mmt) cc_final: 0.8791 (mpp) REVERT: E 355 MET cc_start: 0.9560 (mmt) cc_final: 0.9194 (mpp) REVERT: E 360 GLN cc_start: 0.9322 (mp10) cc_final: 0.9005 (pp30) REVERT: W 93 CYS cc_start: 0.7610 (m) cc_final: 0.7214 (p) REVERT: W 122 ASN cc_start: 0.8188 (t0) cc_final: 0.7884 (t0) REVERT: W 146 MET cc_start: 0.6610 (mmm) cc_final: 0.6406 (mmm) REVERT: W 153 TYR cc_start: 0.8836 (t80) cc_final: 0.8382 (t80) REVERT: W 157 MET cc_start: 0.9082 (mmp) cc_final: 0.8798 (mmp) REVERT: a 115 MET cc_start: 0.9428 (tpt) cc_final: 0.9129 (tpt) REVERT: b 115 MET cc_start: 0.9489 (tpt) cc_final: 0.8884 (tpp) REVERT: c 46 GLN cc_start: 0.9125 (mt0) cc_final: 0.8879 (mt0) REVERT: d 26 GLN cc_start: 0.9351 (mm-40) cc_final: 0.9023 (tm-30) REVERT: d 54 GLN cc_start: 0.9114 (mt0) cc_final: 0.8571 (mp10) REVERT: d 115 MET cc_start: 0.9182 (tpt) cc_final: 0.8853 (tpp) REVERT: e 16 ASN cc_start: 0.9464 (m-40) cc_final: 0.9200 (m110) REVERT: e 21 ARG cc_start: 0.8738 (mpt-90) cc_final: 0.8269 (mpt180) REVERT: e 46 GLN cc_start: 0.9583 (mt0) cc_final: 0.9174 (mt0) REVERT: e 54 GLN cc_start: 0.9016 (mt0) cc_final: 0.8230 (mp10) REVERT: e 115 MET cc_start: 0.9149 (tpt) cc_final: 0.8584 (tpp) outliers start: 11 outliers final: 5 residues processed: 147 average time/residue: 0.1500 time to fit residues: 35.8379 Evaluate side-chains 142 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain d residue 6 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 5 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 213 optimal weight: 0.1980 chunk 175 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.041554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033168 restraints weight = 123664.240| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 4.42 r_work: 0.2558 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22833 Z= 0.133 Angle : 0.509 8.247 30900 Z= 0.250 Chirality : 0.042 0.139 3462 Planarity : 0.003 0.044 3924 Dihedral : 4.692 45.522 3114 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.53 % Allowed : 4.86 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2782 helix: 1.30 (0.16), residues: 1164 sheet: -0.24 (0.22), residues: 565 loop : 0.69 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 45 TYR 0.009 0.001 TYR d 85 PHE 0.010 0.001 PHE B 90 TRP 0.009 0.001 TRP D 79 HIS 0.003 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00294 (22833) covalent geometry : angle 0.50909 (30900) hydrogen bonds : bond 0.02800 ( 1006) hydrogen bonds : angle 4.24162 ( 2877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8914 (tpt) cc_final: 0.8653 (tpp) REVERT: A 176 MET cc_start: 0.8948 (mmp) cc_final: 0.8713 (mmp) REVERT: A 190 MET cc_start: 0.9301 (mtt) cc_final: 0.9063 (mmm) REVERT: A 236 LEU cc_start: 0.9385 (mt) cc_final: 0.9031 (tt) REVERT: A 292 ASP cc_start: 0.9289 (m-30) cc_final: 0.8927 (t0) REVERT: C 121 GLN cc_start: 0.9511 (tt0) cc_final: 0.8995 (tm-30) REVERT: C 132 MET cc_start: 0.8902 (ppp) cc_final: 0.8508 (ppp) REVERT: C 355 MET cc_start: 0.9457 (mmt) cc_final: 0.9060 (mpp) REVERT: E 176 MET cc_start: 0.8475 (mmm) cc_final: 0.7567 (mtt) REVERT: E 355 MET cc_start: 0.9556 (mmt) cc_final: 0.9177 (mpp) REVERT: E 360 GLN cc_start: 0.9330 (mp10) cc_final: 0.9013 (pp30) REVERT: W 93 CYS cc_start: 0.7603 (m) cc_final: 0.7189 (p) REVERT: W 122 ASN cc_start: 0.8238 (t0) cc_final: 0.7912 (t0) REVERT: W 146 MET cc_start: 0.6792 (mmm) cc_final: 0.6583 (mmm) REVERT: W 153 TYR cc_start: 0.8818 (t80) cc_final: 0.8348 (t80) REVERT: W 157 MET cc_start: 0.9028 (mmp) cc_final: 0.8750 (mmp) REVERT: a 115 MET cc_start: 0.9415 (tpt) cc_final: 0.8908 (tpp) REVERT: b 115 MET cc_start: 0.9510 (tpt) cc_final: 0.8870 (tpp) REVERT: c 46 GLN cc_start: 0.9105 (mt0) cc_final: 0.8851 (mt0) REVERT: d 26 GLN cc_start: 0.9362 (mm-40) cc_final: 0.9018 (tm-30) REVERT: d 54 GLN cc_start: 0.9125 (mt0) cc_final: 0.8563 (mp10) REVERT: d 115 MET cc_start: 0.9176 (tpt) cc_final: 0.8814 (tpp) REVERT: e 16 ASN cc_start: 0.9428 (m-40) cc_final: 0.9191 (m110) REVERT: e 21 ARG cc_start: 0.8713 (mpt-90) cc_final: 0.8258 (mpt180) REVERT: e 46 GLN cc_start: 0.9539 (mt0) cc_final: 0.9153 (mt0) REVERT: e 54 GLN cc_start: 0.8968 (mt0) cc_final: 0.8197 (mp10) REVERT: e 115 MET cc_start: 0.9109 (tpt) cc_final: 0.8574 (tpp) outliers start: 13 outliers final: 10 residues processed: 146 average time/residue: 0.1508 time to fit residues: 36.0702 Evaluate side-chains 146 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 3 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 169 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.052518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.044562 restraints weight = 167312.741| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 4.41 r_work: 0.2528 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22833 Z= 0.228 Angle : 0.587 9.121 30900 Z= 0.292 Chirality : 0.043 0.137 3462 Planarity : 0.004 0.048 3924 Dihedral : 4.900 48.853 3114 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.74 % Allowed : 5.02 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2782 helix: 1.31 (0.16), residues: 1148 sheet: -0.18 (0.23), residues: 522 loop : 0.77 (0.20), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG a 45 TYR 0.012 0.001 TYR a 117 PHE 0.016 0.001 PHE D 90 TRP 0.013 0.001 TRP a 104 HIS 0.005 0.001 HIS W 77 Details of bonding type rmsd covalent geometry : bond 0.00495 (22833) covalent geometry : angle 0.58691 (30900) hydrogen bonds : bond 0.03318 ( 1006) hydrogen bonds : angle 4.42821 ( 2877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8977 (tpt) cc_final: 0.8719 (tpp) REVERT: A 190 MET cc_start: 0.9301 (mtt) cc_final: 0.9077 (mmm) REVERT: A 227 MET cc_start: 0.8923 (mmm) cc_final: 0.8714 (mmm) REVERT: A 236 LEU cc_start: 0.9383 (mt) cc_final: 0.9028 (tt) REVERT: A 292 ASP cc_start: 0.9294 (m-30) cc_final: 0.8987 (t0) REVERT: C 62 ARG cc_start: 0.6307 (mmt180) cc_final: 0.4609 (mtm-85) REVERT: C 121 GLN cc_start: 0.9535 (tt0) cc_final: 0.9015 (tm-30) REVERT: C 132 MET cc_start: 0.9045 (ppp) cc_final: 0.8632 (ppp) REVERT: C 355 MET cc_start: 0.9491 (mmt) cc_final: 0.9082 (mpp) REVERT: E 176 MET cc_start: 0.8539 (mmm) cc_final: 0.7616 (mtt) REVERT: E 355 MET cc_start: 0.9579 (mmt) cc_final: 0.9172 (mpp) REVERT: W 93 CYS cc_start: 0.7811 (m) cc_final: 0.7376 (p) REVERT: W 122 ASN cc_start: 0.8274 (t0) cc_final: 0.7925 (t0) REVERT: W 157 MET cc_start: 0.9086 (mmp) cc_final: 0.8812 (mmp) REVERT: a 54 GLN cc_start: 0.9292 (mt0) cc_final: 0.9077 (mp10) REVERT: a 111 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8439 (tp) REVERT: a 115 MET cc_start: 0.9477 (tpt) cc_final: 0.8984 (tpp) REVERT: b 115 MET cc_start: 0.9556 (tpt) cc_final: 0.8833 (tpp) REVERT: d 26 GLN cc_start: 0.9401 (mm-40) cc_final: 0.9021 (tm-30) REVERT: d 54 GLN cc_start: 0.9178 (mt0) cc_final: 0.8613 (mp10) REVERT: d 115 MET cc_start: 0.9225 (tpt) cc_final: 0.8823 (tpp) REVERT: e 16 ASN cc_start: 0.9443 (m-40) cc_final: 0.9205 (m110) REVERT: e 21 ARG cc_start: 0.8737 (mpt-90) cc_final: 0.8298 (mpt180) REVERT: e 46 GLN cc_start: 0.9539 (mt0) cc_final: 0.9124 (mt0) REVERT: e 54 GLN cc_start: 0.9035 (mt0) cc_final: 0.8290 (mp10) REVERT: e 115 MET cc_start: 0.9151 (tpt) cc_final: 0.8607 (tpp) outliers start: 18 outliers final: 14 residues processed: 147 average time/residue: 0.1517 time to fit residues: 36.5779 Evaluate side-chains 146 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain W residue 158 ASN Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain e residue 25 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 232 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 136 optimal weight: 0.2980 chunk 261 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 111 GLN ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.033141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.025260 restraints weight = 234249.367| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 5.10 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22833 Z= 0.130 Angle : 0.520 7.606 30900 Z= 0.255 Chirality : 0.042 0.149 3462 Planarity : 0.003 0.052 3924 Dihedral : 4.784 45.416 3114 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.74 % Allowed : 5.27 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2782 helix: 1.31 (0.16), residues: 1180 sheet: -0.12 (0.24), residues: 487 loop : 0.74 (0.20), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG a 45 TYR 0.017 0.001 TYR W 153 PHE 0.010 0.001 PHE a 38 TRP 0.012 0.001 TRP B 340 HIS 0.003 0.001 HIS W 130 Details of bonding type rmsd covalent geometry : bond 0.00290 (22833) covalent geometry : angle 0.52019 (30900) hydrogen bonds : bond 0.02850 ( 1006) hydrogen bonds : angle 4.20521 ( 2877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8908 (tpt) cc_final: 0.8612 (tpp) REVERT: A 176 MET cc_start: 0.8591 (mmp) cc_final: 0.8301 (mmp) REVERT: A 227 MET cc_start: 0.8874 (mmm) cc_final: 0.8637 (mmm) REVERT: A 236 LEU cc_start: 0.9382 (mt) cc_final: 0.9053 (tt) REVERT: A 292 ASP cc_start: 0.9193 (m-30) cc_final: 0.8985 (t0) REVERT: C 121 GLN cc_start: 0.9454 (tt0) cc_final: 0.8885 (tm-30) REVERT: C 132 MET cc_start: 0.8571 (ppp) cc_final: 0.8213 (ppp) REVERT: C 355 MET cc_start: 0.9371 (mmt) cc_final: 0.8912 (mpp) REVERT: E 176 MET cc_start: 0.8174 (mmm) cc_final: 0.7172 (mtt) REVERT: E 355 MET cc_start: 0.9390 (mmt) cc_final: 0.8971 (mpp) REVERT: W 93 CYS cc_start: 0.7807 (m) cc_final: 0.7355 (p) REVERT: W 122 ASN cc_start: 0.8235 (t0) cc_final: 0.7853 (t0) REVERT: W 162 MET cc_start: 0.9265 (mmm) cc_final: 0.9042 (mmm) REVERT: a 111 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8201 (tp) REVERT: a 115 MET cc_start: 0.9257 (tpt) cc_final: 0.8769 (tpp) REVERT: b 115 MET cc_start: 0.9432 (tpt) cc_final: 0.8664 (tpp) REVERT: d 26 GLN cc_start: 0.9381 (mm-40) cc_final: 0.9180 (mm-40) REVERT: d 54 GLN cc_start: 0.9065 (mt0) cc_final: 0.8596 (mp10) REVERT: d 115 MET cc_start: 0.9109 (tpt) cc_final: 0.8681 (tpp) REVERT: e 16 ASN cc_start: 0.9453 (m-40) cc_final: 0.9209 (m110) REVERT: e 21 ARG cc_start: 0.8728 (mpt-90) cc_final: 0.8332 (mpt180) REVERT: e 46 GLN cc_start: 0.9528 (mt0) cc_final: 0.9119 (mt0) REVERT: e 54 GLN cc_start: 0.9049 (mt0) cc_final: 0.8306 (mp10) REVERT: e 115 MET cc_start: 0.9065 (tpt) cc_final: 0.8562 (tpp) outliers start: 18 outliers final: 11 residues processed: 144 average time/residue: 0.1539 time to fit residues: 35.7151 Evaluate side-chains 142 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain d residue 6 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 251 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 269 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.034856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.027533 restraints weight = 204791.535| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 4.47 r_work: 0.2542 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 22833 Z= 0.255 Angle : 0.601 8.283 30900 Z= 0.298 Chirality : 0.044 0.138 3462 Planarity : 0.004 0.056 3924 Dihedral : 4.929 47.830 3114 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.70 % Allowed : 5.68 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2782 helix: 1.19 (0.16), residues: 1181 sheet: -0.19 (0.23), residues: 517 loop : 0.87 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG a 45 TYR 0.012 0.001 TYR a 117 PHE 0.017 0.001 PHE a 38 TRP 0.014 0.001 TRP a 104 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00560 (22833) covalent geometry : angle 0.60074 (30900) hydrogen bonds : bond 0.03289 ( 1006) hydrogen bonds : angle 4.43270 ( 2877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9009 (tpt) cc_final: 0.8739 (tpp) REVERT: A 123 MET cc_start: 0.9535 (mmp) cc_final: 0.9126 (mmm) REVERT: A 176 MET cc_start: 0.9029 (mmp) cc_final: 0.8786 (mmp) REVERT: A 227 MET cc_start: 0.9002 (mmm) cc_final: 0.8748 (mmm) REVERT: A 292 ASP cc_start: 0.9294 (m-30) cc_final: 0.9068 (t0) REVERT: A 299 MET cc_start: 0.9148 (mtm) cc_final: 0.8891 (mtm) REVERT: C 121 GLN cc_start: 0.9565 (tt0) cc_final: 0.9060 (tm-30) REVERT: C 132 MET cc_start: 0.9098 (ppp) cc_final: 0.8714 (ppp) REVERT: C 355 MET cc_start: 0.9510 (mmt) cc_final: 0.9111 (mpp) REVERT: E 176 MET cc_start: 0.8681 (mmm) cc_final: 0.7807 (mtt) REVERT: E 355 MET cc_start: 0.9579 (mmt) cc_final: 0.9195 (mpp) REVERT: W 93 CYS cc_start: 0.7913 (m) cc_final: 0.7479 (p) REVERT: W 122 ASN cc_start: 0.8308 (t0) cc_final: 0.7909 (t0) REVERT: a 111 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8522 (tp) REVERT: a 115 MET cc_start: 0.9489 (tpt) cc_final: 0.9064 (tpp) REVERT: b 115 MET cc_start: 0.9594 (tpt) cc_final: 0.8883 (tpp) REVERT: d 54 GLN cc_start: 0.9201 (mt0) cc_final: 0.8654 (mp10) REVERT: e 16 ASN cc_start: 0.9454 (m-40) cc_final: 0.9222 (m110) REVERT: e 21 ARG cc_start: 0.8760 (mpt-90) cc_final: 0.8309 (mpt180) REVERT: e 46 GLN cc_start: 0.9551 (mt0) cc_final: 0.9123 (mt0) REVERT: e 54 GLN cc_start: 0.9089 (mt0) cc_final: 0.8333 (mp10) REVERT: e 115 MET cc_start: 0.9208 (tpt) cc_final: 0.8672 (tpp) outliers start: 17 outliers final: 14 residues processed: 140 average time/residue: 0.1491 time to fit residues: 34.3870 Evaluate side-chains 145 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 132 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 134 optimal weight: 0.4980 chunk 234 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.033332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.025470 restraints weight = 233107.551| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 5.10 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22833 Z= 0.096 Angle : 0.520 9.057 30900 Z= 0.252 Chirality : 0.042 0.141 3462 Planarity : 0.003 0.056 3924 Dihedral : 4.723 41.629 3114 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.58 % Allowed : 5.97 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2782 helix: 1.41 (0.16), residues: 1180 sheet: -0.03 (0.24), residues: 477 loop : 0.76 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG a 45 TYR 0.018 0.001 TYR W 153 PHE 0.009 0.001 PHE e 38 TRP 0.013 0.001 TRP B 340 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00216 (22833) covalent geometry : angle 0.51992 (30900) hydrogen bonds : bond 0.02682 ( 1006) hydrogen bonds : angle 4.12451 ( 2877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8898 (tpt) cc_final: 0.8598 (tpp) REVERT: A 176 MET cc_start: 0.8643 (mmp) cc_final: 0.8335 (mmp) REVERT: A 190 MET cc_start: 0.8970 (mtt) cc_final: 0.8765 (mmm) REVERT: A 227 MET cc_start: 0.8885 (mmm) cc_final: 0.8627 (mmm) REVERT: C 62 ARG cc_start: 0.6050 (mmt180) cc_final: 0.5146 (mtm-85) REVERT: C 121 GLN cc_start: 0.9450 (tt0) cc_final: 0.8961 (tm-30) REVERT: C 123 MET cc_start: 0.9247 (mmm) cc_final: 0.9019 (mmm) REVERT: C 132 MET cc_start: 0.8574 (ppp) cc_final: 0.8238 (ppp) REVERT: C 227 MET cc_start: 0.8719 (mmm) cc_final: 0.8377 (tpp) REVERT: C 305 MET cc_start: 0.8913 (mmm) cc_final: 0.8698 (mmt) REVERT: C 355 MET cc_start: 0.9374 (mmt) cc_final: 0.8901 (mpp) REVERT: E 176 MET cc_start: 0.8180 (mmm) cc_final: 0.7529 (mpp) REVERT: E 283 MET cc_start: 0.9005 (mmt) cc_final: 0.8782 (mpp) REVERT: E 355 MET cc_start: 0.9396 (mmt) cc_final: 0.8962 (mpp) REVERT: W 93 CYS cc_start: 0.7831 (m) cc_final: 0.7378 (p) REVERT: W 122 ASN cc_start: 0.8249 (t0) cc_final: 0.7841 (t0) REVERT: a 115 MET cc_start: 0.9238 (tpt) cc_final: 0.8951 (tpp) REVERT: b 115 MET cc_start: 0.9416 (tpt) cc_final: 0.8636 (tpp) REVERT: d 54 GLN cc_start: 0.9063 (mt0) cc_final: 0.8579 (mp10) REVERT: d 115 MET cc_start: 0.9113 (tpp) cc_final: 0.8383 (tpp) REVERT: e 16 ASN cc_start: 0.9435 (m-40) cc_final: 0.9204 (m110) REVERT: e 21 ARG cc_start: 0.8705 (mpt-90) cc_final: 0.8327 (mpt180) REVERT: e 46 GLN cc_start: 0.9519 (mt0) cc_final: 0.9091 (mt0) REVERT: e 54 GLN cc_start: 0.9037 (mt0) cc_final: 0.8294 (mp10) REVERT: e 115 MET cc_start: 0.9060 (tpt) cc_final: 0.8545 (tpp) outliers start: 14 outliers final: 11 residues processed: 141 average time/residue: 0.1497 time to fit residues: 34.4018 Evaluate side-chains 142 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain d residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 139 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 267 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 133 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.035085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.027813 restraints weight = 193782.978| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 4.31 r_work: 0.2561 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 22833 Z= 0.214 Angle : 0.588 8.968 30900 Z= 0.288 Chirality : 0.043 0.138 3462 Planarity : 0.004 0.065 3924 Dihedral : 4.848 44.517 3114 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.49 % Allowed : 6.30 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2782 helix: 1.31 (0.16), residues: 1183 sheet: -0.32 (0.23), residues: 522 loop : 0.83 (0.21), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG a 45 TYR 0.011 0.001 TYR a 117 PHE 0.015 0.001 PHE a 38 TRP 0.012 0.001 TRP a 104 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00469 (22833) covalent geometry : angle 0.58763 (30900) hydrogen bonds : bond 0.03123 ( 1006) hydrogen bonds : angle 4.31517 ( 2877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8998 (tpt) cc_final: 0.8730 (tpp) REVERT: A 227 MET cc_start: 0.9017 (mmm) cc_final: 0.8754 (mmm) REVERT: A 299 MET cc_start: 0.9214 (mtm) cc_final: 0.8874 (mtm) REVERT: A 325 MET cc_start: 0.8865 (mmm) cc_final: 0.8636 (mmm) REVERT: C 121 GLN cc_start: 0.9570 (tt0) cc_final: 0.9146 (tm-30) REVERT: C 123 MET cc_start: 0.9356 (mmm) cc_final: 0.9130 (mmm) REVERT: C 132 MET cc_start: 0.9090 (ppp) cc_final: 0.8764 (ppp) REVERT: C 227 MET cc_start: 0.8935 (mmm) cc_final: 0.8566 (tpp) REVERT: C 355 MET cc_start: 0.9488 (mmt) cc_final: 0.9118 (mpp) REVERT: E 176 MET cc_start: 0.8716 (mmm) cc_final: 0.7882 (mtt) REVERT: E 355 MET cc_start: 0.9562 (mmt) cc_final: 0.9201 (mpp) REVERT: W 93 CYS cc_start: 0.7911 (m) cc_final: 0.7462 (p) REVERT: W 122 ASN cc_start: 0.8276 (t0) cc_final: 0.7890 (t0) REVERT: a 115 MET cc_start: 0.9468 (tpt) cc_final: 0.9094 (tpp) REVERT: b 115 MET cc_start: 0.9570 (tpt) cc_final: 0.8892 (tpp) REVERT: d 54 GLN cc_start: 0.9195 (mt0) cc_final: 0.8674 (mp10) REVERT: e 16 ASN cc_start: 0.9456 (m-40) cc_final: 0.9228 (m110) REVERT: e 21 ARG cc_start: 0.8783 (mpt-90) cc_final: 0.8332 (mpt180) REVERT: e 46 GLN cc_start: 0.9555 (mt0) cc_final: 0.9122 (mt0) REVERT: e 54 GLN cc_start: 0.9093 (mt0) cc_final: 0.8350 (mp10) REVERT: e 115 MET cc_start: 0.9241 (tpt) cc_final: 0.8704 (tpp) outliers start: 12 outliers final: 11 residues processed: 136 average time/residue: 0.1486 time to fit residues: 33.2563 Evaluate side-chains 140 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain d residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 205 optimal weight: 3.9990 chunk 273 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 172 optimal weight: 0.3980 chunk 127 optimal weight: 0.0570 chunk 142 optimal weight: 2.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.033479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.025668 restraints weight = 233095.501| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 5.11 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22833 Z= 0.092 Angle : 0.523 8.738 30900 Z= 0.251 Chirality : 0.042 0.142 3462 Planarity : 0.003 0.056 3924 Dihedral : 4.625 39.611 3114 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.37 % Allowed : 6.46 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.17), residues: 2782 helix: 1.48 (0.16), residues: 1185 sheet: -0.00 (0.24), residues: 475 loop : 0.82 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG a 45 TYR 0.018 0.001 TYR W 153 PHE 0.010 0.001 PHE W 163 TRP 0.012 0.001 TRP B 340 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00209 (22833) covalent geometry : angle 0.52285 (30900) hydrogen bonds : bond 0.02548 ( 1006) hydrogen bonds : angle 4.02665 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5781.76 seconds wall clock time: 100 minutes 2.52 seconds (6002.52 seconds total)