Starting phenix.real_space_refine on Wed May 14 14:43:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmy_27549/05_2025/8dmy_27549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmy_27549/05_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_27549/05_2025/8dmy_27549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmy_27549/05_2025/8dmy_27549.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmy_27549/05_2025/8dmy_27549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmy_27549/05_2025/8dmy_27549.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.14, per 1000 atoms: 0.61 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: 2.49 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.82 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: 3.77 Time building geometry restraints manager: 3.01 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 375 or resid 401 through 402)) selection = (chain 'B' and (resid 3 through 375 or resid 401 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.940 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 356 HIS 0.003 0.001 HIS A 101 PHE 0.004 0.001 PHE B 31 TYR 0.006 0.001 TYR D 306 ARG 0.002 0.000 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.34375 ( 476) hydrogen bonds : angle 7.92257 ( 1188) covalent geometry : bond 0.00359 (12052) covalent geometry : angle 0.62157 (16358) *********************** 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 : 1.235 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: 0.2439 time to fit residues: 70.8986 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 : 1.387 ------------------------------------------------------------------------------- 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 124 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 A 371 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 C 371 HIS D 12 ASN D 101 HIS D 121 GLN D 275 HIS D 353 GLN D 371 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107568 restraints weight = 14990.887| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.79 r_work: 0.3134 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12052 Z= 0.189 Angle : 0.652 6.053 16358 Z= 0.331 Chirality : 0.050 0.143 1814 Planarity : 0.006 0.054 2096 Dihedral : 13.832 177.541 1680 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.96 % Allowed : 19.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1474 helix: -0.88 (0.22), residues: 560 sheet: 0.81 (0.30), residues: 288 loop : -0.88 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 356 HIS 0.005 0.001 HIS A 275 PHE 0.009 0.001 PHE A 255 TYR 0.011 0.001 TYR C 69 ARG 0.004 0.001 ARG A 254 Details of bonding type rmsd hydrogen bonds : bond 0.06258 ( 476) hydrogen bonds : angle 5.11703 ( 1188) covalent geometry : bond 0.00465 (12052) covalent geometry : angle 0.65239 (16358) *********************** 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 197 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 1.285 Fit side-chains REVERT: A 305 MET cc_start: 0.9079 (mtp) cc_final: 0.8675 (mtp) REVERT: B 65 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8388 (pp) REVERT: B 82 MET cc_start: 0.9038 (tpt) cc_final: 0.8619 (tpt) REVERT: B 95 ARG cc_start: 0.7523 (mtm110) cc_final: 0.7118 (mtt90) REVERT: B 326 LYS cc_start: 0.8254 (mttp) cc_final: 0.7373 (tttm) REVERT: B 372 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.7055 (mtm180) REVERT: C 51 ASP cc_start: 0.7670 (p0) cc_final: 0.7226 (t0) REVERT: C 211 ASP cc_start: 0.8671 (t0) cc_final: 0.8322 (t0) REVERT: C 326 LYS cc_start: 0.8354 (mttp) cc_final: 0.7787 (mmtm) REVERT: C 372 ARG cc_start: 0.6978 (ttm170) cc_final: 0.6688 (ttm170) REVERT: D 95 ARG cc_start: 0.7536 (mtm110) cc_final: 0.7277 (mtm110) outliers start: 50 outliers final: 34 residues processed: 181 average time/residue: 0.2189 time to fit residues: 58.1473 Evaluate side-chains 164 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 160 THR 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 6 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU 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 303 THR 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 250 ILE 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 46 optimal weight: 8.9990 chunk 132 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 144 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 121 GLN D 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112189 restraints weight = 15152.306| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.80 r_work: 0.3210 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12052 Z= 0.098 Angle : 0.536 6.144 16358 Z= 0.261 Chirality : 0.044 0.135 1814 Planarity : 0.004 0.054 2096 Dihedral : 12.631 179.170 1678 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.06 % Allowed : 22.35 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1474 helix: 0.10 (0.24), residues: 536 sheet: 0.67 (0.29), residues: 296 loop : -0.65 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 356 HIS 0.002 0.001 HIS D 161 PHE 0.007 0.001 PHE B 375 TYR 0.006 0.001 TYR A 306 ARG 0.004 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 476) hydrogen bonds : angle 4.58858 ( 1188) covalent geometry : bond 0.00211 (12052) covalent geometry : angle 0.53595 (16358) *********************** 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 168 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.433 Fit side-chains REVERT: B 95 ARG cc_start: 0.7528 (mtm110) cc_final: 0.7062 (mtt90) REVERT: B 326 LYS cc_start: 0.8279 (mttp) cc_final: 0.7404 (tttm) REVERT: C 51 ASP cc_start: 0.7530 (p0) cc_final: 0.7137 (t0) REVERT: C 93 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: C 211 ASP cc_start: 0.8605 (t0) cc_final: 0.8265 (t0) REVERT: C 326 LYS cc_start: 0.8333 (mttp) cc_final: 0.7792 (mmtm) REVERT: C 372 ARG cc_start: 0.6896 (ttm170) cc_final: 0.6470 (ttm170) REVERT: D 34 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7839 (pt) REVERT: D 95 ARG cc_start: 0.7538 (mtm110) cc_final: 0.7305 (mtm110) outliers start: 26 outliers final: 16 residues processed: 160 average time/residue: 0.2262 time to fit residues: 52.6556 Evaluate side-chains 149 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 93 GLU 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 160 THR Chi-restraints excluded: chain D residue 211 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 chunk 25 optimal weight: 0.0370 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112595 restraints weight = 15040.199| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.79 r_work: 0.3210 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12052 Z= 0.094 Angle : 0.525 7.260 16358 Z= 0.252 Chirality : 0.044 0.135 1814 Planarity : 0.004 0.051 2096 Dihedral : 10.877 169.762 1678 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.61 % Allowed : 21.87 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1474 helix: 0.50 (0.25), residues: 536 sheet: 0.60 (0.29), residues: 296 loop : -0.53 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 79 HIS 0.003 0.001 HIS D 161 PHE 0.007 0.001 PHE B 375 TYR 0.007 0.001 TYR B 69 ARG 0.004 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 476) hydrogen bonds : angle 4.31179 ( 1188) covalent geometry : bond 0.00211 (12052) covalent geometry : angle 0.52463 (16358) *********************** 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 181 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.333 Fit side-chains REVERT: A 34 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8085 (pt) REVERT: B 65 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8484 (pp) REVERT: B 95 ARG cc_start: 0.7518 (mtm110) cc_final: 0.7066 (mtt90) REVERT: B 176 MET cc_start: 0.8578 (mmt) cc_final: 0.8364 (mmm) REVERT: B 326 LYS cc_start: 0.8259 (mttp) cc_final: 0.7388 (tttm) REVERT: B 372 ARG cc_start: 0.7462 (mmm-85) cc_final: 0.7199 (mtm180) REVERT: C 51 ASP cc_start: 0.7616 (p0) cc_final: 0.7203 (t0) REVERT: C 93 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: C 211 ASP cc_start: 0.8597 (t0) cc_final: 0.8252 (t0) REVERT: C 326 LYS cc_start: 0.8355 (mttp) cc_final: 0.7804 (mmtm) REVERT: D 12 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7735 (m110) REVERT: D 34 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.7848 (pt) REVERT: D 95 ARG cc_start: 0.7516 (mtm110) cc_final: 0.7293 (mtm110) REVERT: D 334 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6800 (pm20) outliers start: 33 outliers final: 19 residues processed: 172 average time/residue: 0.2303 time to fit residues: 57.2706 Evaluate side-chains 159 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 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 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 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 93 GLU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 12 ASN 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 160 THR Chi-restraints excluded: chain D residue 288 ASP 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 90 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS B 12 ASN C 371 HIS D 354 GLN D 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101557 restraints weight = 15213.373| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.78 r_work: 0.3061 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 12052 Z= 0.330 Angle : 0.758 6.995 16358 Z= 0.379 Chirality : 0.055 0.162 1814 Planarity : 0.006 0.054 2096 Dihedral : 11.010 179.322 1678 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.75 % Allowed : 20.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1474 helix: -0.27 (0.23), residues: 550 sheet: 0.19 (0.30), residues: 276 loop : -0.84 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 79 HIS 0.008 0.002 HIS D 161 PHE 0.016 0.002 PHE B 90 TYR 0.024 0.002 TYR B 294 ARG 0.006 0.001 ARG A 254 Details of bonding type rmsd hydrogen bonds : bond 0.06844 ( 476) hydrogen bonds : angle 4.77853 ( 1188) covalent geometry : bond 0.00856 (12052) covalent geometry : angle 0.75843 (16358) *********************** 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 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 131 time to evaluate : 1.467 Fit side-chains REVERT: A 354 GLN cc_start: 0.8493 (tp40) cc_final: 0.8283 (tp40) REVERT: B 65 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8427 (pp) REVERT: B 95 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7307 (mtt90) REVERT: B 284 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8189 (mttm) REVERT: B 326 LYS cc_start: 0.8308 (mttp) cc_final: 0.7422 (tttm) REVERT: B 328 LYS cc_start: 0.8354 (ptpp) cc_final: 0.7985 (ptmm) REVERT: C 51 ASP cc_start: 0.7916 (p0) cc_final: 0.7330 (t0) REVERT: C 93 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: C 211 ASP cc_start: 0.8696 (t0) cc_final: 0.8448 (t0) REVERT: C 278 THR cc_start: 0.8841 (t) cc_final: 0.8641 (m) REVERT: D 95 ARG cc_start: 0.7557 (mtm110) cc_final: 0.7298 (mtm180) REVERT: D 334 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6969 (pm20) outliers start: 60 outliers final: 43 residues processed: 175 average time/residue: 0.2259 time to fit residues: 59.0499 Evaluate side-chains 172 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 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 303 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 178 LEU 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 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 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 247 VAL 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 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 201 VAL 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 325 MET Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 116 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 12 ASN D 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106986 restraints weight = 15255.248| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.79 r_work: 0.3135 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2668 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= 0.127 Angle : 0.575 7.084 16358 Z= 0.281 Chirality : 0.046 0.136 1814 Planarity : 0.005 0.055 2096 Dihedral : 10.367 178.065 1678 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.41 % Allowed : 21.55 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1474 helix: 0.22 (0.24), residues: 536 sheet: 0.16 (0.28), residues: 288 loop : -0.66 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.003 0.001 HIS D 161 PHE 0.007 0.001 PHE C 31 TYR 0.017 0.001 TYR B 294 ARG 0.002 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 476) hydrogen bonds : angle 4.47089 ( 1188) covalent geometry : bond 0.00307 (12052) covalent geometry : angle 0.57519 (16358) *********************** 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 172 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 1.354 Fit side-chains REVERT: A 34 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8173 (pt) REVERT: B 65 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8536 (pp) REVERT: B 95 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7294 (mtt90) REVERT: B 326 LYS cc_start: 0.8279 (mttp) cc_final: 0.7407 (tttm) REVERT: C 51 ASP cc_start: 0.7785 (p0) cc_final: 0.7243 (t0) REVERT: C 93 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: C 211 ASP cc_start: 0.8623 (t0) cc_final: 0.8268 (t0) REVERT: D 334 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6874 (pm20) outliers start: 43 outliers final: 31 residues processed: 159 average time/residue: 0.2414 time to fit residues: 57.0488 Evaluate side-chains 163 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 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 284 LYS 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 247 VAL 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 93 GLU 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 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 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 199 SER 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 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 32 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS C 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103430 restraints weight = 15411.875| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.80 r_work: 0.3083 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2787 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= 0.217 Angle : 0.656 6.664 16358 Z= 0.325 Chirality : 0.050 0.151 1814 Planarity : 0.006 0.054 2096 Dihedral : 9.909 179.324 1678 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.28 % Allowed : 20.52 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1474 helix: 0.01 (0.24), residues: 546 sheet: 0.06 (0.28), residues: 300 loop : -0.87 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 356 HIS 0.006 0.002 HIS D 161 PHE 0.011 0.001 PHE A 223 TYR 0.015 0.001 TYR B 294 ARG 0.003 0.001 ARG D 254 Details of bonding type rmsd hydrogen bonds : bond 0.05527 ( 476) hydrogen bonds : angle 4.59388 ( 1188) covalent geometry : bond 0.00558 (12052) covalent geometry : angle 0.65608 (16358) *********************** 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 178 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 124 time to evaluate : 1.359 Fit side-chains REVERT: B 65 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8480 (pp) REVERT: B 95 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7315 (mtt90) REVERT: B 222 ASP cc_start: 0.7684 (t0) cc_final: 0.7113 (t0) REVERT: B 326 LYS cc_start: 0.8278 (mttp) cc_final: 0.7526 (tttm) REVERT: B 328 LYS cc_start: 0.8372 (ptpp) cc_final: 0.7979 (ptmm) REVERT: C 51 ASP cc_start: 0.7899 (p0) cc_final: 0.7288 (t0) REVERT: C 93 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8493 (mt-10) REVERT: C 211 ASP cc_start: 0.8670 (t0) cc_final: 0.8420 (t0) REVERT: D 334 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7025 (pm20) outliers start: 54 outliers final: 46 residues processed: 166 average time/residue: 0.2255 time to fit residues: 54.5140 Evaluate side-chains 172 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 65 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 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 65 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 29 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 314 GLN D 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107115 restraints weight = 15167.655| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.79 r_work: 0.3141 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2828 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= 0.125 Angle : 0.564 6.064 16358 Z= 0.276 Chirality : 0.046 0.137 1814 Planarity : 0.005 0.055 2096 Dihedral : 8.464 162.067 1678 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.88 % Allowed : 21.08 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.22), residues: 1474 helix: 0.35 (0.24), residues: 536 sheet: 0.13 (0.28), residues: 288 loop : -0.68 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 PHE 0.007 0.001 PHE D 223 TYR 0.013 0.001 TYR B 294 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 476) hydrogen bonds : angle 4.40544 ( 1188) covalent geometry : bond 0.00306 (12052) covalent geometry : angle 0.56385 (16358) *********************** 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 183 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 1.240 Fit side-chains REVERT: B 65 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8508 (pp) REVERT: B 95 ARG cc_start: 0.7507 (mtm110) cc_final: 0.7211 (mtt90) REVERT: B 326 LYS cc_start: 0.8233 (mttp) cc_final: 0.7548 (tttm) REVERT: C 211 ASP cc_start: 0.8631 (t0) cc_final: 0.8368 (t0) REVERT: D 34 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.7966 (pt) REVERT: D 334 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7021 (pm20) outliers start: 49 outliers final: 39 residues processed: 169 average time/residue: 0.2230 time to fit residues: 55.2733 Evaluate side-chains 175 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 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 65 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 216 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 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 199 SER 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 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 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 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 134 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.123892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104866 restraints weight = 15292.997| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.78 r_work: 0.3116 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12052 Z= 0.175 Angle : 0.615 6.296 16358 Z= 0.302 Chirality : 0.048 0.150 1814 Planarity : 0.005 0.054 2096 Dihedral : 7.935 148.342 1678 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.72 % Allowed : 21.24 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1474 helix: 0.23 (0.24), residues: 536 sheet: 0.13 (0.29), residues: 290 loop : -0.77 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 356 HIS 0.005 0.001 HIS D 161 PHE 0.011 0.001 PHE C 31 TYR 0.013 0.001 TYR B 294 ARG 0.003 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 476) hydrogen bonds : angle 4.46077 ( 1188) covalent geometry : bond 0.00446 (12052) covalent geometry : angle 0.61496 (16358) *********************** 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 175 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 1.320 Fit side-chains REVERT: B 65 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8507 (pp) REVERT: B 95 ARG cc_start: 0.7569 (mtm110) cc_final: 0.7235 (mtt90) REVERT: B 222 ASP cc_start: 0.7689 (t0) cc_final: 0.7073 (t0) REVERT: B 284 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7981 (mttm) REVERT: B 326 LYS cc_start: 0.8238 (mttp) cc_final: 0.7563 (tttm) REVERT: B 328 LYS cc_start: 0.8282 (ptpp) cc_final: 0.7891 (ptmm) REVERT: C 51 ASP cc_start: 0.7821 (p0) cc_final: 0.7146 (t0) REVERT: C 211 ASP cc_start: 0.8653 (t0) cc_final: 0.8384 (t0) REVERT: D 334 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6989 (pm20) outliers start: 47 outliers final: 42 residues processed: 165 average time/residue: 0.2293 time to fit residues: 55.0603 Evaluate side-chains 172 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 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 65 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET 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 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 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 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 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 3 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.127466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108655 restraints weight = 14916.969| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.76 r_work: 0.3161 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12052 Z= 0.104 Angle : 0.552 6.127 16358 Z= 0.267 Chirality : 0.045 0.141 1814 Planarity : 0.005 0.056 2096 Dihedral : 7.026 121.358 1678 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.25 % Allowed : 21.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1474 helix: 0.48 (0.25), residues: 538 sheet: 0.20 (0.29), residues: 284 loop : -0.61 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.003 0.001 HIS D 161 PHE 0.009 0.001 PHE C 31 TYR 0.012 0.001 TYR B 294 ARG 0.002 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 476) hydrogen bonds : angle 4.30149 ( 1188) covalent geometry : bond 0.00242 (12052) covalent geometry : angle 0.55188 (16358) ********************** 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 175 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 1.192 Fit side-chains REVERT: A 34 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8176 (pt) REVERT: B 95 ARG cc_start: 0.7633 (mtm110) cc_final: 0.7306 (mtt90) REVERT: B 326 LYS cc_start: 0.8254 (mttp) cc_final: 0.7594 (tttm) REVERT: C 211 ASP cc_start: 0.8654 (t0) cc_final: 0.8411 (t0) REVERT: D 34 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8025 (pt) REVERT: D 334 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6901 (pm20) outliers start: 41 outliers final: 31 residues processed: 161 average time/residue: 0.2178 time to fit residues: 51.8235 Evaluate side-chains 165 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 100 GLU 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 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 216 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 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 66 THR 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 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 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 99 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.128121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109318 restraints weight = 15004.820| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.76 r_work: 0.3169 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12052 Z= 0.103 Angle : 0.552 6.282 16358 Z= 0.264 Chirality : 0.045 0.184 1814 Planarity : 0.005 0.056 2096 Dihedral : 6.730 108.600 1678 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.85 % Allowed : 22.82 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1474 helix: 0.58 (0.25), residues: 538 sheet: 0.30 (0.28), residues: 296 loop : -0.58 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 PHE 0.009 0.001 PHE C 31 TYR 0.011 0.001 TYR B 294 ARG 0.002 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 476) hydrogen bonds : angle 4.22867 ( 1188) covalent geometry : bond 0.00242 (12052) covalent geometry : angle 0.55174 (16358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5465.54 seconds wall clock time: 95 minutes 30.86 seconds (5730.86 seconds total)