Starting phenix.real_space_refine on Tue Jun 10 11:24:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpm_44781/06_2025/9bpm_44781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpm_44781/06_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_44781/06_2025/9bpm_44781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpm_44781/06_2025/9bpm_44781.map" model { file = "/net/cci-nas-00/data/ceres_data/9bpm_44781/06_2025/9bpm_44781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpm_44781/06_2025/9bpm_44781.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.87, per 1000 atoms: 1.10 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: 2.96 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 1.74 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: 3.67 Time building geometry restraints manager: 3.47 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.140 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (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 TRP 0.015 0.002 TRP C 79 HIS 0.002 0.001 HIS C 275 PHE 0.008 0.001 PHE A 90 TYR 0.009 0.001 TYR B 279 ARG 0.005 0.001 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.22463 ( 480) hydrogen bonds : angle 6.49508 ( 1248) covalent geometry : bond 0.00471 (12004) covalent geometry : angle 0.90628 (16300) *********************** 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 : 1.213 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: 0.2161 time to fit residues: 81.8181 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 : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 275 HIS B 12 ASN B 275 HIS C 12 ASN C 121 GLN C 275 HIS D 12 ASN 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 = 0.3560 r_free = 0.3560 target = 0.134600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117164 restraints weight = 41829.518| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.70 r_work: 0.3195 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12004 Z= 0.169 Angle : 0.696 6.775 16300 Z= 0.352 Chirality : 0.049 0.147 1808 Planarity : 0.006 0.091 2084 Dihedral : 14.440 177.617 1676 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.90 % Allowed : 15.63 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1468 helix: -0.31 (0.22), residues: 560 sheet: 0.62 (0.29), residues: 288 loop : -1.22 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 86 HIS 0.011 0.002 HIS A 87 PHE 0.006 0.001 PHE B 31 TYR 0.013 0.002 TYR A 166 ARG 0.009 0.001 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.04679 ( 480) hydrogen bonds : angle 4.99091 ( 1248) covalent geometry : bond 0.00388 (12004) covalent geometry : angle 0.69582 (16300) *********************** 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 181 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.270 Fit side-chains REVERT: A 369 ILE cc_start: 0.7870 (tt) cc_final: 0.7579 (tp) REVERT: B 44 MET cc_start: 0.7885 (mtp) cc_final: 0.7671 (mtt) REVERT: B 57 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7791 (mt-10) REVERT: B 82 MET cc_start: 0.8576 (tpt) cc_final: 0.7585 (tpt) REVERT: B 91 TYR cc_start: 0.8308 (m-80) cc_final: 0.7989 (m-10) REVERT: B 167 GLU cc_start: 0.8547 (tt0) cc_final: 0.8335 (tt0) REVERT: B 346 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7113 (tt) REVERT: C 57 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 82 MET cc_start: 0.8513 (tpt) cc_final: 0.8165 (tpt) REVERT: C 369 ILE cc_start: 0.7726 (tt) cc_final: 0.7422 (tp) outliers start: 24 outliers final: 11 residues processed: 178 average time/residue: 0.2038 time to fit residues: 54.5042 Evaluate side-chains 136 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 139 VAL 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 139 VAL 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 7 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117574 restraints weight = 50653.628| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 4.60 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12004 Z= 0.117 Angle : 0.593 6.158 16300 Z= 0.291 Chirality : 0.046 0.130 1808 Planarity : 0.005 0.050 2084 Dihedral : 12.880 163.594 1676 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.95 % Allowed : 18.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1468 helix: 0.19 (0.23), residues: 584 sheet: 0.60 (0.28), residues: 284 loop : -1.43 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 79 HIS 0.002 0.001 HIS D 87 PHE 0.006 0.001 PHE C 31 TYR 0.007 0.001 TYR A 337 ARG 0.007 0.001 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 480) hydrogen bonds : angle 4.63498 ( 1248) covalent geometry : bond 0.00272 (12004) covalent geometry : angle 0.59339 (16300) *********************** 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 140 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.201 Fit side-chains REVERT: A 369 ILE cc_start: 0.7972 (tt) cc_final: 0.7640 (tp) REVERT: B 269 MET cc_start: 0.8617 (mtt) cc_final: 0.8147 (mtp) REVERT: B 346 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7194 (tt) REVERT: C 82 MET cc_start: 0.8294 (tpt) cc_final: 0.7803 (tpt) REVERT: C 363 ASP cc_start: 0.7163 (m-30) cc_final: 0.6935 (m-30) outliers start: 12 outliers final: 6 residues processed: 136 average time/residue: 0.1913 time to fit residues: 40.0620 Evaluate side-chains 124 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 159 VAL 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 89 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 90 optimal weight: 0.0970 chunk 109 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116108 restraints weight = 33332.019| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.61 r_work: 0.3213 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12004 Z= 0.103 Angle : 0.567 6.257 16300 Z= 0.274 Chirality : 0.045 0.129 1808 Planarity : 0.005 0.049 2084 Dihedral : 10.922 136.812 1676 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.43 % Allowed : 17.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.22), residues: 1468 helix: 0.68 (0.24), residues: 564 sheet: 0.42 (0.28), residues: 284 loop : -1.26 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 79 HIS 0.002 0.001 HIS A 101 PHE 0.006 0.001 PHE A 31 TYR 0.008 0.001 TYR C 306 ARG 0.009 0.000 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 480) hydrogen bonds : angle 4.41240 ( 1248) covalent geometry : bond 0.00237 (12004) covalent geometry : angle 0.56684 (16300) *********************** 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 138 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.219 Fit side-chains REVERT: A 284 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7838 (mttt) REVERT: A 369 ILE cc_start: 0.7776 (tt) cc_final: 0.7464 (tp) REVERT: B 269 MET cc_start: 0.8888 (mtt) cc_final: 0.8435 (mtp) REVERT: B 346 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7316 (tt) REVERT: C 82 MET cc_start: 0.8482 (tpt) cc_final: 0.8191 (tpt) REVERT: C 123 MET cc_start: 0.7972 (mtp) cc_final: 0.7507 (mmt) REVERT: C 284 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7903 (mttt) REVERT: C 363 ASP cc_start: 0.7207 (m-30) cc_final: 0.6994 (m-30) outliers start: 18 outliers final: 6 residues processed: 134 average time/residue: 0.2054 time to fit residues: 41.7499 Evaluate side-chains 123 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 65 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.101086 restraints weight = 50214.749| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 4.34 r_work: 0.2990 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12004 Z= 0.205 Angle : 0.691 7.346 16300 Z= 0.348 Chirality : 0.051 0.147 1808 Planarity : 0.005 0.049 2084 Dihedral : 10.556 132.890 1676 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.83 % Allowed : 16.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1468 helix: 0.30 (0.23), residues: 580 sheet: -0.23 (0.27), residues: 284 loop : -1.55 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 340 HIS 0.003 0.001 HIS A 87 PHE 0.010 0.001 PHE A 255 TYR 0.010 0.001 TYR B 279 ARG 0.008 0.001 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.05459 ( 480) hydrogen bonds : angle 4.38564 ( 1248) covalent geometry : bond 0.00509 (12004) covalent geometry : angle 0.69137 (16300) *********************** 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 150 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.272 Fit side-chains REVERT: B 123 MET cc_start: 0.8603 (mmt) cc_final: 0.8309 (mmt) REVERT: B 269 MET cc_start: 0.9071 (mtt) cc_final: 0.8639 (mtp) REVERT: B 346 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7434 (tt) REVERT: C 82 MET cc_start: 0.8666 (tpt) cc_final: 0.8283 (tpt) REVERT: C 96 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8423 (p) REVERT: C 284 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8119 (mttt) REVERT: D 291 LYS cc_start: 0.8918 (ttpp) cc_final: 0.8704 (tttm) outliers start: 23 outliers final: 14 residues processed: 146 average time/residue: 0.2269 time to fit residues: 48.7830 Evaluate side-chains 130 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 96 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 C residue 229 THR Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 111 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 162 ASN C 162 ASN D 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.106153 restraints weight = 41137.121| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.89 r_work: 0.3078 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4042 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= 0.112 Angle : 0.584 6.101 16300 Z= 0.284 Chirality : 0.046 0.132 1808 Planarity : 0.005 0.050 2084 Dihedral : 10.117 132.005 1676 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.59 % Allowed : 17.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1468 helix: 0.71 (0.24), residues: 556 sheet: -0.24 (0.27), residues: 284 loop : -1.25 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 79 HIS 0.003 0.001 HIS B 101 PHE 0.005 0.001 PHE A 255 TYR 0.007 0.001 TYR A 337 ARG 0.013 0.001 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 480) hydrogen bonds : angle 4.29820 ( 1248) covalent geometry : bond 0.00264 (12004) covalent geometry : angle 0.58371 (16300) *********************** 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 150 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.403 Fit side-chains REVERT: A 8 LEU cc_start: 0.7748 (mt) cc_final: 0.7533 (tt) REVERT: B 65 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8333 (pp) REVERT: B 211 ASP cc_start: 0.8748 (t0) cc_final: 0.8029 (m-30) REVERT: B 269 MET cc_start: 0.9003 (mtt) cc_final: 0.8567 (mtp) REVERT: C 82 MET cc_start: 0.8476 (tpt) cc_final: 0.8103 (tpt) REVERT: D 72 GLU cc_start: 0.7752 (tt0) cc_final: 0.7170 (mt-10) REVERT: D 291 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8682 (tttm) outliers start: 20 outliers final: 16 residues processed: 144 average time/residue: 0.2266 time to fit residues: 48.7823 Evaluate side-chains 138 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 75 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 96 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 C residue 229 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 26 optimal weight: 0.0370 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.126910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109506 restraints weight = 33944.589| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.47 r_work: 0.3142 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12004 Z= 0.096 Angle : 0.557 5.811 16300 Z= 0.265 Chirality : 0.044 0.133 1808 Planarity : 0.005 0.051 2084 Dihedral : 9.623 137.313 1676 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.27 % Allowed : 17.94 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1468 helix: 0.92 (0.24), residues: 556 sheet: -0.16 (0.27), residues: 284 loop : -1.09 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 79 HIS 0.003 0.001 HIS D 101 PHE 0.006 0.001 PHE B 124 TYR 0.005 0.001 TYR D 306 ARG 0.010 0.001 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 480) hydrogen bonds : angle 4.14800 ( 1248) covalent geometry : bond 0.00219 (12004) covalent geometry : angle 0.55724 (16300) *********************** 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 137 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 1.379 Fit side-chains REVERT: A 369 ILE cc_start: 0.7915 (tt) cc_final: 0.7609 (tp) REVERT: B 65 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8366 (pp) REVERT: B 125 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 211 ASP cc_start: 0.8693 (t0) cc_final: 0.7930 (m-30) REVERT: B 269 MET cc_start: 0.8918 (mtt) cc_final: 0.8490 (mtp) REVERT: C 82 MET cc_start: 0.8392 (tpt) cc_final: 0.8020 (tpt) REVERT: C 284 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7864 (mttt) REVERT: D 72 GLU cc_start: 0.7698 (tt0) cc_final: 0.7190 (mt-10) REVERT: D 291 LYS cc_start: 0.8880 (ttpp) cc_final: 0.8669 (tttm) outliers start: 16 outliers final: 12 residues processed: 134 average time/residue: 0.2253 time to fit residues: 45.6284 Evaluate side-chains 133 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 65 LEU 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 B residue 229 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 229 THR 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 132 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 162 ASN D 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.100901 restraints weight = 38039.959| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.65 r_work: 0.3026 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4429 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= 0.169 Angle : 0.636 5.847 16300 Z= 0.314 Chirality : 0.048 0.133 1808 Planarity : 0.005 0.048 2084 Dihedral : 9.649 145.593 1676 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.90 % Allowed : 17.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.22), residues: 1468 helix: 0.53 (0.23), residues: 580 sheet: -0.49 (0.27), residues: 284 loop : -1.38 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 340 HIS 0.004 0.001 HIS D 101 PHE 0.008 0.001 PHE A 352 TYR 0.007 0.001 TYR B 279 ARG 0.009 0.001 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 480) hydrogen bonds : angle 4.13302 ( 1248) covalent geometry : bond 0.00413 (12004) covalent geometry : angle 0.63643 (16300) *********************** 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: 24 poor density : 120 time to evaluate : 1.204 Fit side-chains REVERT: B 65 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8354 (pp) REVERT: B 269 MET cc_start: 0.9071 (mtt) cc_final: 0.8643 (mtp) REVERT: C 82 MET cc_start: 0.8549 (tpt) cc_final: 0.8148 (tpt) REVERT: C 284 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8008 (mttt) REVERT: D 72 GLU cc_start: 0.7800 (tt0) cc_final: 0.7300 (mt-10) REVERT: D 291 LYS cc_start: 0.8901 (ttpp) cc_final: 0.8685 (tttm) outliers start: 24 outliers final: 20 residues processed: 136 average time/residue: 0.2221 time to fit residues: 45.5118 Evaluate side-chains 139 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 229 THR 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 C residue 229 THR Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 244 ASP 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 45 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.102059 restraints weight = 34535.621| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.43 r_work: 0.3038 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12004 Z= 0.165 Angle : 0.631 5.898 16300 Z= 0.310 Chirality : 0.048 0.139 1808 Planarity : 0.005 0.049 2084 Dihedral : 9.652 148.103 1676 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.98 % Allowed : 17.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1468 helix: 0.43 (0.23), residues: 580 sheet: -0.70 (0.27), residues: 284 loop : -1.42 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 356 HIS 0.008 0.001 HIS C 101 PHE 0.008 0.001 PHE B 255 TYR 0.007 0.001 TYR A 337 ARG 0.008 0.001 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 480) hydrogen bonds : angle 4.14672 ( 1248) covalent geometry : bond 0.00409 (12004) covalent geometry : angle 0.63119 (16300) *********************** 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 152 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.405 Fit side-chains REVERT: B 65 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8330 (pp) REVERT: B 269 MET cc_start: 0.9039 (mtt) cc_final: 0.8617 (mtp) REVERT: C 82 MET cc_start: 0.8457 (tpt) cc_final: 0.8135 (tpt) REVERT: C 284 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7997 (mttt) REVERT: D 72 GLU cc_start: 0.7804 (tt0) cc_final: 0.7299 (mt-10) REVERT: D 291 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8672 (tttm) outliers start: 25 outliers final: 21 residues processed: 147 average time/residue: 0.2314 time to fit residues: 50.3315 Evaluate side-chains 144 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 148 THR 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 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 229 THR Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 65 LEU 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 244 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 100 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 chunk 60 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 1.5284 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.121621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.103259 restraints weight = 41995.234| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.91 r_work: 0.3020 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12004 Z= 0.131 Angle : 0.609 8.091 16300 Z= 0.297 Chirality : 0.047 0.138 1808 Planarity : 0.005 0.049 2084 Dihedral : 9.645 147.421 1676 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.67 % Allowed : 17.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1468 helix: 0.46 (0.23), residues: 580 sheet: -0.66 (0.27), residues: 284 loop : -1.37 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 356 HIS 0.005 0.001 HIS C 101 PHE 0.006 0.001 PHE B 255 TYR 0.006 0.001 TYR A 337 ARG 0.009 0.001 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 480) hydrogen bonds : angle 4.06672 ( 1248) covalent geometry : bond 0.00318 (12004) covalent geometry : angle 0.60888 (16300) ********************** 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 150 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.240 Fit side-chains REVERT: A 72 GLU cc_start: 0.7951 (tt0) cc_final: 0.7277 (mt-10) REVERT: B 65 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8344 (pp) REVERT: B 269 MET cc_start: 0.9031 (mtt) cc_final: 0.8627 (mtp) REVERT: B 326 LYS cc_start: 0.7002 (mmmt) cc_final: 0.6509 (mmtt) REVERT: C 82 MET cc_start: 0.8473 (tpt) cc_final: 0.8160 (tpt) REVERT: C 125 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8416 (mm-30) REVERT: C 284 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7991 (mttt) REVERT: D 72 GLU cc_start: 0.7864 (tt0) cc_final: 0.7332 (mt-10) REVERT: D 291 LYS cc_start: 0.8898 (ttpp) cc_final: 0.8690 (tttm) outliers start: 21 outliers final: 16 residues processed: 145 average time/residue: 0.2139 time to fit residues: 47.0902 Evaluate side-chains 148 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 148 THR 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 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 0.9980 chunk 51 optimal weight: 0.0050 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 63 optimal weight: 0.0170 overall best weight: 1.2036 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.121704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104563 restraints weight = 34385.705| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.41 r_work: 0.3070 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4777 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= 0.116 Angle : 0.590 8.098 16300 Z= 0.285 Chirality : 0.046 0.138 1808 Planarity : 0.005 0.048 2084 Dihedral : 9.603 146.887 1676 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.59 % Allowed : 17.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1468 helix: 0.74 (0.23), residues: 556 sheet: -0.61 (0.28), residues: 284 loop : -1.13 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 79 HIS 0.004 0.001 HIS C 101 PHE 0.005 0.001 PHE B 255 TYR 0.006 0.001 TYR A 337 ARG 0.009 0.001 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 480) hydrogen bonds : angle 4.00689 ( 1248) covalent geometry : bond 0.00279 (12004) covalent geometry : angle 0.58991 (16300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5189.24 seconds wall clock time: 89 minutes 52.98 seconds (5392.98 seconds total)