Starting phenix.real_space_refine on Wed Sep 17 21:47:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpm_44781/09_2025/9bpm_44781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpm_44781/09_2025/9bpm_44781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bpm_44781/09_2025/9bpm_44781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpm_44781/09_2025/9bpm_44781.map" model { file = "/net/cci-nas-00/data/ceres_data/9bpm_44781/09_2025/9bpm_44781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpm_44781/09_2025/9bpm_44781.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.050 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 7416 2.51 5 N 1980 2.21 5 O 2252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11740 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2907 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2901 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 371, 2901 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2958 Chain: "B" Number of atoms: 2907 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2901 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 371, 2901 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2958 Chain: "C" Number of atoms: 2907 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2901 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 371, 2901 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2958 Chain: "D" Number of atoms: 2907 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2901 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 371, 2901 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2958 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: 4.84, per 1000 atoms: 0.41 Number of scatterers: 11740 At special positions: 0 Unit cell: (88.209, 95.337, 170.181, 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 2252 8.00 N 1980 7.00 C 7416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 24 sheets defined 48.0% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.700A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.631A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.735A 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: 4.271A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.759A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.875A 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: 3.848A 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 205 through 217 removed outlier: 3.746A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.728A 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 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.770A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.570A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 348 through 355 removed outlier: 6.200A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.208A 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 368 through 373 removed outlier: 4.234A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.700A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.631A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.735A 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: 4.271A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.759A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.876A 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: 3.848A 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 205 through 217 removed outlier: 3.747A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.728A 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 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.770A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.570A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 355 removed outlier: 6.200A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.207A 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 368 through 373 removed outlier: 4.235A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.700A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.631A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.734A 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: 4.272A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.760A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.875A 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: 3.848A 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 205 through 217 removed outlier: 3.746A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.728A 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 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.770A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.570A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 355 removed outlier: 6.200A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.208A 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 368 through 373 removed outlier: 4.234A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.699A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.631A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.735A 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: 4.271A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.759A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.875A 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: 3.849A 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 205 through 217 removed outlier: 3.746A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.728A 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 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.769A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.569A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 355 removed outlier: 6.200A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.207A 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 368 through 373 removed outlier: 4.234A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 4.129A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET A 132 " --> pdb=" O ILE A 357 " (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: 6.381A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 7.020A 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: 3.648A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.438A 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: 4.129A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (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: 6.380A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 7.019A 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: 3.648A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 5.438A 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: 4.130A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (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: 6.381A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 7.020A 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: 3.648A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.439A 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: 4.129A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (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: 6.380A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 7.020A 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: 3.648A pdb=" N LYS D 238 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU D 242 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLN D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1248 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: 1.92 Time building geometry restraints manager: 1.04 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: 3771 1.34 - 1.46: 2127 1.46 - 1.57: 5954 1.57 - 1.69: 12 1.69 - 1.81: 140 Bond restraints: 12004 Sorted by residual: bond pdb=" C LYS D 336 " pdb=" O LYS D 336 " ideal model delta sigma weight residual 1.235 1.329 -0.094 1.26e-02 6.30e+03 5.57e+01 bond pdb=" C LYS A 336 " pdb=" O LYS A 336 " ideal model delta sigma weight residual 1.235 1.329 -0.094 1.26e-02 6.30e+03 5.56e+01 bond pdb=" C LYS B 336 " pdb=" O LYS B 336 " ideal model delta sigma weight residual 1.235 1.329 -0.094 1.26e-02 6.30e+03 5.53e+01 bond pdb=" C LYS C 336 " pdb=" O LYS C 336 " ideal model delta sigma weight residual 1.235 1.329 -0.094 1.26e-02 6.30e+03 5.52e+01 bond pdb=" N ARG C 372 " pdb=" CA ARG C 372 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.17e-02 7.31e+03 7.98e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 15942 2.59 - 5.19: 276 5.19 - 7.78: 46 7.78 - 10.37: 28 10.37 - 12.97: 8 Bond angle restraints: 16300 Sorted by residual: angle pdb=" C THR D 149 " pdb=" CA THR D 149 " pdb=" CB THR D 149 " ideal model delta sigma weight residual 110.62 97.65 12.97 1.51e+00 4.39e-01 7.38e+01 angle pdb=" C THR C 149 " pdb=" CA THR C 149 " pdb=" CB THR C 149 " ideal model delta sigma weight residual 110.62 97.70 12.92 1.51e+00 4.39e-01 7.32e+01 angle pdb=" C THR A 149 " pdb=" CA THR A 149 " pdb=" CB THR A 149 " ideal model delta sigma weight residual 110.62 97.71 12.91 1.51e+00 4.39e-01 7.31e+01 angle pdb=" C THR B 149 " pdb=" CA THR B 149 " pdb=" CB THR B 149 " ideal model delta sigma weight residual 110.62 97.71 12.91 1.51e+00 4.39e-01 7.31e+01 angle pdb=" O LYS D 336 " pdb=" C LYS D 336 " pdb=" CA ALYS D 336 " ideal model delta sigma weight residual 120.51 129.89 -9.38 1.43e+00 4.89e-01 4.31e+01 ... (remaining 16295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 6992 34.99 - 69.97: 216 69.97 - 104.96: 16 104.96 - 139.95: 4 139.95 - 174.93: 8 Dihedral angle restraints: 7236 sinusoidal: 2932 harmonic: 4304 Sorted by residual: 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 -60.00 114.93 -174.93 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 -60.00 114.92 -174.92 1 2.00e+01 2.50e-03 4.79e+01 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 -60.00 114.91 -174.91 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 7233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1112 0.038 - 0.075: 458 0.075 - 0.113: 178 0.113 - 0.151: 44 0.151 - 0.189: 16 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA VAL C 17 " pdb=" N VAL C 17 " pdb=" C VAL C 17 " pdb=" CB VAL C 17 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA VAL D 17 " pdb=" N VAL D 17 " pdb=" C VAL D 17 " pdb=" CB VAL D 17 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CA VAL A 17 " pdb=" N VAL A 17 " pdb=" C VAL A 17 " pdb=" CB VAL A 17 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 372 " 0.878 9.50e-02 1.11e+02 3.94e-01 9.39e+01 pdb=" NE ARG D 372 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG D 372 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 372 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 372 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 372 " -0.878 9.50e-02 1.11e+02 3.94e-01 9.39e+01 pdb=" NE ARG A 372 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 372 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 372 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 372 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 372 " 0.878 9.50e-02 1.11e+02 3.94e-01 9.39e+01 pdb=" NE ARG C 372 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG C 372 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 372 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 372 " 0.024 2.00e-02 2.50e+03 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1882 2.76 - 3.30: 10334 3.30 - 3.83: 17201 3.83 - 4.37: 20140 4.37 - 4.90: 37074 Nonbonded interactions: 86631 Sorted by model distance: nonbonded pdb=" NH1 ARG A 210 " pdb=" OE2 GLU A 214 " model vdw 2.227 3.120 nonbonded pdb=" NH1 ARG D 210 " pdb=" OE2 GLU D 214 " model vdw 2.228 3.120 nonbonded pdb=" NH1 ARG B 210 " pdb=" OE2 GLU B 214 " model vdw 2.228 3.120 nonbonded pdb=" NH1 ARG C 210 " pdb=" OE2 GLU C 214 " model vdw 2.228 3.120 nonbonded pdb=" OD1 ASN C 128 " pdb=" NZ LYS C 359 " model vdw 2.367 3.120 ... (remaining 86626 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' selection = chain 'B' 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.580 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 12004 Z= 0.276 Angle : 0.906 12.968 16300 Z= 0.532 Chirality : 0.051 0.189 1808 Planarity : 0.019 0.394 2084 Dihedral : 16.990 174.932 4484 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.69 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.21), residues: 1468 helix: -1.80 (0.19), residues: 580 sheet: 0.92 (0.32), residues: 288 loop : -1.15 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 147 TYR 0.009 0.001 TYR B 279 PHE 0.008 0.001 PHE A 90 TRP 0.015 0.002 TRP C 79 HIS 0.002 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00471 (12004) covalent geometry : angle 0.90628 (16300) hydrogen bonds : bond 0.22463 ( 480) hydrogen bonds : angle 6.49508 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.408 Fit side-chains REVERT: A 92 ASN cc_start: 0.8033 (t0) cc_final: 0.7646 (t0) REVERT: A 167 GLU cc_start: 0.8279 (tt0) cc_final: 0.8003 (tt0) REVERT: A 176 MET cc_start: 0.8000 (mmm) cc_final: 0.7555 (mtp) REVERT: A 222 ASP cc_start: 0.7754 (m-30) cc_final: 0.7293 (t0) REVERT: A 320 LEU cc_start: 0.8050 (mt) cc_final: 0.7814 (mt) REVERT: B 44 MET cc_start: 0.7599 (mtp) cc_final: 0.7385 (mtt) REVERT: B 57 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7277 (mt-10) REVERT: B 91 TYR cc_start: 0.8105 (m-80) cc_final: 0.7788 (m-10) REVERT: B 167 GLU cc_start: 0.8405 (tt0) cc_final: 0.8147 (tt0) REVERT: B 176 MET cc_start: 0.8097 (mmm) cc_final: 0.7756 (mtp) REVERT: C 47 MET cc_start: 0.6843 (mmm) cc_final: 0.6617 (mmm) REVERT: C 57 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7202 (mt-10) REVERT: C 82 MET cc_start: 0.8340 (tpt) cc_final: 0.7759 (tpt) REVERT: C 91 TYR cc_start: 0.8159 (m-80) cc_final: 0.7869 (m-10) REVERT: C 176 MET cc_start: 0.7968 (mmm) cc_final: 0.7520 (mtp) REVERT: C 222 ASP cc_start: 0.7803 (m-30) cc_final: 0.7311 (t0) REVERT: D 44 MET cc_start: 0.8322 (mtp) cc_final: 0.8020 (mtt) REVERT: D 167 GLU cc_start: 0.8269 (tt0) cc_final: 0.7892 (tt0) REVERT: D 176 MET cc_start: 0.8002 (mmm) cc_final: 0.7707 (mtp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1025 time to fit residues: 39.0001 Evaluate side-chains 149 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS B 12 ASN B 275 HIS C 12 ASN C 121 GLN C 275 HIS D 12 ASN D 121 GLN D 275 HIS D 353 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.138030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121522 restraints weight = 33792.848| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.28 r_work: 0.3259 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12004 Z= 0.151 Angle : 0.674 6.787 16300 Z= 0.340 Chirality : 0.048 0.146 1808 Planarity : 0.006 0.076 2084 Dihedral : 14.370 176.714 1676 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.67 % Allowed : 16.19 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.21), residues: 1468 helix: -0.24 (0.22), residues: 556 sheet: 0.72 (0.29), residues: 288 loop : -1.17 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 372 TYR 0.012 0.002 TYR A 166 PHE 0.005 0.001 PHE B 31 TRP 0.007 0.001 TRP C 86 HIS 0.011 0.002 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00346 (12004) covalent geometry : angle 0.67399 (16300) hydrogen bonds : bond 0.04460 ( 480) hydrogen bonds : angle 5.03780 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.498 Fit side-chains REVERT: A 369 ILE cc_start: 0.7869 (tt) cc_final: 0.7584 (tp) REVERT: B 57 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7739 (mt-10) REVERT: B 82 MET cc_start: 0.8600 (tpt) cc_final: 0.7653 (tpt) REVERT: B 91 TYR cc_start: 0.8298 (m-80) cc_final: 0.8029 (m-10) REVERT: B 346 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7084 (tt) REVERT: C 57 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7807 (mt-10) REVERT: C 82 MET cc_start: 0.8499 (tpt) cc_final: 0.8124 (tpt) REVERT: C 369 ILE cc_start: 0.7734 (tt) cc_final: 0.7439 (tp) outliers start: 21 outliers final: 9 residues processed: 176 average time/residue: 0.0938 time to fit residues: 24.9168 Evaluate side-chains 140 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.117544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.100518 restraints weight = 36662.230| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.49 r_work: 0.3016 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 12004 Z= 0.313 Angle : 0.858 7.507 16300 Z= 0.443 Chirality : 0.057 0.169 1808 Planarity : 0.007 0.051 2084 Dihedral : 13.194 160.749 1676 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.70 % Allowed : 15.32 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.21), residues: 1468 helix: -0.42 (0.22), residues: 572 sheet: -0.02 (0.29), residues: 264 loop : -1.89 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 196 TYR 0.015 0.002 TYR A 337 PHE 0.011 0.002 PHE A 255 TRP 0.012 0.002 TRP B 86 HIS 0.007 0.002 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00774 (12004) covalent geometry : angle 0.85772 (16300) hydrogen bonds : bond 0.07818 ( 480) hydrogen bonds : angle 4.81060 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.469 Fit side-chains REVERT: A 291 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8624 (tttp) REVERT: B 91 TYR cc_start: 0.8545 (m-80) cc_final: 0.8256 (m-80) REVERT: B 269 MET cc_start: 0.9138 (mtt) cc_final: 0.8747 (mtp) REVERT: C 47 MET cc_start: 0.7548 (mmm) cc_final: 0.7227 (mmm) REVERT: C 57 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8237 (mt-10) REVERT: C 82 MET cc_start: 0.8650 (tpt) cc_final: 0.8376 (tpt) REVERT: D 82 MET cc_start: 0.8550 (tpt) cc_final: 0.8133 (tpt) REVERT: D 211 ASP cc_start: 0.8731 (t0) cc_final: 0.7968 (m-30) REVERT: D 291 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8618 (tttm) outliers start: 34 outliers final: 22 residues processed: 161 average time/residue: 0.1028 time to fit residues: 24.2394 Evaluate side-chains 136 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.121848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.104353 restraints weight = 34660.898| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.51 r_work: 0.3062 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12004 Z= 0.118 Angle : 0.615 6.650 16300 Z= 0.308 Chirality : 0.047 0.133 1808 Planarity : 0.005 0.051 2084 Dihedral : 11.691 145.381 1676 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.11 % Allowed : 17.14 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.21), residues: 1468 helix: 0.26 (0.23), residues: 552 sheet: -0.21 (0.28), residues: 284 loop : -1.51 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 147 TYR 0.007 0.001 TYR A 337 PHE 0.005 0.001 PHE A 255 TRP 0.007 0.001 TRP D 79 HIS 0.008 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00268 (12004) covalent geometry : angle 0.61524 (16300) hydrogen bonds : bond 0.04090 ( 480) hydrogen bonds : angle 4.55633 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.472 Fit side-chains REVERT: A 65 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8503 (pt) REVERT: A 211 ASP cc_start: 0.8550 (t0) cc_final: 0.7914 (m-30) REVERT: A 291 LYS cc_start: 0.8801 (ttpp) cc_final: 0.8547 (tttp) REVERT: B 91 TYR cc_start: 0.8349 (m-80) cc_final: 0.8118 (m-10) REVERT: B 211 ASP cc_start: 0.8747 (t0) cc_final: 0.8165 (m-30) REVERT: B 269 MET cc_start: 0.9033 (mtt) cc_final: 0.8652 (mtp) REVERT: B 313 MET cc_start: 0.7721 (ttm) cc_final: 0.7459 (ttt) REVERT: C 47 MET cc_start: 0.7548 (mmm) cc_final: 0.7260 (mmm) REVERT: C 82 MET cc_start: 0.8414 (tpt) cc_final: 0.8126 (tpt) REVERT: D 82 MET cc_start: 0.8386 (tpt) cc_final: 0.8058 (tpt) REVERT: D 211 ASP cc_start: 0.8662 (t0) cc_final: 0.7857 (m-30) REVERT: D 291 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8602 (tttm) outliers start: 14 outliers final: 8 residues processed: 141 average time/residue: 0.0917 time to fit residues: 19.3186 Evaluate side-chains 127 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 26 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104903 restraints weight = 43123.388| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.13 r_work: 0.3036 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12004 Z= 0.117 Angle : 0.590 6.447 16300 Z= 0.288 Chirality : 0.046 0.133 1808 Planarity : 0.005 0.049 2084 Dihedral : 10.839 133.792 1676 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.43 % Allowed : 17.06 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.22), residues: 1468 helix: 0.53 (0.23), residues: 556 sheet: -0.38 (0.28), residues: 284 loop : -1.36 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 372 TYR 0.008 0.001 TYR B 362 PHE 0.005 0.001 PHE A 352 TRP 0.008 0.001 TRP C 79 HIS 0.008 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00276 (12004) covalent geometry : angle 0.59038 (16300) hydrogen bonds : bond 0.03725 ( 480) hydrogen bonds : angle 4.37327 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.457 Fit side-chains REVERT: A 211 ASP cc_start: 0.8660 (t0) cc_final: 0.7965 (m-30) REVERT: A 291 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8619 (tttp) REVERT: B 211 ASP cc_start: 0.8748 (t0) cc_final: 0.8139 (m-30) REVERT: B 269 MET cc_start: 0.9051 (mtt) cc_final: 0.8685 (mtp) REVERT: B 313 MET cc_start: 0.7772 (ttm) cc_final: 0.7500 (ttt) REVERT: C 47 MET cc_start: 0.7584 (mmm) cc_final: 0.7336 (mmm) REVERT: C 82 MET cc_start: 0.8482 (tpt) cc_final: 0.8203 (tpt) REVERT: D 72 GLU cc_start: 0.7739 (tt0) cc_final: 0.7239 (mt-10) REVERT: D 82 MET cc_start: 0.8477 (tpt) cc_final: 0.8134 (tpt) REVERT: D 291 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8649 (tttm) outliers start: 18 outliers final: 9 residues processed: 138 average time/residue: 0.1074 time to fit residues: 22.1633 Evaluate side-chains 131 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 244 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.124402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106224 restraints weight = 40092.181| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.82 r_work: 0.3086 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12004 Z= 0.103 Angle : 0.568 6.094 16300 Z= 0.274 Chirality : 0.045 0.132 1808 Planarity : 0.005 0.049 2084 Dihedral : 10.276 134.093 1676 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.03 % Allowed : 17.78 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.22), residues: 1468 helix: 0.71 (0.24), residues: 556 sheet: -0.40 (0.28), residues: 284 loop : -1.25 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 372 TYR 0.007 0.001 TYR B 91 PHE 0.005 0.001 PHE A 31 TRP 0.006 0.001 TRP D 79 HIS 0.007 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00238 (12004) covalent geometry : angle 0.56759 (16300) hydrogen bonds : bond 0.03187 ( 480) hydrogen bonds : angle 4.23048 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.470 Fit side-chains REVERT: A 72 GLU cc_start: 0.7592 (tt0) cc_final: 0.7047 (mt-10) REVERT: A 211 ASP cc_start: 0.8644 (t0) cc_final: 0.7910 (m-30) REVERT: A 291 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8608 (tttp) REVERT: B 211 ASP cc_start: 0.8745 (t0) cc_final: 0.7965 (m-30) REVERT: B 269 MET cc_start: 0.9000 (mtt) cc_final: 0.8612 (mtp) REVERT: B 313 MET cc_start: 0.7657 (ttm) cc_final: 0.7394 (ttt) REVERT: C 47 MET cc_start: 0.7612 (mmm) cc_final: 0.7340 (mmm) REVERT: C 82 MET cc_start: 0.8395 (tpt) cc_final: 0.7959 (tpt) REVERT: D 72 GLU cc_start: 0.7673 (tt0) cc_final: 0.7145 (mt-10) REVERT: D 82 MET cc_start: 0.8395 (tpt) cc_final: 0.8051 (tpt) REVERT: D 167 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8291 (tp30) REVERT: D 291 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8662 (tttm) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.1049 time to fit residues: 22.1686 Evaluate side-chains 133 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 167 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 7 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.104881 restraints weight = 39156.340| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.74 r_work: 0.3064 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12004 Z= 0.117 Angle : 0.580 6.001 16300 Z= 0.280 Chirality : 0.046 0.139 1808 Planarity : 0.005 0.048 2084 Dihedral : 9.932 136.279 1676 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.27 % Allowed : 17.54 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.22), residues: 1468 helix: 0.80 (0.24), residues: 556 sheet: -0.51 (0.28), residues: 284 loop : -1.21 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 372 TYR 0.005 0.001 TYR A 337 PHE 0.005 0.001 PHE A 255 TRP 0.006 0.001 TRP B 356 HIS 0.007 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00281 (12004) covalent geometry : angle 0.57988 (16300) hydrogen bonds : bond 0.03538 ( 480) hydrogen bonds : angle 4.16250 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.354 Fit side-chains REVERT: A 72 GLU cc_start: 0.7695 (tt0) cc_final: 0.7081 (mt-10) REVERT: A 211 ASP cc_start: 0.8664 (t0) cc_final: 0.7907 (m-30) REVERT: A 291 LYS cc_start: 0.8859 (ttpp) cc_final: 0.8611 (tttp) REVERT: B 125 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 269 MET cc_start: 0.9038 (mtt) cc_final: 0.8639 (mtp) REVERT: B 313 MET cc_start: 0.7727 (ttm) cc_final: 0.7459 (ttt) REVERT: C 47 MET cc_start: 0.7577 (mmm) cc_final: 0.7363 (mmm) REVERT: C 82 MET cc_start: 0.8426 (tpt) cc_final: 0.8052 (tpt) REVERT: D 72 GLU cc_start: 0.7711 (tt0) cc_final: 0.7175 (mt-10) REVERT: D 82 MET cc_start: 0.8440 (tpt) cc_final: 0.8015 (tpt) REVERT: D 291 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8662 (tttm) outliers start: 16 outliers final: 11 residues processed: 140 average time/residue: 0.0941 time to fit residues: 19.8798 Evaluate side-chains 135 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 244 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 112 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 17 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.117651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.099728 restraints weight = 41674.601| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.81 r_work: 0.2990 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12004 Z= 0.184 Angle : 0.659 5.905 16300 Z= 0.326 Chirality : 0.049 0.138 1808 Planarity : 0.005 0.048 2084 Dihedral : 9.765 142.826 1676 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.27 % Allowed : 17.86 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.22), residues: 1468 helix: 0.61 (0.23), residues: 556 sheet: -0.76 (0.28), residues: 284 loop : -1.32 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 95 TYR 0.008 0.001 TYR B 279 PHE 0.009 0.001 PHE A 255 TRP 0.007 0.001 TRP B 356 HIS 0.007 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00452 (12004) covalent geometry : angle 0.65864 (16300) hydrogen bonds : bond 0.04903 ( 480) hydrogen bonds : angle 4.21815 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.410 Fit side-chains REVERT: A 72 GLU cc_start: 0.7858 (tt0) cc_final: 0.7232 (mt-10) REVERT: A 291 LYS cc_start: 0.8886 (ttpp) cc_final: 0.8661 (tttp) REVERT: B 269 MET cc_start: 0.9081 (mtt) cc_final: 0.8675 (mtp) REVERT: C 82 MET cc_start: 0.8520 (tpt) cc_final: 0.8157 (tpt) REVERT: D 72 GLU cc_start: 0.7778 (tt0) cc_final: 0.7297 (mt-10) REVERT: D 291 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8677 (tttm) outliers start: 16 outliers final: 13 residues processed: 140 average time/residue: 0.1049 time to fit residues: 21.7295 Evaluate side-chains 134 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.118572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.100829 restraints weight = 39140.491| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.67 r_work: 0.3012 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12004 Z= 0.156 Angle : 0.626 5.976 16300 Z= 0.309 Chirality : 0.048 0.140 1808 Planarity : 0.005 0.048 2084 Dihedral : 9.678 146.997 1676 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.11 % Allowed : 17.78 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.22), residues: 1468 helix: 0.57 (0.23), residues: 556 sheet: -0.82 (0.27), residues: 284 loop : -1.30 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 372 TYR 0.007 0.001 TYR A 337 PHE 0.007 0.001 PHE A 255 TRP 0.006 0.001 TRP B 356 HIS 0.007 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00384 (12004) covalent geometry : angle 0.62640 (16300) hydrogen bonds : bond 0.04282 ( 480) hydrogen bonds : angle 4.14807 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.376 Fit side-chains REVERT: A 72 GLU cc_start: 0.7880 (tt0) cc_final: 0.7255 (mt-10) REVERT: A 291 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8647 (tttp) REVERT: B 65 LEU cc_start: 0.8680 (pp) cc_final: 0.8472 (pp) REVERT: B 125 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8268 (mm-30) REVERT: B 269 MET cc_start: 0.9064 (mtt) cc_final: 0.8668 (mtp) REVERT: B 313 MET cc_start: 0.7864 (ttm) cc_final: 0.7599 (ttt) REVERT: B 326 LYS cc_start: 0.6984 (mmmt) cc_final: 0.6485 (mmtt) REVERT: C 82 MET cc_start: 0.8459 (tpt) cc_final: 0.8165 (tpt) REVERT: C 125 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8525 (mm-30) REVERT: D 72 GLU cc_start: 0.7807 (tt0) cc_final: 0.7319 (mt-10) REVERT: D 291 LYS cc_start: 0.8903 (ttpp) cc_final: 0.8676 (tttm) outliers start: 14 outliers final: 14 residues processed: 142 average time/residue: 0.0936 time to fit residues: 20.1228 Evaluate side-chains 145 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 95 optimal weight: 0.0470 chunk 63 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 chunk 84 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.124580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107633 restraints weight = 31988.841| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.28 r_work: 0.3118 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12004 Z= 0.100 Angle : 0.567 6.134 16300 Z= 0.276 Chirality : 0.044 0.145 1808 Planarity : 0.005 0.048 2084 Dihedral : 9.477 147.154 1676 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.63 % Allowed : 18.41 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.22), residues: 1468 helix: 0.77 (0.24), residues: 556 sheet: -0.57 (0.28), residues: 284 loop : -1.10 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 372 TYR 0.008 0.001 TYR A 306 PHE 0.006 0.000 PHE A 31 TRP 0.009 0.001 TRP D 79 HIS 0.007 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00226 (12004) covalent geometry : angle 0.56747 (16300) hydrogen bonds : bond 0.02835 ( 480) hydrogen bonds : angle 4.09866 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.451 Fit side-chains REVERT: A 72 GLU cc_start: 0.7740 (tt0) cc_final: 0.7198 (mt-10) REVERT: A 291 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8581 (tttm) REVERT: B 211 ASP cc_start: 0.8598 (t0) cc_final: 0.7932 (m-30) REVERT: B 269 MET cc_start: 0.8971 (mtt) cc_final: 0.8579 (mtp) REVERT: B 326 LYS cc_start: 0.6840 (mmmt) cc_final: 0.6364 (mmtt) REVERT: C 72 GLU cc_start: 0.7606 (tt0) cc_final: 0.7122 (mt-10) REVERT: C 82 MET cc_start: 0.8241 (tpt) cc_final: 0.7952 (tpt) REVERT: D 72 GLU cc_start: 0.7835 (tt0) cc_final: 0.7295 (mt-10) REVERT: D 291 LYS cc_start: 0.8897 (ttpp) cc_final: 0.8662 (tttm) outliers start: 8 outliers final: 6 residues processed: 139 average time/residue: 0.0991 time to fit residues: 20.7085 Evaluate side-chains 139 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.119844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101411 restraints weight = 45585.992| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.00 r_work: 0.3013 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12004 Z= 0.147 Angle : 0.614 5.766 16300 Z= 0.301 Chirality : 0.047 0.140 1808 Planarity : 0.005 0.047 2084 Dihedral : 9.565 149.793 1676 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.87 % Allowed : 18.65 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.22), residues: 1468 helix: 0.78 (0.24), residues: 556 sheet: -0.75 (0.28), residues: 284 loop : -1.15 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 372 TYR 0.007 0.001 TYR A 279 PHE 0.007 0.001 PHE B 255 TRP 0.007 0.001 TRP B 356 HIS 0.007 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00361 (12004) covalent geometry : angle 0.61362 (16300) hydrogen bonds : bond 0.04082 ( 480) hydrogen bonds : angle 4.01885 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.98 seconds wall clock time: 41 minutes 5.73 seconds (2465.73 seconds total)