Starting phenix.real_space_refine on Tue Apr 7 00:07:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y9m_72711/04_2026/9y9m_72711.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y9m_72711/04_2026/9y9m_72711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y9m_72711/04_2026/9y9m_72711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y9m_72711/04_2026/9y9m_72711.map" model { file = "/net/cci-nas-00/data/ceres_data/9y9m_72711/04_2026/9y9m_72711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y9m_72711/04_2026/9y9m_72711.cif" } resolution = 3.06 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= 0.003 sd= 0.011 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 126 5.16 5 C 14310 2.51 5 N 3819 2.21 5 O 4385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s 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: 22655 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2846 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 2891 Chain: "B" Number of atoms: 2846 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 2891 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: "Y" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2195 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 259} Chain: "Y" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 29 Classifications: {'peptide': 6} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 5} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2131 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 9, 'TRANS': 260} 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: "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: 6.09, per 1000 atoms: 0.27 Number of scatterers: 22655 At special positions: 0 Unit cell: (102.06, 119.88, 220.32, 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 126 16.00 P 10 15.00 Mg 5 11.99 O 4385 8.00 N 3819 7.00 C 14310 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 Links applied TRANS " UNK Y 278 " - " TYR Y 277 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 1.3 seconds 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5346 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 37 sheets defined 46.8% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.901A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.712A 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 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.769A 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: 3.928A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.674A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.586A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.685A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 4.111A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.279A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.532A 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 353 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.757A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.859A 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: 3.567A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.752A 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: 4.045A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.660A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.599A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.698A pdb=" N THR B 260 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix 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: 4.026A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.169A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.585A pdb=" N LEU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 353 removed outlier: 4.197A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 353' Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.532A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 181 through 197 removed outlier: 4.051A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.722A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.556A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.665A pdb=" N THR C 260 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.529A 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 290 through 295 removed outlier: 4.161A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.210A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.517A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 62 removed outlier: 3.996A pdb=" N ARG D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.771A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.620A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.599A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 181 through 197 removed outlier: 4.195A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY D 197 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.624A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.694A pdb=" N THR D 260 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 293 removed outlier: 3.710A pdb=" N ILE D 289 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.293A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 57 through 65 removed outlier: 3.774A pdb=" N LYS E 61 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG E 62 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY E 63 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 65 " --> pdb=" O ARG E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.648A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.571A 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 removed outlier: 3.566A pdb=" N THR E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.547A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 203 through 217 removed outlier: 3.958A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.883A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 294 removed outlier: 3.911A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 293 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.203A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 352 through 356 removed outlier: 3.650A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.890A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.625A pdb=" N HIS Y 23 " --> pdb=" O LYS Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 41 Processing helix chain 'Y' and resid 42 through 47 removed outlier: 4.012A pdb=" N LEU Y 46 " --> pdb=" O ASN Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 61 removed outlier: 4.087A pdb=" N ASN Y 58 " --> pdb=" O PHE Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 135 Processing helix chain 'Y' and resid 220 through 250 Processing helix chain 'Y' and resid 254 through 259 removed outlier: 3.865A pdb=" N LEU Y 258 " --> pdb=" O THR Y 254 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG Y 259 " --> pdb=" O PHE Y 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 254 through 259' Processing helix chain 'Y' and resid 270 through 275 removed outlier: 4.001A pdb=" N ILE Y 274 " --> pdb=" O ASP Y 270 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 15 removed outlier: 3.664A pdb=" N ARG Z 15 " --> pdb=" O ASP Z 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 20 through 32 removed outlier: 4.776A pdb=" N ASP Z 30 " --> pdb=" O SER Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 35 through 43 Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.689A pdb=" N GLU Z 99 " --> pdb=" O LYS Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 208 through 244 removed outlier: 4.390A pdb=" N TYR Z 232 " --> pdb=" O LEU Z 228 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE Z 233 " --> pdb=" O ASN Z 229 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG Z 244 " --> pdb=" O VAL Z 240 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 271 removed outlier: 4.074A pdb=" N GLU Z 256 " --> pdb=" O LYS Z 252 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN Z 271 " --> pdb=" O LYS Z 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 20 removed outlier: 3.778A pdb=" N ILE a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) removed outlier: 3.633A 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 128 removed outlier: 5.196A pdb=" N ASP a 122 " --> pdb=" O ALA a 118 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE a 124 " --> pdb=" O SER a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 143 removed outlier: 3.542A pdb=" N ASP a 142 " --> pdb=" O GLY a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 153 removed outlier: 4.224A 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: 3.767A pdb=" N ILE b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) removed outlier: 3.513A 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 74 Processing helix chain 'b' and resid 110 through 128 removed outlier: 5.184A pdb=" N ASP b 122 " --> pdb=" O ALA b 118 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ALA b 123 " --> pdb=" O SER b 119 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE b 124 " --> pdb=" O SER b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 143 removed outlier: 3.566A pdb=" N ASP b 142 " --> pdb=" O GLY b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 153 removed outlier: 4.183A pdb=" N LEU b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) 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: 3.764A pdb=" N ILE c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) removed outlier: 3.547A 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 74 removed outlier: 3.776A pdb=" N SER c 70 " --> pdb=" O ASP c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 110 through 128 removed outlier: 5.224A pdb=" N ASP c 122 " --> pdb=" O ALA c 118 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA c 123 " --> pdb=" O SER c 119 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE c 124 " --> pdb=" O SER c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 removed outlier: 3.543A pdb=" N ASP c 142 " --> pdb=" O GLY c 139 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.718A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.017A 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 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: 6.231A 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 8 through 12 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 105 through 107 removed outlier: 6.806A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.292A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.777A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.365A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.713A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 357 " --> pdb=" O MET D 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.725A pdb=" N TYR D 53 " --> pdb=" O GLY D 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.716A pdb=" N TYR D 169 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN D 162 " --> pdb=" O MET D 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.716A pdb=" N TYR D 169 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 6.145A 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: 3.721A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (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 removed outlier: 3.669A pdb=" N TYR E 169 " --> pdb=" O TYR E 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.669A pdb=" N TYR E 169 " --> pdb=" O TYR E 166 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.497A 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 'Y' and resid 63 through 65 removed outlier: 3.850A pdb=" N THR Y 63 " --> pdb=" O ILE Y 76 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 86 through 89 removed outlier: 3.727A pdb=" N LYS Y 97 " --> pdb=" O ASP Y 107 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASP Y 107 " --> pdb=" O LYS Y 97 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASP Y 99 " --> pdb=" O ALA Y 105 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA Y 105 " --> pdb=" O ASP Y 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 139 through 148 removed outlier: 3.510A pdb=" N ILE Y 148 " --> pdb=" O GLN Y 151 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR Y 180 " --> pdb=" O GLN Y 187 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLN Y 187 " --> pdb=" O THR Y 180 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 48 through 52 removed outlier: 4.179A pdb=" N LYS Z 48 " --> pdb=" O LEU Z 61 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.562A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU a 50 " --> pdb=" O LEU a 37 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS a 133 " --> pdb=" O LEU a 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.562A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU a 50 " --> pdb=" O LEU a 37 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.528A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL b 49 " --> pdb=" O LEU b 40 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU b 40 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N GLU b 51 " --> pdb=" O PHE b 38 " (cutoff:3.500A) removed outlier: 10.810A pdb=" N PHE b 38 " --> pdb=" O GLU b 51 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS b 53 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL b 36 " --> pdb=" O LYS b 53 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE b 55 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N HIS b 133 " --> pdb=" O LEU b 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.528A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL b 49 " --> pdb=" O LEU b 40 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU b 40 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N GLU b 51 " --> pdb=" O PHE b 38 " (cutoff:3.500A) removed outlier: 10.810A pdb=" N PHE b 38 " --> pdb=" O GLU b 51 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS b 53 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL b 36 " --> pdb=" O LYS b 53 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE b 55 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.487A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS c 133 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.487A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6905 1.34 - 1.46: 4934 1.46 - 1.58: 11043 1.58 - 1.70: 18 1.70 - 1.83: 213 Bond restraints: 23113 Sorted by residual: bond pdb=" C PRO Z 81 " pdb=" N PRO Z 82 " ideal model delta sigma weight residual 1.332 1.385 -0.053 1.34e-02 5.57e+03 1.55e+01 bond pdb=" CA ASP Z 67 " pdb=" CB ASP Z 67 " ideal model delta sigma weight residual 1.530 1.575 -0.044 1.69e-02 3.50e+03 6.89e+00 bond pdb=" N THR b 63 " pdb=" CA THR b 63 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.22e+00 bond pdb=" CB ASP Z 67 " pdb=" CG ASP Z 67 " ideal model delta sigma weight residual 1.516 1.578 -0.062 2.50e-02 1.60e+03 6.20e+00 bond pdb=" N THR a 63 " pdb=" CA THR a 63 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.18e+00 ... (remaining 23108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 30416 2.98 - 5.97: 765 5.97 - 8.95: 92 8.95 - 11.94: 19 11.94 - 14.92: 6 Bond angle restraints: 31298 Sorted by residual: angle pdb=" C ARG Z 66 " pdb=" N ASP Z 67 " pdb=" CA ASP Z 67 " ideal model delta sigma weight residual 121.54 133.93 -12.39 1.91e+00 2.74e-01 4.21e+01 angle pdb=" C SER Z 76 " pdb=" N ASN Z 77 " pdb=" CA ASN Z 77 " ideal model delta sigma weight residual 121.54 133.33 -11.79 1.91e+00 2.74e-01 3.81e+01 angle pdb=" N THR c 63 " pdb=" CA THR c 63 " pdb=" CB THR c 63 " ideal model delta sigma weight residual 114.17 107.85 6.32 1.14e+00 7.69e-01 3.08e+01 angle pdb=" N ILE Z 144 " pdb=" CA ILE Z 144 " pdb=" C ILE Z 144 " ideal model delta sigma weight residual 112.29 107.27 5.02 9.40e-01 1.13e+00 2.86e+01 angle pdb=" CA ASP Z 67 " pdb=" CB ASP Z 67 " pdb=" CG ASP Z 67 " ideal model delta sigma weight residual 112.60 117.88 -5.28 1.00e+00 1.00e+00 2.79e+01 ... (remaining 31293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12837 17.91 - 35.82: 944 35.82 - 53.73: 177 53.73 - 71.64: 37 71.64 - 89.55: 24 Dihedral angle restraints: 14019 sinusoidal: 5716 harmonic: 8303 Sorted by residual: dihedral pdb=" CA ASP Z 80 " pdb=" C ASP Z 80 " pdb=" N PRO Z 81 " pdb=" CA PRO Z 81 " ideal model delta harmonic sigma weight residual -180.00 -100.20 -79.80 0 5.00e+00 4.00e-02 2.55e+02 dihedral pdb=" CA PRO Z 81 " pdb=" C PRO Z 81 " pdb=" N PRO Z 82 " pdb=" CA PRO Z 82 " ideal model delta harmonic sigma weight residual -180.00 -150.48 -29.52 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PHE E 352 " pdb=" C PHE E 352 " pdb=" N GLN E 353 " pdb=" CA GLN E 353 " ideal model delta harmonic sigma weight residual 180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 14016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2750 0.069 - 0.139: 632 0.139 - 0.208: 89 0.208 - 0.278: 9 0.278 - 0.347: 5 Chirality restraints: 3485 Sorted by residual: chirality pdb=" CB ILE E 64 " pdb=" CA ILE E 64 " pdb=" CG1 ILE E 64 " pdb=" CG2 ILE E 64 " both_signs ideal model delta sigma weight residual False 2.64 2.99 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CB VAL Y 8 " pdb=" CA VAL Y 8 " pdb=" CG1 VAL Y 8 " pdb=" CG2 VAL Y 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB THR Z 179 " pdb=" CA THR Z 179 " pdb=" OG1 THR Z 179 " pdb=" CG2 THR Z 179 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 3482 not shown) Planarity restraints: 4004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP Z 80 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO Z 81 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO Z 81 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO Z 81 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 370 " -0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C VAL D 370 " 0.071 2.00e-02 2.50e+03 pdb=" O VAL D 370 " -0.026 2.00e-02 2.50e+03 pdb=" N HIS D 371 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU Y 262 " 0.060 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO Y 263 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO Y 263 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO Y 263 " 0.049 5.00e-02 4.00e+02 ... (remaining 4001 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 40 2.66 - 3.22: 19041 3.22 - 3.78: 33597 3.78 - 4.34: 47606 4.34 - 4.90: 78352 Nonbonded interactions: 178636 Sorted by model distance: nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.103 2.170 nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.109 2.170 nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.112 2.170 nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.113 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.134 2.170 ... (remaining 178631 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 172 or resid 174 through 401)) selection = (chain 'B' and (resid 4 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' } 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: 30.600 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: 0.800 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.240 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 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 : 0.006 0.067 23114 Z= 0.280 Angle : 1.107 14.921 31301 Z= 0.599 Chirality : 0.060 0.347 3485 Planarity : 0.009 0.104 4003 Dihedral : 13.773 89.551 8670 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -2.00 (0.14), residues: 2805 helix: -2.27 (0.12), residues: 1052 sheet: -0.40 (0.20), residues: 593 loop : -0.64 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 62 TYR 0.031 0.002 TYR D 166 PHE 0.044 0.003 PHE A 90 TRP 0.045 0.003 TRP Y 173 HIS 0.009 0.002 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00552 (23113) covalent geometry : angle 1.10720 (31298) hydrogen bonds : bond 0.16760 ( 1109) hydrogen bonds : angle 7.05689 ( 3075) link_TRANS : bond 0.00387 ( 1) link_TRANS : angle 1.66305 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8807 (tpt) cc_final: 0.8600 (mmm) REVERT: B 227 MET cc_start: 0.9031 (mmt) cc_final: 0.8803 (mmm) REVERT: C 283 MET cc_start: 0.9080 (tpp) cc_final: 0.8816 (mpp) REVERT: C 305 MET cc_start: 0.9436 (mmm) cc_final: 0.9049 (mmt) REVERT: C 355 MET cc_start: 0.9377 (mmm) cc_final: 0.8770 (mpp) REVERT: D 355 MET cc_start: 0.8888 (ttp) cc_final: 0.8349 (ttp) REVERT: E 246 GLN cc_start: 0.9206 (mt0) cc_final: 0.8863 (mt0) REVERT: E 325 MET cc_start: 0.8361 (mmm) cc_final: 0.8067 (mmm) REVERT: E 355 MET cc_start: 0.9428 (mtp) cc_final: 0.9079 (mtm) REVERT: Y 157 CYS cc_start: 0.9039 (m) cc_final: 0.8719 (m) REVERT: Z 126 HIS cc_start: 0.9056 (m90) cc_final: 0.8681 (m90) REVERT: Z 163 ARG cc_start: 0.8967 (mmm160) cc_final: 0.8496 (mmm160) REVERT: Z 197 MET cc_start: 0.8963 (ttm) cc_final: 0.8643 (tmm) REVERT: a 26 GLN cc_start: 0.8668 (mp10) cc_final: 0.8442 (mm-40) REVERT: a 78 ASN cc_start: 0.9317 (p0) cc_final: 0.9061 (p0) REVERT: c 45 ARG cc_start: 0.8872 (ttm110) cc_final: 0.8563 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1482 time to fit residues: 35.9950 Evaluate side-chains 140 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0470 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 overall best weight: 2.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 101 HIS C 59 GLN D 121 GLN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS E 246 GLN Y 23 HIS Y 135 HIS Z 45 GLN a 54 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.045364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.034002 restraints weight = 112970.259| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.89 r_work: 0.2584 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23114 Z= 0.169 Angle : 0.606 8.953 31301 Z= 0.309 Chirality : 0.044 0.134 3485 Planarity : 0.005 0.102 4003 Dihedral : 5.615 59.680 3156 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.89 % Favored : 95.93 % Rotamer: Outliers : 0.12 % Allowed : 2.97 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 2805 helix: -0.26 (0.15), residues: 1105 sheet: -0.18 (0.21), residues: 600 loop : -0.27 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 37 TYR 0.020 0.001 TYR Y 277 PHE 0.023 0.002 PHE E 223 TRP 0.023 0.002 TRP Y 173 HIS 0.010 0.001 HIS Y 209 Details of bonding type rmsd covalent geometry : bond 0.00385 (23113) covalent geometry : angle 0.60615 (31298) hydrogen bonds : bond 0.04252 ( 1109) hydrogen bonds : angle 4.86294 ( 3075) link_TRANS : bond 0.00238 ( 1) link_TRANS : angle 1.18578 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7734 (tpm170) cc_final: 0.7358 (tpm170) REVERT: B 353 GLN cc_start: 0.8990 (mm110) cc_final: 0.8713 (mm-40) REVERT: Y 124 CYS cc_start: 0.9283 (m) cc_final: 0.8506 (p) REVERT: Y 157 CYS cc_start: 0.9026 (m) cc_final: 0.8769 (m) REVERT: Z 126 HIS cc_start: 0.9050 (m90) cc_final: 0.8685 (m90) REVERT: Z 163 ARG cc_start: 0.8947 (mmm160) cc_final: 0.8490 (mmm160) REVERT: Z 197 MET cc_start: 0.9033 (ttm) cc_final: 0.8667 (tmm) REVERT: a 26 GLN cc_start: 0.8748 (mp10) cc_final: 0.8500 (mm-40) REVERT: a 78 ASN cc_start: 0.9308 (p0) cc_final: 0.9008 (p0) REVERT: c 45 ARG cc_start: 0.8850 (ttm110) cc_final: 0.8539 (mtp-110) outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.1502 time to fit residues: 35.9538 Evaluate side-chains 139 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 169 optimal weight: 0.0040 chunk 42 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 242 optimal weight: 0.2980 chunk 171 optimal weight: 0.0980 chunk 126 optimal weight: 3.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 D 162 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN E 162 ASN Y 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.046514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.034548 restraints weight = 166878.827| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.75 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23114 Z= 0.089 Angle : 0.524 6.693 31301 Z= 0.263 Chirality : 0.042 0.140 3485 Planarity : 0.004 0.086 4003 Dihedral : 5.095 56.319 3156 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.18 % Favored : 96.68 % Rotamer: Outliers : 0.33 % Allowed : 3.86 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2805 helix: 0.61 (0.16), residues: 1107 sheet: 0.04 (0.21), residues: 633 loop : -0.14 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 45 TYR 0.008 0.001 TYR A 91 PHE 0.014 0.001 PHE Z 128 TRP 0.018 0.001 TRP Y 173 HIS 0.006 0.001 HIS Y 209 Details of bonding type rmsd covalent geometry : bond 0.00184 (23113) covalent geometry : angle 0.52352 (31298) hydrogen bonds : bond 0.03044 ( 1109) hydrogen bonds : angle 4.40477 ( 3075) link_TRANS : bond 0.00291 ( 1) link_TRANS : angle 0.99428 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.8788 (tpt) cc_final: 0.8565 (mmm) REVERT: C 283 MET cc_start: 0.8584 (tpp) cc_final: 0.8135 (mpp) REVERT: E 355 MET cc_start: 0.9386 (mtm) cc_final: 0.9006 (mtm) REVERT: Y 124 CYS cc_start: 0.9293 (m) cc_final: 0.8496 (p) REVERT: Y 274 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9271 (tt) REVERT: Z 99 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8847 (pm20) REVERT: Z 126 HIS cc_start: 0.8840 (m90) cc_final: 0.8590 (m90) REVERT: Z 163 ARG cc_start: 0.8886 (mmm160) cc_final: 0.8458 (mmm160) REVERT: a 26 GLN cc_start: 0.8623 (mp10) cc_final: 0.8408 (mm-40) REVERT: a 78 ASN cc_start: 0.9088 (p0) cc_final: 0.8828 (p0) REVERT: c 45 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8402 (mtp-110) outliers start: 8 outliers final: 1 residues processed: 152 average time/residue: 0.1475 time to fit residues: 36.7208 Evaluate side-chains 141 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain Y residue 274 ILE Chi-restraints excluded: chain Z residue 99 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 154 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 259 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.044925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.033236 restraints weight = 144180.169| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 4.37 r_work: 0.2540 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23114 Z= 0.170 Angle : 0.561 8.460 31301 Z= 0.282 Chirality : 0.044 0.136 3485 Planarity : 0.004 0.085 4003 Dihedral : 5.144 57.961 3156 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % Rotamer: Outliers : 0.57 % Allowed : 4.35 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2805 helix: 1.03 (0.16), residues: 1108 sheet: 0.01 (0.20), residues: 652 loop : 0.01 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 62 TYR 0.016 0.001 TYR Y 277 PHE 0.015 0.001 PHE A 90 TRP 0.015 0.002 TRP Y 173 HIS 0.005 0.001 HIS Y 209 Details of bonding type rmsd covalent geometry : bond 0.00390 (23113) covalent geometry : angle 0.56083 (31298) hydrogen bonds : bond 0.03786 ( 1109) hydrogen bonds : angle 4.36253 ( 3075) link_TRANS : bond 0.00264 ( 1) link_TRANS : angle 1.23034 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7737 (tpm170) cc_final: 0.7406 (tpm170) REVERT: C 82 MET cc_start: 0.9063 (tpt) cc_final: 0.8806 (tpt) REVERT: C 283 MET cc_start: 0.9067 (tpp) cc_final: 0.8810 (tpp) REVERT: E 325 MET cc_start: 0.8878 (mmm) cc_final: 0.8391 (mmm) REVERT: Y 59 MET cc_start: 0.9037 (mmm) cc_final: 0.8813 (mmm) REVERT: Z 99 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.9076 (pm20) REVERT: Z 126 HIS cc_start: 0.8998 (m90) cc_final: 0.8676 (m90) REVERT: Z 163 ARG cc_start: 0.9030 (mmm160) cc_final: 0.8571 (mmm160) REVERT: a 78 ASN cc_start: 0.9241 (p0) cc_final: 0.8988 (p0) REVERT: c 45 ARG cc_start: 0.8888 (ttm110) cc_final: 0.8595 (mtp-110) outliers start: 14 outliers final: 7 residues processed: 147 average time/residue: 0.1484 time to fit residues: 35.5352 Evaluate side-chains 145 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain Z residue 99 GLU Chi-restraints excluded: chain Z residue 206 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 117 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN Y 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.044405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.032799 restraints weight = 144991.733| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 4.35 r_work: 0.2522 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23114 Z= 0.189 Angle : 0.574 12.327 31301 Z= 0.288 Chirality : 0.044 0.137 3485 Planarity : 0.004 0.083 4003 Dihedral : 5.218 63.915 3156 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.82 % Favored : 96.04 % Rotamer: Outliers : 0.73 % Allowed : 4.80 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: 0.76 (0.16), residues: 2805 helix: 1.33 (0.17), residues: 1078 sheet: 0.02 (0.20), residues: 652 loop : 0.14 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.014 0.001 TYR Y 277 PHE 0.016 0.001 PHE B 352 TRP 0.015 0.002 TRP Y 173 HIS 0.005 0.001 HIS Y 209 Details of bonding type rmsd covalent geometry : bond 0.00438 (23113) covalent geometry : angle 0.57386 (31298) hydrogen bonds : bond 0.03779 ( 1109) hydrogen bonds : angle 4.35736 ( 3075) link_TRANS : bond 0.00295 ( 1) link_TRANS : angle 1.13798 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 GLN cc_start: 0.8822 (pm20) cc_final: 0.8415 (pm20) REVERT: C 283 MET cc_start: 0.9136 (tpp) cc_final: 0.8528 (mpp) REVERT: E 283 MET cc_start: 0.9124 (tpp) cc_final: 0.8494 (mpp) REVERT: E 355 MET cc_start: 0.9485 (mtm) cc_final: 0.9215 (mtm) REVERT: Z 99 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.9032 (pm20) REVERT: Z 126 HIS cc_start: 0.9031 (m90) cc_final: 0.8680 (m90) REVERT: Z 163 ARG cc_start: 0.9063 (mmm160) cc_final: 0.8615 (mmm160) REVERT: Z 249 PHE cc_start: 0.9012 (m-80) cc_final: 0.8686 (m-80) REVERT: a 26 GLN cc_start: 0.8751 (mm110) cc_final: 0.8477 (mm-40) REVERT: a 78 ASN cc_start: 0.9224 (p0) cc_final: 0.8978 (p0) REVERT: c 45 ARG cc_start: 0.8888 (ttm110) cc_final: 0.8616 (mtp-110) outliers start: 18 outliers final: 9 residues processed: 158 average time/residue: 0.1485 time to fit residues: 37.6258 Evaluate side-chains 152 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain Z residue 99 GLU Chi-restraints excluded: chain Z residue 206 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 261 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN E 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.043758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.032076 restraints weight = 151455.504| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 4.44 r_work: 0.2496 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23114 Z= 0.226 Angle : 0.605 12.079 31301 Z= 0.302 Chirality : 0.045 0.139 3485 Planarity : 0.004 0.081 4003 Dihedral : 5.318 64.777 3156 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.17 % Favored : 95.72 % Rotamer: Outliers : 0.57 % Allowed : 5.57 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: 0.72 (0.16), residues: 2805 helix: 1.24 (0.16), residues: 1105 sheet: 0.00 (0.20), residues: 647 loop : 0.15 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.017 0.001 TYR Y 277 PHE 0.014 0.001 PHE Z 104 TRP 0.015 0.002 TRP C 356 HIS 0.004 0.001 HIS Y 209 Details of bonding type rmsd covalent geometry : bond 0.00522 (23113) covalent geometry : angle 0.60481 (31298) hydrogen bonds : bond 0.04108 ( 1109) hydrogen bonds : angle 4.41891 ( 3075) link_TRANS : bond 0.00315 ( 1) link_TRANS : angle 1.37966 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8833 (mm-30) REVERT: E 132 MET cc_start: 0.9220 (tmm) cc_final: 0.8806 (tmm) REVERT: E 325 MET cc_start: 0.8804 (mmm) cc_final: 0.8558 (mmm) REVERT: Z 99 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.9016 (pm20) REVERT: Z 163 ARG cc_start: 0.9085 (mmm160) cc_final: 0.8650 (mmm160) REVERT: a 26 GLN cc_start: 0.8789 (mm110) cc_final: 0.8522 (mm-40) REVERT: a 78 ASN cc_start: 0.9245 (p0) cc_final: 0.8999 (p0) outliers start: 14 outliers final: 11 residues processed: 147 average time/residue: 0.1435 time to fit residues: 34.1917 Evaluate side-chains 149 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain Z residue 99 GLU Chi-restraints excluded: chain Z residue 206 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 187 optimal weight: 20.0000 chunk 267 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.044175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.032737 restraints weight = 144958.890| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 4.35 r_work: 0.2521 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23114 Z= 0.141 Angle : 0.554 12.045 31301 Z= 0.275 Chirality : 0.043 0.140 3485 Planarity : 0.004 0.079 4003 Dihedral : 5.155 62.461 3156 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.64 % Favored : 96.25 % Rotamer: Outliers : 0.49 % Allowed : 6.10 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: 0.90 (0.17), residues: 2805 helix: 1.42 (0.17), residues: 1098 sheet: 0.02 (0.20), residues: 657 loop : 0.29 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG c 45 TYR 0.017 0.001 TYR Y 277 PHE 0.012 0.001 PHE Y 179 TRP 0.014 0.001 TRP Y 173 HIS 0.005 0.001 HIS Y 209 Details of bonding type rmsd covalent geometry : bond 0.00324 (23113) covalent geometry : angle 0.55366 (31298) hydrogen bonds : bond 0.03473 ( 1109) hydrogen bonds : angle 4.24297 ( 3075) link_TRANS : bond 0.00425 ( 1) link_TRANS : angle 1.41357 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8835 (mm-30) REVERT: B 132 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8919 (ttp) REVERT: C 82 MET cc_start: 0.9081 (tpt) cc_final: 0.8845 (mmm) REVERT: C 283 MET cc_start: 0.9217 (tpp) cc_final: 0.8281 (mpp) REVERT: C 353 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: D 246 GLN cc_start: 0.8631 (mt0) cc_final: 0.8053 (mt0) REVERT: E 132 MET cc_start: 0.9191 (tmm) cc_final: 0.8789 (tmm) REVERT: E 283 MET cc_start: 0.9017 (tpp) cc_final: 0.8577 (mpp) REVERT: E 325 MET cc_start: 0.8865 (mmm) cc_final: 0.8633 (mmm) REVERT: E 355 MET cc_start: 0.9477 (mtm) cc_final: 0.9197 (mtm) REVERT: Z 99 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8973 (pm20) REVERT: Z 126 HIS cc_start: 0.9194 (m-70) cc_final: 0.8795 (m90) REVERT: Z 163 ARG cc_start: 0.9075 (mmm160) cc_final: 0.8649 (mmm160) REVERT: Z 249 PHE cc_start: 0.8957 (m-80) cc_final: 0.8550 (m-80) REVERT: a 26 GLN cc_start: 0.8764 (mm110) cc_final: 0.8528 (mm-40) REVERT: a 78 ASN cc_start: 0.9242 (p0) cc_final: 0.8989 (p0) REVERT: c 45 ARG cc_start: 0.8867 (ttm110) cc_final: 0.8570 (mtp-110) outliers start: 12 outliers final: 7 residues processed: 151 average time/residue: 0.1509 time to fit residues: 37.7017 Evaluate side-chains 150 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain Z residue 99 GLU Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 107 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 251 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.043515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.031853 restraints weight = 172004.779| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 4.69 r_work: 0.2477 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23114 Z= 0.228 Angle : 0.601 11.898 31301 Z= 0.301 Chirality : 0.045 0.143 3485 Planarity : 0.004 0.079 4003 Dihedral : 5.277 64.798 3156 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.65 % Rotamer: Outliers : 0.53 % Allowed : 6.14 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: 0.80 (0.17), residues: 2805 helix: 1.26 (0.16), residues: 1123 sheet: 0.05 (0.20), residues: 647 loop : 0.22 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG c 45 TYR 0.017 0.001 TYR Y 277 PHE 0.013 0.001 PHE Z 104 TRP 0.014 0.002 TRP C 356 HIS 0.004 0.001 HIS Y 209 Details of bonding type rmsd covalent geometry : bond 0.00526 (23113) covalent geometry : angle 0.60110 (31298) hydrogen bonds : bond 0.04051 ( 1109) hydrogen bonds : angle 4.36648 ( 3075) link_TRANS : bond 0.00419 ( 1) link_TRANS : angle 1.51216 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8850 (mm-30) REVERT: C 283 MET cc_start: 0.9245 (tpp) cc_final: 0.8564 (mpp) REVERT: C 353 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: E 132 MET cc_start: 0.9221 (tmm) cc_final: 0.8818 (tmm) REVERT: E 355 MET cc_start: 0.9508 (mtm) cc_final: 0.9164 (mtm) REVERT: Z 99 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8976 (pm20) REVERT: Z 163 ARG cc_start: 0.9091 (mmm160) cc_final: 0.8663 (mmm160) REVERT: a 78 ASN cc_start: 0.9259 (p0) cc_final: 0.9010 (p0) REVERT: c 45 ARG cc_start: 0.8892 (ttm110) cc_final: 0.8625 (mtp-110) outliers start: 13 outliers final: 10 residues processed: 145 average time/residue: 0.1440 time to fit residues: 34.1905 Evaluate side-chains 149 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain Z residue 99 GLU Chi-restraints excluded: chain Z residue 206 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 207 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 135 optimal weight: 0.0870 chunk 160 optimal weight: 6.9990 chunk 222 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.044244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.032874 restraints weight = 139381.770| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 4.27 r_work: 0.2531 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23114 Z= 0.125 Angle : 0.547 11.809 31301 Z= 0.273 Chirality : 0.043 0.139 3485 Planarity : 0.004 0.077 4003 Dihedral : 5.101 61.610 3156 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.67 % Favored : 96.18 % Rotamer: Outliers : 0.69 % Allowed : 6.22 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: 0.93 (0.17), residues: 2805 helix: 1.36 (0.17), residues: 1127 sheet: 0.12 (0.21), residues: 647 loop : 0.32 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 45 TYR 0.018 0.001 TYR Y 277 PHE 0.012 0.001 PHE Y 179 TRP 0.014 0.001 TRP Y 173 HIS 0.005 0.001 HIS Y 209 Details of bonding type rmsd covalent geometry : bond 0.00285 (23113) covalent geometry : angle 0.54727 (31298) hydrogen bonds : bond 0.03351 ( 1109) hydrogen bonds : angle 4.17750 ( 3075) link_TRANS : bond 0.00410 ( 1) link_TRANS : angle 1.50368 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 364 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8860 (mm-30) REVERT: B 132 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8885 (ttp) REVERT: C 82 MET cc_start: 0.9062 (tpt) cc_final: 0.8824 (mmm) REVERT: C 283 MET cc_start: 0.9175 (tpp) cc_final: 0.8543 (mpp) REVERT: C 353 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: E 132 MET cc_start: 0.9181 (tmm) cc_final: 0.8780 (tmm) REVERT: E 355 MET cc_start: 0.9497 (mtm) cc_final: 0.9153 (mtm) REVERT: Z 99 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8963 (pm20) REVERT: Z 163 ARG cc_start: 0.9081 (mmm160) cc_final: 0.8653 (mmm160) REVERT: Z 249 PHE cc_start: 0.8928 (m-80) cc_final: 0.8484 (m-80) REVERT: a 26 GLN cc_start: 0.8798 (mm110) cc_final: 0.8564 (mm-40) REVERT: a 78 ASN cc_start: 0.9239 (p0) cc_final: 0.9000 (p0) REVERT: c 45 ARG cc_start: 0.8879 (ttm110) cc_final: 0.8610 (mtp-110) outliers start: 17 outliers final: 12 residues processed: 148 average time/residue: 0.1455 time to fit residues: 35.4858 Evaluate side-chains 155 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain Y residue 59 MET Chi-restraints excluded: chain Z residue 99 GLU Chi-restraints excluded: chain Z residue 206 CYS Chi-restraints excluded: chain a residue 91 THR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 117 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 98 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 257 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN C 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.045022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.033669 restraints weight = 131798.474| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 4.18 r_work: 0.2567 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23114 Z= 0.096 Angle : 0.524 11.607 31301 Z= 0.259 Chirality : 0.042 0.140 3485 Planarity : 0.004 0.075 4003 Dihedral : 4.802 51.780 3156 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 0.45 % Allowed : 6.38 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: 1.10 (0.17), residues: 2805 helix: 1.51 (0.17), residues: 1121 sheet: 0.13 (0.20), residues: 657 loop : 0.46 (0.21), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 45 TYR 0.021 0.001 TYR Y 277 PHE 0.012 0.001 PHE Y 179 TRP 0.017 0.001 TRP B 86 HIS 0.005 0.001 HIS Y 209 Details of bonding type rmsd covalent geometry : bond 0.00214 (23113) covalent geometry : angle 0.52340 (31298) hydrogen bonds : bond 0.02890 ( 1109) hydrogen bonds : angle 3.98389 ( 3075) link_TRANS : bond 0.00340 ( 1) link_TRANS : angle 1.25582 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8847 (mm-30) REVERT: B 132 MET cc_start: 0.9033 (ptm) cc_final: 0.8789 (ttp) REVERT: C 283 MET cc_start: 0.9093 (tpp) cc_final: 0.8530 (mpp) REVERT: C 353 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: D 154 ASP cc_start: 0.8705 (t70) cc_final: 0.8339 (p0) REVERT: E 132 MET cc_start: 0.9134 (tmm) cc_final: 0.8735 (tmm) REVERT: E 325 MET cc_start: 0.8905 (mmm) cc_final: 0.8661 (mmm) REVERT: E 355 MET cc_start: 0.9483 (mtm) cc_final: 0.9127 (mtm) REVERT: Z 99 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8983 (pm20) REVERT: Z 126 HIS cc_start: 0.9150 (m-70) cc_final: 0.8778 (m90) REVERT: Z 163 ARG cc_start: 0.9076 (mmm160) cc_final: 0.8633 (mmm160) REVERT: Z 249 PHE cc_start: 0.8934 (m-80) cc_final: 0.8497 (m-80) REVERT: a 26 GLN cc_start: 0.8830 (mm110) cc_final: 0.8556 (mm-40) REVERT: a 78 ASN cc_start: 0.9220 (p0) cc_final: 0.8998 (p0) REVERT: c 45 ARG cc_start: 0.8878 (ttm110) cc_final: 0.8583 (mtp-110) outliers start: 11 outliers final: 7 residues processed: 154 average time/residue: 0.1506 time to fit residues: 37.6448 Evaluate side-chains 154 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain Z residue 99 GLU Chi-restraints excluded: chain Z residue 206 CYS Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 6 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 94 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 205 optimal weight: 0.2980 chunk 4 optimal weight: 8.9990 chunk 74 optimal weight: 0.2980 chunk 142 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.044819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.033546 restraints weight = 123735.370| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 4.05 r_work: 0.2566 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23114 Z= 0.109 Angle : 0.526 11.579 31301 Z= 0.260 Chirality : 0.042 0.139 3485 Planarity : 0.004 0.076 4003 Dihedral : 4.780 52.966 3156 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.35 % Favored : 96.54 % Rotamer: Outliers : 0.45 % Allowed : 6.38 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 1.15 (0.17), residues: 2805 helix: 1.54 (0.17), residues: 1121 sheet: 0.17 (0.20), residues: 657 loop : 0.49 (0.21), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 45 TYR 0.019 0.001 TYR Y 277 PHE 0.012 0.001 PHE Y 179 TRP 0.016 0.001 TRP B 86 HIS 0.005 0.001 HIS Y 209 Details of bonding type rmsd covalent geometry : bond 0.00248 (23113) covalent geometry : angle 0.52625 (31298) hydrogen bonds : bond 0.03024 ( 1109) hydrogen bonds : angle 3.98088 ( 3075) link_TRANS : bond 0.00390 ( 1) link_TRANS : angle 1.38776 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5996.52 seconds wall clock time: 103 minutes 47.01 seconds (6227.01 seconds total)