Starting phenix.real_space_refine on Mon Apr 6 19:45:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q7k_72305/04_2026/9q7k_72305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q7k_72305/04_2026/9q7k_72305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q7k_72305/04_2026/9q7k_72305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q7k_72305/04_2026/9q7k_72305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q7k_72305/04_2026/9q7k_72305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q7k_72305/04_2026/9q7k_72305.map" } resolution = 3.13 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= 0.002 sd= 0.007 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 120 5.16 5 C 13275 2.51 5 N 3500 2.21 5 O 4045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 20955 Number of models: 1 Model: "" Number of chains: 15 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: 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: "D" 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: "E" 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: "a" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "b" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "c" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "d" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "e" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.03, per 1000 atoms: 0.38 Number of scatterers: 20955 At special positions: 0 Unit cell: (115.56, 127.44, 206.82, 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 120 16.00 P 10 15.00 Mg 5 11.99 O 4045 8.00 N 3500 7.00 C 13275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.7 seconds 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 33 sheets defined 47.5% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.890A 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 removed outlier: 3.647A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.765A 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: 3.973A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.628A 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 Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.571A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.523A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) 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: 4.088A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.214A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.549A pdb=" N PHE A 352 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.807A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.683A 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: 3.633A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.713A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.882A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.698A 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: 3.582A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.668A pdb=" N THR B 260 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.567A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) 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: 4.049A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.220A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.537A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 349 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 61 removed outlier: 3.783A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.708A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.760A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 197 removed outlier: 4.024A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.695A 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 256 removed outlier: 3.553A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.722A pdb=" N THR C 260 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.513A pdb=" N PHE C 266 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 263 through 267' Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 4.101A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.220A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.515A pdb=" N PHE C 352 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.677A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.591A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.695A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 197 removed outlier: 4.149A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D 197 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.667A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.548A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.670A pdb=" N THR D 260 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 4.093A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.157A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.548A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) 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 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.519A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.690A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.670A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 197 removed outlier: 4.146A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.663A 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 251 through 256 removed outlier: 3.602A pdb=" N ARG E 254 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 removed outlier: 3.662A pdb=" N THR E 260 " --> pdb=" O CYS E 257 " (cutoff:3.500A) 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 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.992A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.214A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.548A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 352 through 356 removed outlier: 3.602A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'a' and resid 8 through 20 removed outlier: 3.781A pdb=" N ILE a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL a 20 " --> pdb=" O ASN a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 31 Processing helix chain 'a' and resid 58 through 60 No H-bonds generated for 'chain 'a' and resid 58 through 60' Processing helix chain 'a' and resid 66 through 74 Processing helix chain 'a' and resid 110 through 120 Processing helix chain 'a' and resid 120 through 128 removed outlier: 4.191A pdb=" N ILE a 124 " --> pdb=" O SER a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 143 removed outlier: 3.575A pdb=" N ASP a 142 " --> pdb=" O GLY a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 153 removed outlier: 4.217A 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: 3.892A pdb=" N ILE b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) removed outlier: 3.654A 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 120 Processing helix chain 'b' and resid 120 through 128 removed outlier: 4.056A pdb=" N ILE b 124 " --> pdb=" O SER b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 143 removed outlier: 3.591A pdb=" N ASP b 142 " --> pdb=" O GLY b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 153 removed outlier: 4.224A 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: 3.770A pdb=" N ILE c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) removed outlier: 3.550A 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 Processing helix chain 'c' and resid 110 through 120 Processing helix chain 'c' and resid 120 through 128 removed outlier: 3.950A pdb=" N ILE c 124 " --> pdb=" O SER c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 removed outlier: 3.576A 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 helix chain 'd' and resid 8 through 20 removed outlier: 3.768A pdb=" N ILE d 12 " --> pdb=" O ASN d 8 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL d 20 " --> pdb=" O ASN d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 31 Processing helix chain 'd' and resid 58 through 60 No H-bonds generated for 'chain 'd' and resid 58 through 60' Processing helix chain 'd' and resid 66 through 74 removed outlier: 3.519A pdb=" N SER d 70 " --> pdb=" O ASP d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 120 Processing helix chain 'd' and resid 120 through 128 removed outlier: 3.990A pdb=" N ILE d 124 " --> pdb=" O SER d 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 143 removed outlier: 3.533A pdb=" N ASP d 142 " --> pdb=" O GLY d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 145 through 153 removed outlier: 4.212A pdb=" N LEU d 149 " --> pdb=" O ASP d 145 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing helix chain 'e' and resid 8 through 20 removed outlier: 3.831A pdb=" N ILE e 12 " --> pdb=" O ASN e 8 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL e 20 " --> pdb=" O ASN e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 25 through 31 Processing helix chain 'e' and resid 58 through 60 No H-bonds generated for 'chain 'e' and resid 58 through 60' Processing helix chain 'e' and resid 66 through 74 Processing helix chain 'e' and resid 110 through 120 Processing helix chain 'e' and resid 120 through 128 removed outlier: 3.960A pdb=" N ILE e 124 " --> pdb=" O SER e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 139 through 143 removed outlier: 3.552A pdb=" N ASP e 142 " --> pdb=" O GLY e 139 " (cutoff:3.500A) Processing helix chain 'e' and resid 145 through 153 removed outlier: 4.224A pdb=" N LEU e 149 " --> pdb=" O ASP e 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.697A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.236A 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 240 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.740A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.187A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.793A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.203A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.797A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.226A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.697A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC4, first strand: chain 'E' and resid 169 through 170 removed outlier: 7.569A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC6, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.624A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 10.947A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS a 133 " --> pdb=" O LEU a 99 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.624A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 10.947A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.511A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU b 37 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ALA b 52 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 10.895A pdb=" N ALA b 35 " --> pdb=" O ALA b 52 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N GLN b 54 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N LYS b 33 " --> pdb=" O GLN b 54 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS b 133 " --> pdb=" O LEU b 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.511A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU b 37 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ALA b 52 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 10.895A pdb=" N ALA b 35 " --> pdb=" O ALA b 52 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N GLN b 54 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N LYS b 33 " --> pdb=" O GLN b 54 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.485A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS c 133 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.485A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.465A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL d 49 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU d 40 " --> pdb=" O VAL d 49 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N GLU d 51 " --> pdb=" O PHE d 38 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N PHE d 38 " --> pdb=" O GLU d 51 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N LYS d 53 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL d 36 " --> pdb=" O LYS d 53 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE d 55 " --> pdb=" O LYS d 34 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS d 133 " --> pdb=" O LEU d 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.465A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL d 49 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU d 40 " --> pdb=" O VAL d 49 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N GLU d 51 " --> pdb=" O PHE d 38 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N PHE d 38 " --> pdb=" O GLU d 51 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N LYS d 53 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL d 36 " --> pdb=" O LYS d 53 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE d 55 " --> pdb=" O LYS d 34 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.566A pdb=" N THR e 6 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N VAL e 49 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU e 37 " --> pdb=" O GLU e 50 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N ALA e 52 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 10.963A pdb=" N ALA e 35 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N GLN e 54 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N LYS e 33 " --> pdb=" O GLN e 54 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS e 34 " --> pdb=" O ASP e 86 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS e 133 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.566A pdb=" N THR e 6 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N VAL e 49 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU e 37 " --> pdb=" O GLU e 50 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N ALA e 52 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 10.963A pdb=" N ALA e 35 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N GLN e 54 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N LYS e 33 " --> pdb=" O GLN e 54 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS e 34 " --> pdb=" O ASP e 86 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2655 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: 4.36 Time building geometry restraints manager: 2.36 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: 6641 1.34 - 1.46: 4668 1.46 - 1.59: 9846 1.59 - 1.71: 15 1.71 - 1.83: 205 Bond restraints: 21375 Sorted by residual: bond pdb=" C LEU A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.335 1.390 -0.055 1.28e-02 6.10e+03 1.85e+01 bond pdb=" N THR e 63 " pdb=" CA THR e 63 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.04e+00 bond pdb=" N THR d 63 " pdb=" CA THR d 63 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.15e-02 7.56e+03 6.90e+00 bond pdb=" N THR a 63 " pdb=" CA THR a 63 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.15e-02 7.56e+03 6.54e+00 bond pdb=" N THR c 63 " pdb=" CA THR c 63 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.15e-02 7.56e+03 6.47e+00 ... (remaining 21370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 28330 3.23 - 6.46: 534 6.46 - 9.70: 55 9.70 - 12.93: 10 12.93 - 16.16: 6 Bond angle restraints: 28935 Sorted by residual: angle pdb=" CB MET C 123 " pdb=" CG MET C 123 " pdb=" SD MET C 123 " ideal model delta sigma weight residual 112.70 128.86 -16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" CA GLN A 246 " pdb=" CB GLN A 246 " pdb=" CG GLN A 246 " ideal model delta sigma weight residual 114.10 124.85 -10.75 2.00e+00 2.50e-01 2.89e+01 angle pdb=" CB MET A 325 " pdb=" CG MET A 325 " pdb=" SD MET A 325 " ideal model delta sigma weight residual 112.70 128.11 -15.41 3.00e+00 1.11e-01 2.64e+01 angle pdb=" CB MET A 227 " pdb=" CG MET A 227 " pdb=" SD MET A 227 " ideal model delta sigma weight residual 112.70 127.95 -15.25 3.00e+00 1.11e-01 2.59e+01 angle pdb=" CB MET C 227 " pdb=" CG MET C 227 " pdb=" SD MET C 227 " ideal model delta sigma weight residual 112.70 127.72 -15.02 3.00e+00 1.11e-01 2.51e+01 ... (remaining 28930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 11920 17.87 - 35.74: 859 35.74 - 53.60: 174 53.60 - 71.47: 25 71.47 - 89.34: 22 Dihedral angle restraints: 13000 sinusoidal: 5310 harmonic: 7690 Sorted by residual: dihedral pdb=" CA TYR B 337 " pdb=" C TYR B 337 " pdb=" N SER B 338 " pdb=" CA SER B 338 " ideal model delta harmonic sigma weight residual -180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG e 81 " pdb=" C ARG e 81 " pdb=" N TYR e 82 " pdb=" CA TYR e 82 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ARG d 81 " pdb=" C ARG d 81 " pdb=" N TYR d 82 " pdb=" CA TYR d 82 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 12997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2418 0.059 - 0.119: 673 0.119 - 0.178: 121 0.178 - 0.237: 24 0.237 - 0.297: 9 Chirality restraints: 3245 Sorted by residual: chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA GLN A 246 " pdb=" N GLN A 246 " pdb=" C GLN A 246 " pdb=" CB GLN A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3242 not shown) Planarity restraints: 3675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 370 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.35e+00 pdb=" C VAL B 370 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL B 370 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS B 371 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 370 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C VAL D 370 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL D 370 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS D 371 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO B 164 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.039 5.00e-02 4.00e+02 ... (remaining 3672 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 20 2.64 - 3.21: 16979 3.21 - 3.77: 30778 3.77 - 4.34: 44488 4.34 - 4.90: 72827 Nonbonded interactions: 165092 Sorted by model distance: nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.076 2.170 nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.079 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.084 2.170 nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.086 2.170 nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.092 2.170 ... (remaining 165087 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: 0.01 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' selection = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 25.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.170 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 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 : 0.005 0.059 21375 Z= 0.264 Angle : 1.060 16.158 28935 Z= 0.565 Chirality : 0.059 0.297 3245 Planarity : 0.009 0.089 3675 Dihedral : 13.609 89.338 8050 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.15), residues: 2600 helix: -2.35 (0.12), residues: 950 sheet: -0.36 (0.22), residues: 490 loop : -0.25 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG d 45 TYR 0.031 0.002 TYR A 306 PHE 0.046 0.003 PHE D 90 TRP 0.022 0.003 TRP B 86 HIS 0.010 0.002 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00534 (21375) covalent geometry : angle 1.06039 (28935) hydrogen bonds : bond 0.16841 ( 960) hydrogen bonds : angle 7.23625 ( 2655) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 121 GLN cc_start: 0.9480 (tt0) cc_final: 0.9032 (tm-30) REVERT: A 305 MET cc_start: 0.9021 (tpp) cc_final: 0.8751 (tpp) REVERT: A 314 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8225 (tm-30) REVERT: B 82 MET cc_start: 0.9149 (tpt) cc_final: 0.8777 (mmm) REVERT: B 121 GLN cc_start: 0.9485 (tt0) cc_final: 0.9242 (tp40) REVERT: C 246 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8968 (mm-40) REVERT: C 313 MET cc_start: 0.9330 (mmm) cc_final: 0.9122 (tpt) REVERT: D 299 MET cc_start: 0.9447 (mmm) cc_final: 0.9239 (mtp) REVERT: E 59 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7794 (tm-30) REVERT: E 82 MET cc_start: 0.8889 (tpt) cc_final: 0.8517 (mmm) REVERT: E 176 MET cc_start: 0.8745 (mmt) cc_final: 0.8459 (mmt) REVERT: E 246 GLN cc_start: 0.8909 (mt0) cc_final: 0.8706 (mt0) REVERT: E 313 MET cc_start: 0.9260 (mmm) cc_final: 0.8961 (tpt) REVERT: a 115 MET cc_start: 0.9008 (tpt) cc_final: 0.8305 (tpp) REVERT: b 115 MET cc_start: 0.9465 (tpt) cc_final: 0.8894 (tpp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1265 time to fit residues: 26.9541 Evaluate side-chains 124 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN C 59 GLN C 101 HIS ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS D 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.037935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.028160 restraints weight = 236983.102| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 5.33 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21375 Z= 0.132 Angle : 0.574 7.674 28935 Z= 0.292 Chirality : 0.044 0.178 3245 Planarity : 0.005 0.056 3675 Dihedral : 5.377 51.043 2925 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.13 % Allowed : 2.02 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.29 (0.16), residues: 2600 helix: -0.37 (0.16), residues: 965 sheet: -0.10 (0.23), residues: 515 loop : 0.18 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 45 TYR 0.010 0.001 TYR A 133 PHE 0.016 0.001 PHE D 90 TRP 0.012 0.002 TRP C 340 HIS 0.003 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00294 (21375) covalent geometry : angle 0.57448 (28935) hydrogen bonds : bond 0.03878 ( 960) hydrogen bonds : angle 4.98236 ( 2655) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.802 Fit side-chains REVERT: A 121 GLN cc_start: 0.9464 (tt0) cc_final: 0.9099 (tm-30) REVERT: A 283 MET cc_start: 0.9142 (tpp) cc_final: 0.8530 (mpp) REVERT: B 121 GLN cc_start: 0.9310 (tt0) cc_final: 0.9046 (tp40) REVERT: C 325 MET cc_start: 0.9082 (mmm) cc_final: 0.8856 (mmp) REVERT: E 246 GLN cc_start: 0.8778 (mt0) cc_final: 0.8192 (mt0) REVERT: E 283 MET cc_start: 0.9102 (mmt) cc_final: 0.8566 (mpp) REVERT: a 115 MET cc_start: 0.8981 (tpt) cc_final: 0.8383 (tpp) REVERT: b 115 MET cc_start: 0.9109 (tpt) cc_final: 0.8611 (tpp) outliers start: 3 outliers final: 3 residues processed: 127 average time/residue: 0.1266 time to fit residues: 26.9670 Evaluate side-chains 127 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain b residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 176 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.036918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.027434 restraints weight = 254956.091| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 5.43 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21375 Z= 0.178 Angle : 0.582 7.986 28935 Z= 0.294 Chirality : 0.044 0.147 3245 Planarity : 0.004 0.053 3675 Dihedral : 5.081 48.648 2925 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.26 % Allowed : 3.20 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.17), residues: 2600 helix: 0.62 (0.17), residues: 970 sheet: -0.15 (0.23), residues: 530 loop : 0.37 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.010 0.001 TYR C 91 PHE 0.017 0.001 PHE c 38 TRP 0.015 0.002 TRP C 340 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00402 (21375) covalent geometry : angle 0.58190 (28935) hydrogen bonds : bond 0.03965 ( 960) hydrogen bonds : angle 4.62004 ( 2655) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.917 Fit side-chains REVERT: A 121 GLN cc_start: 0.9446 (tt0) cc_final: 0.9046 (tm-30) REVERT: B 82 MET cc_start: 0.9218 (tpt) cc_final: 0.8906 (mmm) REVERT: B 121 GLN cc_start: 0.9339 (tt0) cc_final: 0.8822 (tm-30) REVERT: C 132 MET cc_start: 0.8423 (ttp) cc_final: 0.8222 (ttp) REVERT: C 325 MET cc_start: 0.9024 (mmm) cc_final: 0.8780 (mmp) REVERT: D 82 MET cc_start: 0.8690 (tpt) cc_final: 0.8126 (mmm) REVERT: E 82 MET cc_start: 0.8840 (tpt) cc_final: 0.8012 (mmm) REVERT: E 246 GLN cc_start: 0.8683 (mt0) cc_final: 0.8416 (mt0) REVERT: a 115 MET cc_start: 0.8951 (tpt) cc_final: 0.8309 (tpp) REVERT: b 115 MET cc_start: 0.9215 (tpt) cc_final: 0.8696 (tpp) outliers start: 6 outliers final: 3 residues processed: 128 average time/residue: 0.1270 time to fit residues: 27.4842 Evaluate side-chains 126 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain e residue 166 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 161 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 GLN ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.035792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.026444 restraints weight = 230204.634| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 5.09 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 21375 Z= 0.300 Angle : 0.660 9.938 28935 Z= 0.333 Chirality : 0.047 0.155 3245 Planarity : 0.004 0.056 3675 Dihedral : 5.267 53.834 2925 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.39 % Allowed : 3.60 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.17), residues: 2600 helix: 0.98 (0.17), residues: 960 sheet: -0.20 (0.23), residues: 540 loop : 0.41 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 45 TYR 0.016 0.001 TYR a 117 PHE 0.028 0.002 PHE c 38 TRP 0.017 0.002 TRP C 340 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00680 (21375) covalent geometry : angle 0.66005 (28935) hydrogen bonds : bond 0.04584 ( 960) hydrogen bonds : angle 4.71930 ( 2655) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8903 (tpp) cc_final: 0.8244 (tmm) REVERT: A 121 GLN cc_start: 0.9453 (tt0) cc_final: 0.9035 (tm-30) REVERT: C 325 MET cc_start: 0.8974 (mmm) cc_final: 0.8736 (mmp) REVERT: E 132 MET cc_start: 0.8905 (ptm) cc_final: 0.8483 (tmm) REVERT: a 115 MET cc_start: 0.9003 (tpt) cc_final: 0.8315 (tpp) REVERT: b 111 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8683 (tt) REVERT: b 115 MET cc_start: 0.9238 (tpt) cc_final: 0.8742 (tpp) outliers start: 9 outliers final: 5 residues processed: 128 average time/residue: 0.1181 time to fit residues: 25.4523 Evaluate side-chains 129 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain e residue 166 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 25 optimal weight: 0.4980 chunk 185 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.036078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.026959 restraints weight = 192951.224| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 4.72 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 21375 Z= 0.199 Angle : 0.582 9.281 28935 Z= 0.292 Chirality : 0.045 0.153 3245 Planarity : 0.004 0.052 3675 Dihedral : 5.103 51.677 2925 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.31 % Allowed : 4.52 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.17), residues: 2600 helix: 1.10 (0.17), residues: 1000 sheet: -0.12 (0.23), residues: 525 loop : 0.41 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.011 0.001 TYR E 306 PHE 0.017 0.001 PHE c 38 TRP 0.015 0.002 TRP C 340 HIS 0.003 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00455 (21375) covalent geometry : angle 0.58197 (28935) hydrogen bonds : bond 0.03880 ( 960) hydrogen bonds : angle 4.48142 ( 2655) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 GLN cc_start: 0.9456 (tt0) cc_final: 0.9109 (tm-30) REVERT: B 82 MET cc_start: 0.9219 (tpt) cc_final: 0.8915 (mmm) REVERT: E 132 MET cc_start: 0.8873 (ptm) cc_final: 0.8462 (tmm) REVERT: a 115 MET cc_start: 0.8989 (tpt) cc_final: 0.8305 (tpp) REVERT: b 111 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8622 (tt) REVERT: b 115 MET cc_start: 0.9220 (tpt) cc_final: 0.8715 (tpp) outliers start: 7 outliers final: 5 residues processed: 130 average time/residue: 0.1277 time to fit residues: 27.6955 Evaluate side-chains 129 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain e residue 166 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 157 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 228 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 chunk 195 optimal weight: 0.0980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.036415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.026959 restraints weight = 258186.242| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 5.42 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21375 Z= 0.148 Angle : 0.553 8.998 28935 Z= 0.274 Chirality : 0.044 0.161 3245 Planarity : 0.004 0.049 3675 Dihedral : 4.898 47.684 2925 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.26 % Allowed : 4.87 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2600 helix: 1.35 (0.17), residues: 995 sheet: 0.02 (0.23), residues: 515 loop : 0.48 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.010 0.001 TYR E 306 PHE 0.013 0.001 PHE c 38 TRP 0.013 0.002 TRP C 340 HIS 0.002 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00337 (21375) covalent geometry : angle 0.55340 (28935) hydrogen bonds : bond 0.03469 ( 960) hydrogen bonds : angle 4.29634 ( 2655) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8856 (mmm) cc_final: 0.8335 (mmm) REVERT: A 121 GLN cc_start: 0.9471 (tt0) cc_final: 0.9112 (tm-30) REVERT: D 82 MET cc_start: 0.8663 (tpt) cc_final: 0.8018 (mmm) REVERT: D 227 MET cc_start: 0.8762 (mmm) cc_final: 0.8375 (tpp) REVERT: E 82 MET cc_start: 0.8831 (tpt) cc_final: 0.8171 (mmm) REVERT: E 132 MET cc_start: 0.8839 (ptm) cc_final: 0.8442 (tmm) REVERT: a 115 MET cc_start: 0.8968 (tpt) cc_final: 0.8318 (tpp) REVERT: b 111 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8581 (tt) REVERT: b 115 MET cc_start: 0.9216 (tpt) cc_final: 0.8682 (tpp) outliers start: 6 outliers final: 5 residues processed: 128 average time/residue: 0.1299 time to fit residues: 27.7753 Evaluate side-chains 129 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 364 GLU Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 30 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN d 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.036202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.026758 restraints weight = 268542.471| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 5.48 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21375 Z= 0.173 Angle : 0.562 8.809 28935 Z= 0.280 Chirality : 0.044 0.162 3245 Planarity : 0.004 0.049 3675 Dihedral : 4.873 47.628 2925 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.35 % Allowed : 5.09 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2600 helix: 1.35 (0.18), residues: 1000 sheet: -0.05 (0.23), residues: 525 loop : 0.51 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 372 TYR 0.010 0.001 TYR C 91 PHE 0.016 0.001 PHE c 38 TRP 0.014 0.002 TRP C 340 HIS 0.002 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00395 (21375) covalent geometry : angle 0.56172 (28935) hydrogen bonds : bond 0.03633 ( 960) hydrogen bonds : angle 4.28981 ( 2655) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8845 (mmm) cc_final: 0.8283 (mmm) REVERT: A 121 GLN cc_start: 0.9471 (tt0) cc_final: 0.9119 (tm-30) REVERT: B 82 MET cc_start: 0.9202 (tpt) cc_final: 0.8940 (mmm) REVERT: D 227 MET cc_start: 0.8760 (mmm) cc_final: 0.8352 (tpp) REVERT: E 82 MET cc_start: 0.8830 (tpt) cc_final: 0.8191 (mmm) REVERT: E 132 MET cc_start: 0.8849 (ptm) cc_final: 0.8435 (tmm) REVERT: a 115 MET cc_start: 0.8973 (tpt) cc_final: 0.8323 (tpp) REVERT: b 111 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8601 (tt) REVERT: b 115 MET cc_start: 0.9226 (tpt) cc_final: 0.8698 (tpp) outliers start: 8 outliers final: 7 residues processed: 127 average time/residue: 0.1358 time to fit residues: 28.3712 Evaluate side-chains 129 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 364 GLU Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain e residue 166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 94 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.036400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.027110 restraints weight = 223610.707| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 5.07 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21375 Z= 0.146 Angle : 0.550 8.521 28935 Z= 0.272 Chirality : 0.043 0.151 3245 Planarity : 0.003 0.048 3675 Dihedral : 4.786 45.511 2925 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.35 % Allowed : 5.22 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2600 helix: 1.19 (0.17), residues: 1055 sheet: -0.03 (0.23), residues: 525 loop : 0.64 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 372 TYR 0.009 0.001 TYR E 306 PHE 0.013 0.001 PHE c 38 TRP 0.013 0.001 TRP C 340 HIS 0.002 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00335 (21375) covalent geometry : angle 0.54952 (28935) hydrogen bonds : bond 0.03374 ( 960) hydrogen bonds : angle 4.19634 ( 2655) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8838 (mmm) cc_final: 0.8294 (mmm) REVERT: A 121 GLN cc_start: 0.9467 (tt0) cc_final: 0.9122 (tm-30) REVERT: B 82 MET cc_start: 0.9203 (tpt) cc_final: 0.8897 (mmm) REVERT: C 325 MET cc_start: 0.8890 (mmp) cc_final: 0.8581 (mmm) REVERT: D 82 MET cc_start: 0.8696 (tpt) cc_final: 0.7773 (mmm) REVERT: D 227 MET cc_start: 0.8753 (mmm) cc_final: 0.8356 (tpp) REVERT: E 82 MET cc_start: 0.8832 (tpt) cc_final: 0.8195 (mmm) REVERT: E 132 MET cc_start: 0.8824 (ptm) cc_final: 0.8421 (tmm) REVERT: a 115 MET cc_start: 0.8967 (tpt) cc_final: 0.8342 (tpp) REVERT: b 111 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8595 (tt) REVERT: b 115 MET cc_start: 0.9213 (tpt) cc_final: 0.8673 (tpp) outliers start: 8 outliers final: 6 residues processed: 130 average time/residue: 0.1298 time to fit residues: 28.1075 Evaluate side-chains 130 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 364 GLU Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 44 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.035863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.026362 restraints weight = 280944.196| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 5.51 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 21375 Z= 0.247 Angle : 0.617 9.795 28935 Z= 0.307 Chirality : 0.045 0.144 3245 Planarity : 0.004 0.051 3675 Dihedral : 4.983 50.562 2925 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.31 % Allowed : 5.44 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.17), residues: 2600 helix: 1.21 (0.17), residues: 1030 sheet: -0.03 (0.23), residues: 525 loop : 0.52 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 372 TYR 0.012 0.001 TYR C 91 PHE 0.018 0.001 PHE c 38 TRP 0.015 0.002 TRP C 340 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00561 (21375) covalent geometry : angle 0.61689 (28935) hydrogen bonds : bond 0.04115 ( 960) hydrogen bonds : angle 4.42130 ( 2655) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8887 (mmm) cc_final: 0.8282 (mmm) REVERT: A 121 GLN cc_start: 0.9473 (tt0) cc_final: 0.9133 (tm-30) REVERT: B 82 MET cc_start: 0.9243 (tpt) cc_final: 0.8955 (mmm) REVERT: C 325 MET cc_start: 0.8930 (mmp) cc_final: 0.8612 (mmm) REVERT: E 132 MET cc_start: 0.8873 (ptm) cc_final: 0.8657 (tmm) REVERT: a 115 MET cc_start: 0.8985 (tpt) cc_final: 0.8299 (tpp) REVERT: b 111 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8703 (tt) REVERT: b 115 MET cc_start: 0.9246 (tpt) cc_final: 0.8755 (tpp) outliers start: 7 outliers final: 5 residues processed: 127 average time/residue: 0.1266 time to fit residues: 26.5560 Evaluate side-chains 128 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 364 GLU Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 65 optimal weight: 0.0170 chunk 228 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 212 optimal weight: 0.0030 chunk 32 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 221 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 overall best weight: 0.5230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.036936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.027433 restraints weight = 272263.716| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 5.57 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21375 Z= 0.092 Angle : 0.542 9.358 28935 Z= 0.266 Chirality : 0.043 0.145 3245 Planarity : 0.003 0.048 3675 Dihedral : 4.698 42.385 2925 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.22 % Allowed : 5.70 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2600 helix: 1.26 (0.17), residues: 1055 sheet: 0.13 (0.23), residues: 515 loop : 0.64 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.009 0.001 TYR C 306 PHE 0.010 0.001 PHE D 223 TRP 0.013 0.001 TRP D 340 HIS 0.002 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00200 (21375) covalent geometry : angle 0.54241 (28935) hydrogen bonds : bond 0.02962 ( 960) hydrogen bonds : angle 4.06831 ( 2655) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8804 (mmm) cc_final: 0.8274 (mmm) REVERT: A 121 GLN cc_start: 0.9471 (tt0) cc_final: 0.9137 (tm-30) REVERT: B 82 MET cc_start: 0.9194 (tpt) cc_final: 0.8885 (mmm) REVERT: D 82 MET cc_start: 0.8656 (tpt) cc_final: 0.7810 (mmm) REVERT: E 82 MET cc_start: 0.8775 (tpt) cc_final: 0.8120 (mmm) REVERT: a 115 MET cc_start: 0.8943 (tpt) cc_final: 0.8373 (tpp) REVERT: b 115 MET cc_start: 0.9190 (tpt) cc_final: 0.8680 (tpp) REVERT: d 26 GLN cc_start: 0.8894 (mm110) cc_final: 0.8686 (mm110) outliers start: 5 outliers final: 3 residues processed: 127 average time/residue: 0.1307 time to fit residues: 27.3924 Evaluate side-chains 124 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain E residue 59 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 254 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 229 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 87 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3114 r_free = 0.3114 target = 0.036742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.027460 restraints weight = 222190.206| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 5.07 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21375 Z= 0.111 Angle : 0.548 9.604 28935 Z= 0.266 Chirality : 0.043 0.141 3245 Planarity : 0.003 0.046 3675 Dihedral : 4.618 40.251 2925 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.13 % Allowed : 5.70 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.17), residues: 2600 helix: 1.29 (0.17), residues: 1055 sheet: 0.17 (0.23), residues: 515 loop : 0.66 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.008 0.001 TYR C 91 PHE 0.013 0.001 PHE D 223 TRP 0.012 0.001 TRP C 340 HIS 0.002 0.000 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00252 (21375) covalent geometry : angle 0.54754 (28935) hydrogen bonds : bond 0.03103 ( 960) hydrogen bonds : angle 4.01282 ( 2655) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5746.82 seconds wall clock time: 99 minutes 5.98 seconds (5945.98 seconds total)