Starting phenix.real_space_refine on Sat Aug 23 11:56:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmy_27549/08_2025/8dmy_27549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmy_27549/08_2025/8dmy_27549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmy_27549/08_2025/8dmy_27549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmy_27549/08_2025/8dmy_27549.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmy_27549/08_2025/8dmy_27549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmy_27549/08_2025/8dmy_27549.cif" } resolution = 3.07 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= 0.049 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 8 5.49 5 Mg 4 5.21 5 S 80 5.16 5 C 7436 2.51 5 N 1986 2.21 5 O 2282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11796 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2925 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2925 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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} Time building chain proxies: 3.37, per 1000 atoms: 0.29 Number of scatterers: 11796 At special positions: 0 Unit cell: (78.408, 110.484, 169.29, 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 80 16.00 P 8 15.00 Mg 4 11.99 O 2282 8.00 N 1986 7.00 C 7436 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: 0.95 Conformation dependent library (CDL) restraints added in 565.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 48.5% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.859A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.808A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.715A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.106A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.830A 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 194 removed outlier: 3.768A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.578A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.732A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.695A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.586A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.756A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.527A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.589A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 348 through 355 removed outlier: 6.204A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.778A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.859A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.808A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.715A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.106A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.830A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.769A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.578A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.732A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.695A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.586A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.756A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.527A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.590A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 355 removed outlier: 6.204A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.778A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.859A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.807A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.715A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.106A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.829A 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 194 removed outlier: 3.768A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.579A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.732A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.695A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.586A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.757A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.528A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.591A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 355 removed outlier: 6.204A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.778A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.859A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.808A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.714A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.106A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.830A 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 194 removed outlier: 3.768A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.578A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.731A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.695A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.587A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.756A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.527A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.590A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 355 removed outlier: 6.204A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.778A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 4.151A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (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 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242 removed outlier: 4.592A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.151A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 242 removed outlier: 4.593A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.150A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 242 removed outlier: 4.593A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.150A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 242 removed outlier: 4.593A pdb=" N LEU D 242 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1188 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: 2.03 Time building geometry restraints manager: 1.31 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: 3660 1.34 - 1.45: 1670 1.45 - 1.57: 6570 1.57 - 1.69: 12 1.69 - 1.81: 140 Bond restraints: 12052 Sorted by residual: bond pdb=" N VAL B 45 " pdb=" CA VAL B 45 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" N VAL C 45 " pdb=" CA VAL C 45 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.22e+01 bond pdb=" N VAL D 45 " pdb=" CA VAL D 45 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N VAL A 45 " pdb=" CA VAL A 45 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.12e-02 7.97e+03 1.07e+01 ... (remaining 12047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15813 1.55 - 3.10: 422 3.10 - 4.65: 95 4.65 - 6.21: 27 6.21 - 7.76: 1 Bond angle restraints: 16358 Sorted by residual: angle pdb=" N VAL A 45 " pdb=" CA VAL A 45 " pdb=" CB VAL A 45 " ideal model delta sigma weight residual 112.36 104.60 7.76 1.85e+00 2.92e-01 1.76e+01 angle pdb=" CA VAL A 45 " pdb=" C VAL A 45 " pdb=" O VAL A 45 " ideal model delta sigma weight residual 121.63 117.98 3.65 9.90e-01 1.02e+00 1.36e+01 angle pdb=" CA VAL D 45 " pdb=" C VAL D 45 " pdb=" O VAL D 45 " ideal model delta sigma weight residual 121.63 117.98 3.65 9.90e-01 1.02e+00 1.36e+01 angle pdb=" CA VAL C 45 " pdb=" C VAL C 45 " pdb=" O VAL C 45 " ideal model delta sigma weight residual 121.63 118.02 3.61 9.90e-01 1.02e+00 1.33e+01 angle pdb=" CA VAL B 45 " pdb=" C VAL B 45 " pdb=" O VAL B 45 " ideal model delta sigma weight residual 121.63 118.06 3.57 9.90e-01 1.02e+00 1.30e+01 ... (remaining 16353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 6943 35.00 - 69.99: 283 69.99 - 104.99: 12 104.99 - 139.98: 4 139.98 - 174.98: 8 Dihedral angle restraints: 7250 sinusoidal: 2932 harmonic: 4318 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.98 -174.98 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.97 -174.97 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.97 -174.96 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 7247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1595 0.075 - 0.150: 202 0.150 - 0.225: 13 0.225 - 0.300: 1 0.300 - 0.375: 3 Chirality restraints: 1814 Sorted by residual: chirality pdb=" CA ILE C 71 " pdb=" N ILE C 71 " pdb=" C ILE C 71 " pdb=" CB ILE C 71 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 1811 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 70 " 0.020 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C PRO D 70 " -0.067 2.00e-02 2.50e+03 pdb=" O PRO D 70 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE D 71 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 111 " -0.033 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO D 112 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO C 112 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " -0.028 5.00e-02 4.00e+02 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 4368 2.88 - 3.39: 9838 3.39 - 3.89: 17453 3.89 - 4.40: 20097 4.40 - 4.90: 36152 Nonbonded interactions: 87908 Sorted by model distance: nonbonded pdb=" O ALA D 174 " pdb=" OG SER D 281 " model vdw 2.379 3.040 nonbonded pdb=" O ALA A 174 " pdb=" OG SER A 281 " model vdw 2.380 3.040 nonbonded pdb=" O ALA B 174 " pdb=" OG SER B 281 " model vdw 2.380 3.040 nonbonded pdb=" O ALA C 174 " pdb=" OG SER C 281 " model vdw 2.381 3.040 nonbonded pdb=" NH1 ARG B 210 " pdb=" OE2 GLU B 214 " model vdw 2.412 3.120 ... (remaining 87903 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 3 through 402) selection = (chain 'B' and resid 3 through 402) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.900 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12052 Z= 0.242 Angle : 0.622 7.757 16358 Z= 0.353 Chirality : 0.049 0.375 1814 Planarity : 0.004 0.051 2096 Dihedral : 18.681 174.978 4486 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.63 % Allowed : 21.71 % Favored : 77.65 % 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 aren not related in a simple way. whole: -1.24 (0.21), residues: 1474 helix: -1.77 (0.20), residues: 528 sheet: 0.76 (0.30), residues: 268 loop : -0.52 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 37 TYR 0.006 0.001 TYR D 306 PHE 0.004 0.001 PHE B 31 TRP 0.007 0.001 TRP B 356 HIS 0.003 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00359 (12052) covalent geometry : angle 0.62157 (16358) hydrogen bonds : bond 0.34375 ( 476) hydrogen bonds : angle 7.92257 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.464 Fit side-chains REVERT: A 224 GLU cc_start: 0.7798 (mm-30) cc_final: 0.6732 (mp0) REVERT: B 95 ARG cc_start: 0.6816 (mtm110) cc_final: 0.6327 (mtt90) REVERT: B 211 ASP cc_start: 0.8154 (t0) cc_final: 0.7849 (t0) REVERT: B 326 LYS cc_start: 0.8294 (mttp) cc_final: 0.7513 (tttm) REVERT: C 51 ASP cc_start: 0.7386 (p0) cc_final: 0.6942 (t0) REVERT: C 80 ASP cc_start: 0.8122 (m-30) cc_final: 0.7770 (m-30) REVERT: C 95 ARG cc_start: 0.6814 (mtm110) cc_final: 0.6552 (mtm-85) REVERT: C 132 MET cc_start: 0.9013 (ptm) cc_final: 0.8783 (ptm) REVERT: C 211 ASP cc_start: 0.8289 (t0) cc_final: 0.7916 (t0) REVERT: C 326 LYS cc_start: 0.8043 (mttp) cc_final: 0.7675 (mmtt) REVERT: C 372 ARG cc_start: 0.6742 (ttm170) cc_final: 0.6208 (mtm180) REVERT: D 95 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6649 (mtp-110) REVERT: D 358 SER cc_start: 0.8685 (m) cc_final: 0.8414 (t) outliers start: 8 outliers final: 1 residues processed: 206 average time/residue: 0.1080 time to fit residues: 31.4986 Evaluate side-chains 150 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 101 HIS A 121 GLN A 275 HIS B 12 ASN B 101 HIS B 121 GLN B 275 HIS C 12 ASN C 101 HIS C 121 GLN C 275 HIS D 12 ASN D 121 GLN D 275 HIS D 353 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.129501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110209 restraints weight = 15072.566| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.80 r_work: 0.3167 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12052 Z= 0.149 Angle : 0.613 6.040 16358 Z= 0.311 Chirality : 0.048 0.144 1814 Planarity : 0.005 0.053 2096 Dihedral : 13.912 179.417 1680 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.49 % Allowed : 20.29 % Favored : 76.23 % 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 aren not related in a simple way. whole: -0.59 (0.22), residues: 1474 helix: -0.57 (0.23), residues: 548 sheet: 0.97 (0.31), residues: 288 loop : -0.75 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 210 TYR 0.009 0.001 TYR C 69 PHE 0.007 0.001 PHE A 223 TRP 0.006 0.001 TRP A 356 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00347 (12052) covalent geometry : angle 0.61283 (16358) hydrogen bonds : bond 0.05558 ( 476) hydrogen bonds : angle 5.04092 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.491 Fit side-chains REVERT: B 65 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8338 (pp) REVERT: B 82 MET cc_start: 0.9027 (tpt) cc_final: 0.8573 (tpt) REVERT: B 95 ARG cc_start: 0.7449 (mtm110) cc_final: 0.7040 (mtt90) REVERT: B 326 LYS cc_start: 0.8278 (mttp) cc_final: 0.7348 (tttm) REVERT: B 372 ARG cc_start: 0.7345 (mmm-85) cc_final: 0.7032 (mtm180) REVERT: C 51 ASP cc_start: 0.7630 (p0) cc_final: 0.7202 (t0) REVERT: C 80 ASP cc_start: 0.8278 (m-30) cc_final: 0.8066 (m-30) REVERT: C 211 ASP cc_start: 0.8652 (t0) cc_final: 0.8296 (t0) REVERT: C 326 LYS cc_start: 0.8293 (mttp) cc_final: 0.7703 (mmtm) REVERT: C 372 ARG cc_start: 0.6937 (ttm170) cc_final: 0.6660 (ttm170) REVERT: D 95 ARG cc_start: 0.7531 (mtm110) cc_final: 0.7275 (mtm110) outliers start: 44 outliers final: 27 residues processed: 185 average time/residue: 0.1025 time to fit residues: 27.8321 Evaluate side-chains 166 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 134 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS B 12 ASN C 371 HIS D 101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103359 restraints weight = 15374.051| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.80 r_work: 0.3082 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12052 Z= 0.247 Angle : 0.694 6.684 16358 Z= 0.350 Chirality : 0.052 0.154 1814 Planarity : 0.006 0.053 2096 Dihedral : 12.939 178.630 1678 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.99 % Allowed : 19.10 % Favored : 75.91 % 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 aren not related in a simple way. whole: -0.90 (0.21), residues: 1474 helix: -0.53 (0.23), residues: 560 sheet: 0.27 (0.29), residues: 288 loop : -0.94 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 177 TYR 0.013 0.001 TYR B 69 PHE 0.012 0.002 PHE B 90 TRP 0.010 0.002 TRP C 356 HIS 0.006 0.002 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00632 (12052) covalent geometry : angle 0.69418 (16358) hydrogen bonds : bond 0.06699 ( 476) hydrogen bonds : angle 4.90063 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 136 time to evaluate : 0.425 Fit side-chains REVERT: A 199 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8475 (t) REVERT: B 65 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8453 (pp) REVERT: B 95 ARG cc_start: 0.7593 (mtm110) cc_final: 0.7269 (mtt90) REVERT: B 284 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8167 (mttm) REVERT: B 326 LYS cc_start: 0.8322 (mttp) cc_final: 0.7437 (tttm) REVERT: B 328 LYS cc_start: 0.8344 (ptpp) cc_final: 0.7986 (ptmm) REVERT: C 51 ASP cc_start: 0.7845 (p0) cc_final: 0.7324 (t0) REVERT: C 80 ASP cc_start: 0.8479 (m-30) cc_final: 0.8265 (m-30) REVERT: C 93 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8387 (mt-10) REVERT: C 211 ASP cc_start: 0.8689 (t0) cc_final: 0.8432 (t0) REVERT: C 278 THR cc_start: 0.8837 (t) cc_final: 0.8627 (m) REVERT: D 95 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7290 (mtm180) REVERT: D 334 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6850 (pm20) outliers start: 63 outliers final: 44 residues processed: 183 average time/residue: 0.1002 time to fit residues: 26.6189 Evaluate side-chains 177 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 5 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.124959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.105242 restraints weight = 15180.099| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.90 r_work: 0.3108 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12052 Z= 0.153 Angle : 0.598 6.474 16358 Z= 0.297 Chirality : 0.048 0.141 1814 Planarity : 0.005 0.055 2096 Dihedral : 12.020 174.755 1678 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.96 % Allowed : 21.32 % Favored : 74.72 % 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 aren not related in a simple way. whole: -0.56 (0.22), residues: 1474 helix: -0.07 (0.24), residues: 548 sheet: 0.02 (0.29), residues: 282 loop : -0.69 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 210 TYR 0.008 0.001 TYR C 69 PHE 0.008 0.001 PHE A 223 TRP 0.009 0.002 TRP C 356 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00383 (12052) covalent geometry : angle 0.59839 (16358) hydrogen bonds : bond 0.04814 ( 476) hydrogen bonds : angle 4.63094 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.353 Fit side-chains REVERT: A 354 GLN cc_start: 0.8417 (tp40) cc_final: 0.8196 (tp40) REVERT: B 65 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8457 (pp) REVERT: B 95 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7250 (mtt90) REVERT: B 326 LYS cc_start: 0.8266 (mttp) cc_final: 0.7389 (tttm) REVERT: B 328 LYS cc_start: 0.8321 (ptpp) cc_final: 0.7947 (ptmm) REVERT: B 372 ARG cc_start: 0.7380 (mmm-85) cc_final: 0.7123 (mtm180) REVERT: C 51 ASP cc_start: 0.7777 (p0) cc_final: 0.7267 (t0) REVERT: C 93 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: C 211 ASP cc_start: 0.8646 (t0) cc_final: 0.8388 (t0) REVERT: D 34 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.7937 (pt) REVERT: D 95 ARG cc_start: 0.7566 (mtm110) cc_final: 0.7268 (mtm180) REVERT: D 334 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6881 (pm20) outliers start: 50 outliers final: 33 residues processed: 171 average time/residue: 0.0963 time to fit residues: 23.9137 Evaluate side-chains 168 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.0270 chunk 107 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109174 restraints weight = 15045.732| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.90 r_work: 0.3163 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12052 Z= 0.097 Angle : 0.536 6.919 16358 Z= 0.259 Chirality : 0.044 0.132 1814 Planarity : 0.004 0.055 2096 Dihedral : 10.991 175.854 1678 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.77 % Allowed : 22.58 % Favored : 74.64 % 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 aren not related in a simple way. whole: -0.13 (0.22), residues: 1474 helix: 0.43 (0.25), residues: 536 sheet: 0.34 (0.28), residues: 296 loop : -0.63 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 210 TYR 0.008 0.001 TYR A 306 PHE 0.007 0.001 PHE D 31 TRP 0.008 0.001 TRP D 79 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00219 (12052) covalent geometry : angle 0.53568 (16358) hydrogen bonds : bond 0.03349 ( 476) hydrogen bonds : angle 4.36118 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.301 Fit side-chains REVERT: A 34 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8188 (pt) REVERT: A 93 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: A 354 GLN cc_start: 0.8424 (tp40) cc_final: 0.8195 (tp40) REVERT: B 95 ARG cc_start: 0.7591 (mtm110) cc_final: 0.7236 (mtt90) REVERT: B 326 LYS cc_start: 0.8257 (mttp) cc_final: 0.7359 (tttm) REVERT: C 51 ASP cc_start: 0.7660 (p0) cc_final: 0.7156 (t0) REVERT: C 93 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: C 211 ASP cc_start: 0.8641 (t0) cc_final: 0.8284 (t0) outliers start: 35 outliers final: 23 residues processed: 167 average time/residue: 0.0956 time to fit residues: 23.5928 Evaluate side-chains 155 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 288 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 68 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 117 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104949 restraints weight = 15274.608| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.79 r_work: 0.3110 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12052 Z= 0.195 Angle : 0.628 7.217 16358 Z= 0.308 Chirality : 0.049 0.143 1814 Planarity : 0.005 0.055 2096 Dihedral : 10.742 179.029 1678 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.52 % Allowed : 20.13 % Favored : 75.36 % 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 aren not related in a simple way. whole: -0.32 (0.22), residues: 1474 helix: 0.25 (0.24), residues: 536 sheet: 0.24 (0.28), residues: 300 loop : -0.72 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 37 TYR 0.009 0.001 TYR C 143 PHE 0.011 0.001 PHE A 223 TRP 0.009 0.002 TRP C 356 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00499 (12052) covalent geometry : angle 0.62791 (16358) hydrogen bonds : bond 0.05025 ( 476) hydrogen bonds : angle 4.50656 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 136 time to evaluate : 0.303 Fit side-chains REVERT: A 354 GLN cc_start: 0.8382 (tp40) cc_final: 0.8140 (tp40) REVERT: B 95 ARG cc_start: 0.7548 (mtm110) cc_final: 0.7232 (mtt90) REVERT: B 326 LYS cc_start: 0.8273 (mttp) cc_final: 0.7360 (tttm) REVERT: B 328 LYS cc_start: 0.8260 (ptpp) cc_final: 0.7866 (ptmm) REVERT: C 51 ASP cc_start: 0.7799 (p0) cc_final: 0.7176 (t0) REVERT: C 93 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8399 (mt-10) REVERT: C 211 ASP cc_start: 0.8675 (t0) cc_final: 0.8413 (t0) REVERT: D 34 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.7926 (pt) REVERT: D 334 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6952 (pm20) outliers start: 57 outliers final: 46 residues processed: 178 average time/residue: 0.0940 time to fit residues: 24.6801 Evaluate side-chains 183 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 104 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 97 optimal weight: 0.0770 chunk 142 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107350 restraints weight = 15146.428| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.79 r_work: 0.3146 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12052 Z= 0.125 Angle : 0.564 6.569 16358 Z= 0.275 Chirality : 0.046 0.137 1814 Planarity : 0.005 0.056 2096 Dihedral : 9.462 177.121 1678 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.04 % Allowed : 21.08 % Favored : 74.88 % 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 aren not related in a simple way. whole: -0.17 (0.22), residues: 1474 helix: 0.40 (0.24), residues: 536 sheet: 0.16 (0.28), residues: 288 loop : -0.56 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.007 0.001 TYR A 306 PHE 0.007 0.001 PHE A 223 TRP 0.009 0.001 TRP D 79 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00307 (12052) covalent geometry : angle 0.56391 (16358) hydrogen bonds : bond 0.03928 ( 476) hydrogen bonds : angle 4.36736 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.497 Fit side-chains REVERT: A 354 GLN cc_start: 0.8407 (tp40) cc_final: 0.8163 (tp40) REVERT: B 95 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7294 (mtt90) REVERT: B 222 ASP cc_start: 0.7666 (t0) cc_final: 0.7094 (t0) REVERT: B 284 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7949 (mttm) REVERT: B 326 LYS cc_start: 0.8262 (mttp) cc_final: 0.7491 (tttm) REVERT: C 51 ASP cc_start: 0.7757 (p0) cc_final: 0.7171 (t0) REVERT: C 93 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: C 211 ASP cc_start: 0.8665 (t0) cc_final: 0.8320 (t0) REVERT: D 34 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.7995 (pt) REVERT: D 334 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6935 (pm20) outliers start: 51 outliers final: 41 residues processed: 171 average time/residue: 0.1111 time to fit residues: 27.8801 Evaluate side-chains 178 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.126440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107391 restraints weight = 15138.147| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.78 r_work: 0.3147 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12052 Z= 0.129 Angle : 0.566 6.121 16358 Z= 0.275 Chirality : 0.046 0.137 1814 Planarity : 0.005 0.055 2096 Dihedral : 7.916 150.872 1678 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.20 % Allowed : 20.84 % Favored : 74.96 % 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 aren not related in a simple way. whole: -0.13 (0.22), residues: 1474 helix: 0.41 (0.24), residues: 538 sheet: 0.34 (0.28), residues: 296 loop : -0.61 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 37 TYR 0.007 0.001 TYR A 143 PHE 0.008 0.001 PHE A 223 TRP 0.009 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00315 (12052) covalent geometry : angle 0.56570 (16358) hydrogen bonds : bond 0.03969 ( 476) hydrogen bonds : angle 4.33231 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.494 Fit side-chains REVERT: B 95 ARG cc_start: 0.7624 (mtm110) cc_final: 0.7297 (mtt90) REVERT: B 284 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7975 (mttm) REVERT: B 326 LYS cc_start: 0.8263 (mttp) cc_final: 0.7581 (tttm) REVERT: C 51 ASP cc_start: 0.7809 (p0) cc_final: 0.7190 (t0) REVERT: C 93 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: C 211 ASP cc_start: 0.8668 (t0) cc_final: 0.8322 (t0) REVERT: D 34 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.7989 (pt) REVERT: D 334 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6959 (pm20) outliers start: 53 outliers final: 47 residues processed: 180 average time/residue: 0.0986 time to fit residues: 26.0686 Evaluate side-chains 190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104776 restraints weight = 15143.859| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.77 r_work: 0.3114 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12052 Z= 0.186 Angle : 0.622 6.368 16358 Z= 0.305 Chirality : 0.049 0.144 1814 Planarity : 0.005 0.055 2096 Dihedral : 7.554 137.535 1678 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.28 % Allowed : 20.76 % Favored : 74.96 % 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 aren not related in a simple way. whole: -0.33 (0.22), residues: 1474 helix: 0.26 (0.24), residues: 536 sheet: 0.09 (0.29), residues: 278 loop : -0.64 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.009 0.001 TYR C 143 PHE 0.010 0.001 PHE A 223 TRP 0.009 0.002 TRP D 79 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00477 (12052) covalent geometry : angle 0.62226 (16358) hydrogen bonds : bond 0.04914 ( 476) hydrogen bonds : angle 4.47300 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 0.488 Fit side-chains REVERT: B 95 ARG cc_start: 0.7659 (mtm110) cc_final: 0.7314 (mtt90) REVERT: B 222 ASP cc_start: 0.7726 (t0) cc_final: 0.7137 (t0) REVERT: B 284 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8077 (mttm) REVERT: B 326 LYS cc_start: 0.8270 (mttp) cc_final: 0.7602 (tttm) REVERT: B 328 LYS cc_start: 0.8330 (ptpp) cc_final: 0.7959 (ptmm) REVERT: C 51 ASP cc_start: 0.7862 (p0) cc_final: 0.7246 (t0) REVERT: C 211 ASP cc_start: 0.8698 (t0) cc_final: 0.8360 (t0) REVERT: D 34 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.7982 (pt) REVERT: D 334 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7017 (pm20) outliers start: 54 outliers final: 48 residues processed: 179 average time/residue: 0.1022 time to fit residues: 26.9937 Evaluate side-chains 188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 111 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN D 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107801 restraints weight = 15149.975| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.78 r_work: 0.3157 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12052 Z= 0.118 Angle : 0.564 6.185 16358 Z= 0.273 Chirality : 0.046 0.135 1814 Planarity : 0.005 0.055 2096 Dihedral : 6.890 114.621 1678 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.04 % Allowed : 20.84 % Favored : 75.12 % 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 aren not related in a simple way. whole: -0.14 (0.22), residues: 1474 helix: 0.46 (0.25), residues: 536 sheet: 0.17 (0.28), residues: 288 loop : -0.57 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.008 0.001 TYR A 306 PHE 0.008 0.001 PHE D 223 TRP 0.010 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00286 (12052) covalent geometry : angle 0.56351 (16358) hydrogen bonds : bond 0.03695 ( 476) hydrogen bonds : angle 4.32046 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 0.366 Fit side-chains REVERT: B 95 ARG cc_start: 0.7557 (mtm110) cc_final: 0.7218 (mtt90) REVERT: B 157 ASP cc_start: 0.8282 (t0) cc_final: 0.8060 (t70) REVERT: B 222 ASP cc_start: 0.7744 (t0) cc_final: 0.7158 (t0) REVERT: B 284 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7867 (mttm) REVERT: B 326 LYS cc_start: 0.8218 (mttp) cc_final: 0.7533 (tttm) REVERT: B 328 LYS cc_start: 0.8266 (ptpp) cc_final: 0.7889 (ptmm) REVERT: C 51 ASP cc_start: 0.7843 (p0) cc_final: 0.7168 (t0) REVERT: C 211 ASP cc_start: 0.8639 (t0) cc_final: 0.8381 (t0) REVERT: D 334 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6946 (pm20) outliers start: 51 outliers final: 48 residues processed: 177 average time/residue: 0.1020 time to fit residues: 26.5947 Evaluate side-chains 188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 14 optimal weight: 0.0470 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110435 restraints weight = 15035.805| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.78 r_work: 0.3191 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12052 Z= 0.094 Angle : 0.535 6.292 16358 Z= 0.255 Chirality : 0.044 0.132 1814 Planarity : 0.004 0.055 2096 Dihedral : 6.508 101.608 1678 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.65 % Allowed : 21.39 % Favored : 74.96 % 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 aren not related in a simple way. whole: 0.07 (0.22), residues: 1474 helix: 0.60 (0.25), residues: 540 sheet: 0.35 (0.29), residues: 296 loop : -0.46 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.008 0.001 TYR A 306 PHE 0.009 0.001 PHE C 31 TRP 0.010 0.001 TRP D 79 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00214 (12052) covalent geometry : angle 0.53546 (16358) hydrogen bonds : bond 0.03010 ( 476) hydrogen bonds : angle 4.17511 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2647.88 seconds wall clock time: 46 minutes 3.10 seconds (2763.10 seconds total)