Starting phenix.real_space_refine on Sun May 3 18:35:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v30_42939/05_2026/8v30_42939_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v30_42939/05_2026/8v30_42939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v30_42939/05_2026/8v30_42939_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v30_42939/05_2026/8v30_42939_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v30_42939/05_2026/8v30_42939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v30_42939/05_2026/8v30_42939.map" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 115 5.16 5 C 9405 2.51 5 N 2495 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14910 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.31, per 1000 atoms: 0.29 Number of scatterers: 14910 At special positions: 0 Unit cell: (79.92, 104.76, 194.4, 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 115 16.00 P 10 15.00 Mg 5 11.99 O 2880 8.00 N 2495 7.00 C 9405 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=4, symmetry=0 Links applied TRANS " TRP F 1 " - " ALA F 7 " " DTH F 4 " - " ALA F 3 " " TRP G 1 " - " ALA G 7 " " DTH G 4 " - " ALA G 3 " " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 835.5 milliseconds 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH F 4 " pdb=" CB DTH G 4 " pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 30 sheets defined 48.8% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.690A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.974A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.567A pdb=" N GLY A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.623A 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 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.690A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.632A pdb=" N ARG A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.976A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.747A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.526A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.689A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.932A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.533A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.655A 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 193 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.674A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.513A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.983A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.725A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.683A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.983A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.561A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.672A 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 193 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.735A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.627A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.997A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.744A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.501A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.503A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.647A 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: 3.940A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.576A pdb=" N GLY D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.641A 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 193 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.674A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.591A pdb=" N ARG D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.920A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.671A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.975A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.540A pdb=" N GLY E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.601A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.685A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 3.592A pdb=" N ARG E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.943A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.762A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.633A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (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: 6.435A 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 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.653A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (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: 6.468A 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 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.615A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (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: 6.445A 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 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.607A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (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: 6.459A 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 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.658A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.474A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 705 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 2480 1.32 - 1.46: 5021 1.46 - 1.60: 7534 1.60 - 1.74: 15 1.74 - 1.89: 190 Bond restraints: 15240 Sorted by residual: bond pdb=" C CYS G 5 " pdb=" N HYP G 6 " ideal model delta sigma weight residual 1.329 1.490 -0.161 1.40e-02 5.10e+03 1.32e+02 bond pdb=" C CYS H 5 " pdb=" N HYP H 6 " ideal model delta sigma weight residual 1.329 1.489 -0.160 1.40e-02 5.10e+03 1.31e+02 bond pdb=" C CYS J 5 " pdb=" N HYP J 6 " ideal model delta sigma weight residual 1.329 1.489 -0.160 1.40e-02 5.10e+03 1.31e+02 bond pdb=" C CYS F 5 " pdb=" N HYP F 6 " ideal model delta sigma weight residual 1.329 1.489 -0.160 1.40e-02 5.10e+03 1.30e+02 bond pdb=" C CYS I 5 " pdb=" N HYP I 6 " ideal model delta sigma weight residual 1.329 1.489 -0.160 1.40e-02 5.10e+03 1.30e+02 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 20400 3.23 - 6.46: 228 6.46 - 9.69: 47 9.69 - 12.92: 11 12.92 - 16.15: 9 Bond angle restraints: 20695 Sorted by residual: angle pdb=" CA CYS F 5 " pdb=" C CYS F 5 " pdb=" N HYP F 6 " ideal model delta sigma weight residual 116.20 132.35 -16.15 2.00e+00 2.50e-01 6.52e+01 angle pdb=" CA CYS J 5 " pdb=" C CYS J 5 " pdb=" N HYP J 6 " ideal model delta sigma weight residual 116.20 132.35 -16.15 2.00e+00 2.50e-01 6.52e+01 angle pdb=" CA CYS H 5 " pdb=" C CYS H 5 " pdb=" N HYP H 6 " ideal model delta sigma weight residual 116.20 132.34 -16.14 2.00e+00 2.50e-01 6.51e+01 angle pdb=" CA CYS G 5 " pdb=" C CYS G 5 " pdb=" N HYP G 6 " ideal model delta sigma weight residual 116.20 132.28 -16.08 2.00e+00 2.50e-01 6.47e+01 angle pdb=" CA CYS I 5 " pdb=" C CYS I 5 " pdb=" N HYP I 6 " ideal model delta sigma weight residual 116.20 132.19 -15.99 2.00e+00 2.50e-01 6.39e+01 ... (remaining 20690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 8734 27.39 - 54.79: 419 54.79 - 82.18: 29 82.18 - 109.57: 3 109.57 - 136.96: 5 Dihedral angle restraints: 9190 sinusoidal: 3720 harmonic: 5470 Sorted by residual: dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 76.97 -136.96 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 73.39 -133.39 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 73.31 -133.30 1 2.00e+01 2.50e-03 4.05e+01 ... (remaining 9187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1763 0.054 - 0.109: 420 0.109 - 0.163: 108 0.163 - 0.218: 4 0.218 - 0.272: 5 Chirality restraints: 2300 Sorted by residual: chirality pdb=" CA EEP J 2 " pdb=" N EEP J 2 " pdb=" C EEP J 2 " pdb=" CB EEP J 2 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA EEP G 2 " pdb=" N EEP G 2 " pdb=" C EEP G 2 " pdb=" CB EEP G 2 " both_signs ideal model delta sigma weight residual False 2.48 2.23 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA EEP I 2 " pdb=" N EEP I 2 " pdb=" C EEP I 2 " pdb=" CB EEP I 2 " both_signs ideal model delta sigma weight residual False 2.48 2.23 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2297 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 354 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" CD GLN A 354 " 0.047 2.00e-02 2.50e+03 pdb=" OE1 GLN A 354 " -0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN A 354 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO C 243 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO D 243 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.028 5.00e-02 4.00e+02 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 102 2.50 - 3.10: 9398 3.10 - 3.70: 22345 3.70 - 4.30: 33676 4.30 - 4.90: 56774 Nonbonded interactions: 122295 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.900 3.620 nonbonded pdb=" CD1 TRP G 1 " pdb=" SG CYS G 5 " model vdw 1.901 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.901 3.620 nonbonded pdb=" CD1 TRP F 1 " pdb=" SG CYS F 5 " model vdw 1.902 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.902 3.620 ... (remaining 122290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 375) selection = (chain 'B' and resid 4 through 375) selection = (chain 'C' and resid 4 through 375) selection = (chain 'D' and resid 4 through 375) selection = (chain 'E' and resid 4 through 375) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.710 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 : 0.009 0.161 15254 Z= 0.560 Angle : 0.949 16.151 20725 Z= 0.498 Chirality : 0.051 0.272 2300 Planarity : 0.006 0.051 2630 Dihedral : 15.153 136.963 5660 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.51 % Allowed : 9.49 % Favored : 90.00 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.19), residues: 1835 helix: -1.49 (0.15), residues: 785 sheet: 0.67 (0.29), residues: 370 loop : -0.50 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 290 TYR 0.008 0.001 TYR E 306 PHE 0.017 0.002 PHE C 255 TRP 0.012 0.002 TRP B 356 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00807 (15240) covalent geometry : angle 0.94190 (20695) hydrogen bonds : bond 0.17373 ( 695) hydrogen bonds : angle 6.63065 ( 1809) Misc. bond : bond 0.00114 ( 4) link_TRANS : bond 0.14368 ( 10) link_TRANS : angle 3.27791 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.396 Fit side-chains REVERT: A 49 GLN cc_start: 0.8195 (mt0) cc_final: 0.7982 (mt0) REVERT: E 41 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8589 (mp10) outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.7632 time to fit residues: 88.4928 Evaluate side-chains 104 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN D 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.052582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.041283 restraints weight = 35705.357| |-----------------------------------------------------------------------------| r_work (start): 0.2451 rms_B_bonded: 2.66 r_work: 0.2311 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2182 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15254 Z= 0.137 Angle : 0.650 9.297 20725 Z= 0.304 Chirality : 0.047 0.248 2300 Planarity : 0.004 0.034 2630 Dihedral : 8.970 118.201 2175 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.89 % Allowed : 8.23 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1835 helix: 0.10 (0.19), residues: 795 sheet: 0.70 (0.29), residues: 365 loop : 0.10 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 116 TYR 0.005 0.001 TYR B 188 PHE 0.007 0.001 PHE C 127 TRP 0.008 0.001 TRP C 340 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00317 (15240) covalent geometry : angle 0.64924 (20695) hydrogen bonds : bond 0.03320 ( 695) hydrogen bonds : angle 4.58083 ( 1809) Misc. bond : bond 0.00102 ( 4) link_TRANS : bond 0.00107 ( 10) link_TRANS : angle 0.96105 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.596 Fit side-chains REVERT: A 41 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8899 (mp10) REVERT: A 44 MET cc_start: -0.0035 (OUTLIER) cc_final: -0.1043 (pmt) REVERT: A 49 GLN cc_start: 0.8547 (mt0) cc_final: 0.7537 (mt0) REVERT: A 305 MET cc_start: 0.9333 (mmm) cc_final: 0.9115 (mmm) REVERT: B 325 MET cc_start: 0.9132 (mmp) cc_final: 0.8796 (mmm) REVERT: D 355 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8917 (ptm) REVERT: E 47 MET cc_start: 0.7820 (pmm) cc_final: 0.7584 (pmm) outliers start: 14 outliers final: 2 residues processed: 103 average time/residue: 0.7700 time to fit residues: 85.7140 Evaluate side-chains 100 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 130 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN D 49 GLN E 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.050362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.039232 restraints weight = 36289.306| |-----------------------------------------------------------------------------| r_work (start): 0.2376 rms_B_bonded: 2.62 r_work: 0.2234 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2102 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15254 Z= 0.246 Angle : 0.692 9.179 20725 Z= 0.329 Chirality : 0.050 0.280 2300 Planarity : 0.004 0.034 2630 Dihedral : 7.737 97.542 2170 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.95 % Allowed : 7.85 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1835 helix: 0.62 (0.20), residues: 795 sheet: 0.73 (0.28), residues: 360 loop : 0.15 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 254 TYR 0.008 0.001 TYR A 188 PHE 0.014 0.001 PHE A 127 TRP 0.010 0.002 TRP D 79 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00581 (15240) covalent geometry : angle 0.69020 (20695) hydrogen bonds : bond 0.04020 ( 695) hydrogen bonds : angle 4.41565 ( 1809) Misc. bond : bond 0.00123 ( 4) link_TRANS : bond 0.00240 ( 10) link_TRANS : angle 1.61897 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.584 Fit side-chains REVERT: A 41 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8932 (mp10) REVERT: A 305 MET cc_start: 0.9375 (mmm) cc_final: 0.9136 (mmm) REVERT: A 314 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: B 49 GLN cc_start: 0.8762 (mt0) cc_final: 0.8539 (mt0) REVERT: B 50 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8766 (mtmm) REVERT: B 283 MET cc_start: 0.9157 (mmm) cc_final: 0.8912 (mmm) REVERT: E 314 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8232 (tt0) outliers start: 15 outliers final: 3 residues processed: 107 average time/residue: 0.7926 time to fit residues: 91.4606 Evaluate side-chains 102 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 120 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN C 49 GLN D 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.053275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.042198 restraints weight = 35404.899| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 2.60 r_work: 0.2319 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2190 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15254 Z= 0.103 Angle : 0.589 6.973 20725 Z= 0.273 Chirality : 0.045 0.267 2300 Planarity : 0.003 0.031 2630 Dihedral : 7.020 77.509 2170 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.01 % Allowed : 8.61 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1835 helix: 0.98 (0.20), residues: 795 sheet: 0.73 (0.28), residues: 360 loop : 0.34 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 206 TYR 0.006 0.001 TYR C 69 PHE 0.008 0.001 PHE C 255 TRP 0.010 0.001 TRP C 79 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00238 (15240) covalent geometry : angle 0.58659 (20695) hydrogen bonds : bond 0.02503 ( 695) hydrogen bonds : angle 4.18442 ( 1809) Misc. bond : bond 0.00052 ( 4) link_TRANS : bond 0.00077 ( 10) link_TRANS : angle 1.45142 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.743 Fit side-chains REVERT: A 44 MET cc_start: 0.0102 (OUTLIER) cc_final: -0.0959 (pmt) REVERT: A 49 GLN cc_start: 0.8491 (mt0) cc_final: 0.7350 (mt0) REVERT: A 305 MET cc_start: 0.9333 (mmm) cc_final: 0.9126 (mmm) REVERT: A 314 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: B 314 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7805 (tp40) REVERT: C 314 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: E 314 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8084 (tt0) outliers start: 16 outliers final: 1 residues processed: 108 average time/residue: 0.8807 time to fit residues: 102.6314 Evaluate side-chains 105 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN D 49 GLN D 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.051868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.040547 restraints weight = 35900.164| |-----------------------------------------------------------------------------| r_work (start): 0.2434 rms_B_bonded: 2.65 r_work: 0.2295 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2166 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15254 Z= 0.130 Angle : 0.593 6.940 20725 Z= 0.275 Chirality : 0.046 0.280 2300 Planarity : 0.003 0.030 2630 Dihedral : 6.689 74.194 2170 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.95 % Allowed : 8.92 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.21), residues: 1835 helix: 1.40 (0.20), residues: 765 sheet: 0.66 (0.28), residues: 365 loop : 0.69 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 254 TYR 0.005 0.001 TYR B 188 PHE 0.007 0.001 PHE C 127 TRP 0.009 0.001 TRP D 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00307 (15240) covalent geometry : angle 0.59138 (20695) hydrogen bonds : bond 0.02780 ( 695) hydrogen bonds : angle 4.11457 ( 1809) Misc. bond : bond 0.00063 ( 4) link_TRANS : bond 0.00107 ( 10) link_TRANS : angle 1.39448 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.605 Fit side-chains REVERT: A 49 GLN cc_start: 0.8621 (mt0) cc_final: 0.8247 (mt0) REVERT: A 305 MET cc_start: 0.9313 (mmm) cc_final: 0.9084 (mmm) REVERT: A 314 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: B 314 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7785 (tp40) REVERT: B 325 MET cc_start: 0.9101 (mmp) cc_final: 0.8846 (mmm) REVERT: C 314 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: E 47 MET cc_start: 0.7991 (pmm) cc_final: 0.7755 (pmm) REVERT: E 314 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8065 (tt0) outliers start: 15 outliers final: 2 residues processed: 104 average time/residue: 0.8902 time to fit residues: 99.9793 Evaluate side-chains 105 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN C 49 GLN D 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.051189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.039903 restraints weight = 35855.690| |-----------------------------------------------------------------------------| r_work (start): 0.2413 rms_B_bonded: 2.65 r_work: 0.2271 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2140 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15254 Z= 0.169 Angle : 0.613 7.074 20725 Z= 0.286 Chirality : 0.047 0.272 2300 Planarity : 0.003 0.031 2630 Dihedral : 6.647 75.706 2170 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.89 % Allowed : 9.18 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.21), residues: 1835 helix: 1.44 (0.21), residues: 765 sheet: 0.65 (0.29), residues: 365 loop : 0.73 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 116 TYR 0.007 0.001 TYR B 188 PHE 0.009 0.001 PHE B 127 TRP 0.010 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00401 (15240) covalent geometry : angle 0.61084 (20695) hydrogen bonds : bond 0.03056 ( 695) hydrogen bonds : angle 4.12879 ( 1809) Misc. bond : bond 0.00078 ( 4) link_TRANS : bond 0.00137 ( 10) link_TRANS : angle 1.38683 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.599 Fit side-chains REVERT: A 44 MET cc_start: -0.0346 (OUTLIER) cc_final: -0.1384 (pmt) REVERT: A 49 GLN cc_start: 0.8627 (mt0) cc_final: 0.7670 (mt0) REVERT: A 305 MET cc_start: 0.9338 (mmm) cc_final: 0.9103 (mmm) REVERT: A 314 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: B 314 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.7797 (tp40) REVERT: C 107 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.8864 (tt0) REVERT: C 314 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: D 314 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8228 (tp40) REVERT: E 47 MET cc_start: 0.8049 (pmm) cc_final: 0.7820 (pmm) REVERT: E 314 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8098 (tt0) outliers start: 14 outliers final: 3 residues processed: 106 average time/residue: 0.9005 time to fit residues: 102.6734 Evaluate side-chains 108 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN D 49 GLN D 246 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.050804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.039556 restraints weight = 35855.551| |-----------------------------------------------------------------------------| r_work (start): 0.2401 rms_B_bonded: 2.64 r_work: 0.2261 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2130 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15254 Z= 0.179 Angle : 0.620 7.398 20725 Z= 0.290 Chirality : 0.048 0.276 2300 Planarity : 0.003 0.030 2630 Dihedral : 6.612 78.221 2170 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.82 % Allowed : 9.30 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.21), residues: 1835 helix: 1.44 (0.20), residues: 765 sheet: 0.74 (0.28), residues: 360 loop : 0.72 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 335 TYR 0.006 0.001 TYR B 188 PHE 0.009 0.001 PHE A 127 TRP 0.010 0.001 TRP D 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00426 (15240) covalent geometry : angle 0.61824 (20695) hydrogen bonds : bond 0.03142 ( 695) hydrogen bonds : angle 4.13649 ( 1809) Misc. bond : bond 0.00082 ( 4) link_TRANS : bond 0.00130 ( 10) link_TRANS : angle 1.36351 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.724 Fit side-chains REVERT: A 49 GLN cc_start: 0.8651 (mt0) cc_final: 0.8256 (mt0) REVERT: A 305 MET cc_start: 0.9357 (mmm) cc_final: 0.9126 (mmm) REVERT: A 314 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: B 314 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7788 (tp40) REVERT: C 107 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.8868 (tt0) REVERT: C 314 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: E 314 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8109 (tt0) outliers start: 13 outliers final: 4 residues processed: 105 average time/residue: 0.8763 time to fit residues: 99.2942 Evaluate side-chains 107 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 169 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN C 49 GLN C 354 GLN D 49 GLN E 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.053790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.042683 restraints weight = 35242.549| |-----------------------------------------------------------------------------| r_work (start): 0.2466 rms_B_bonded: 2.62 r_work: 0.2328 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2198 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15254 Z= 0.096 Angle : 0.570 8.133 20725 Z= 0.263 Chirality : 0.045 0.231 2300 Planarity : 0.003 0.030 2630 Dihedral : 6.240 68.716 2170 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.70 % Allowed : 9.30 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.21), residues: 1835 helix: 1.61 (0.20), residues: 760 sheet: 1.04 (0.30), residues: 320 loop : 0.76 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 335 TYR 0.006 0.001 TYR E 69 PHE 0.006 0.001 PHE B 255 TRP 0.012 0.001 TRP D 79 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00228 (15240) covalent geometry : angle 0.56837 (20695) hydrogen bonds : bond 0.02381 ( 695) hydrogen bonds : angle 4.02888 ( 1809) Misc. bond : bond 0.00036 ( 4) link_TRANS : bond 0.00077 ( 10) link_TRANS : angle 1.18211 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.515 Fit side-chains REVERT: A 49 GLN cc_start: 0.8479 (mt0) cc_final: 0.8176 (mt0) REVERT: A 305 MET cc_start: 0.9355 (mmm) cc_final: 0.9136 (mmm) REVERT: A 314 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: B 314 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7851 (tp40) REVERT: B 325 MET cc_start: 0.9170 (mmp) cc_final: 0.8863 (mmm) REVERT: C 246 GLN cc_start: 0.8826 (mt0) cc_final: 0.8355 (mt0) REVERT: C 314 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: D 314 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8319 (tp40) REVERT: E 314 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8053 (tt0) outliers start: 11 outliers final: 2 residues processed: 109 average time/residue: 0.8922 time to fit residues: 104.4208 Evaluate side-chains 107 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 109 optimal weight: 6.9990 chunk 128 optimal weight: 0.4980 chunk 91 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 178 optimal weight: 0.0870 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 overall best weight: 2.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN C 49 GLN D 49 GLN D 354 GLN E 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.051527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.040388 restraints weight = 35765.683| |-----------------------------------------------------------------------------| r_work (start): 0.2406 rms_B_bonded: 2.62 r_work: 0.2266 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2134 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15254 Z= 0.186 Angle : 0.620 8.895 20725 Z= 0.289 Chirality : 0.048 0.261 2300 Planarity : 0.003 0.029 2630 Dihedral : 6.390 73.721 2170 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.63 % Allowed : 9.62 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.21), residues: 1835 helix: 1.52 (0.21), residues: 765 sheet: 0.77 (0.28), residues: 360 loop : 0.80 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 177 TYR 0.007 0.001 TYR B 188 PHE 0.010 0.001 PHE D 127 TRP 0.009 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00441 (15240) covalent geometry : angle 0.61912 (20695) hydrogen bonds : bond 0.03190 ( 695) hydrogen bonds : angle 4.10945 ( 1809) Misc. bond : bond 0.00071 ( 4) link_TRANS : bond 0.00090 ( 10) link_TRANS : angle 1.14929 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.616 Fit side-chains REVERT: A 49 GLN cc_start: 0.8698 (mt0) cc_final: 0.8385 (mt0) REVERT: A 305 MET cc_start: 0.9405 (mmm) cc_final: 0.9173 (mmm) REVERT: A 314 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: B 314 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.7875 (tp40) REVERT: B 325 MET cc_start: 0.9187 (mmp) cc_final: 0.8874 (mmm) REVERT: C 314 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: D 314 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8251 (tp40) REVERT: E 314 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8144 (tt0) outliers start: 10 outliers final: 3 residues processed: 106 average time/residue: 0.8844 time to fit residues: 100.8096 Evaluate side-chains 107 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN C 49 GLN C 354 GLN D 49 GLN E 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.053032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.041928 restraints weight = 35403.184| |-----------------------------------------------------------------------------| r_work (start): 0.2447 rms_B_bonded: 2.61 r_work: 0.2308 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2178 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15254 Z= 0.114 Angle : 0.584 10.257 20725 Z= 0.268 Chirality : 0.045 0.237 2300 Planarity : 0.003 0.029 2630 Dihedral : 6.175 69.131 2170 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.51 % Allowed : 9.68 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.21), residues: 1835 helix: 1.64 (0.20), residues: 760 sheet: 0.79 (0.29), residues: 360 loop : 0.80 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 116 TYR 0.006 0.001 TYR D 69 PHE 0.007 0.001 PHE A 127 TRP 0.011 0.001 TRP D 79 HIS 0.003 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00276 (15240) covalent geometry : angle 0.58269 (20695) hydrogen bonds : bond 0.02572 ( 695) hydrogen bonds : angle 4.04093 ( 1809) Misc. bond : bond 0.00040 ( 4) link_TRANS : bond 0.00059 ( 10) link_TRANS : angle 1.04835 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.592 Fit side-chains REVERT: A 49 GLN cc_start: 0.8727 (mt0) cc_final: 0.8397 (mt0) REVERT: A 305 MET cc_start: 0.9374 (mmm) cc_final: 0.9149 (mmm) REVERT: B 314 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.7857 (tp40) REVERT: B 325 MET cc_start: 0.9167 (mmp) cc_final: 0.8854 (mmm) REVERT: C 51 ASP cc_start: 0.9319 (m-30) cc_final: 0.8950 (p0) REVERT: C 314 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: D 314 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8266 (tp40) REVERT: E 314 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8081 (tt0) outliers start: 8 outliers final: 2 residues processed: 106 average time/residue: 0.8386 time to fit residues: 95.9781 Evaluate side-chains 106 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 76 optimal weight: 0.3980 chunk 137 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 63 optimal weight: 0.0370 chunk 96 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN C 49 GLN D 49 GLN D 354 GLN E 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.052069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.040974 restraints weight = 35492.923| |-----------------------------------------------------------------------------| r_work (start): 0.2422 rms_B_bonded: 2.61 r_work: 0.2282 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2152 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15254 Z= 0.154 Angle : 0.601 10.231 20725 Z= 0.278 Chirality : 0.046 0.246 2300 Planarity : 0.003 0.028 2630 Dihedral : 6.212 70.703 2170 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.63 % Allowed : 9.81 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.21), residues: 1835 helix: 1.58 (0.20), residues: 765 sheet: 0.80 (0.28), residues: 360 loop : 0.80 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 254 TYR 0.006 0.001 TYR B 188 PHE 0.009 0.001 PHE D 127 TRP 0.010 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00367 (15240) covalent geometry : angle 0.59994 (20695) hydrogen bonds : bond 0.02940 ( 695) hydrogen bonds : angle 4.06681 ( 1809) Misc. bond : bond 0.00058 ( 4) link_TRANS : bond 0.00047 ( 10) link_TRANS : angle 0.94987 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4450.37 seconds wall clock time: 76 minutes 51.80 seconds (4611.80 seconds total)