Starting phenix.real_space_refine on Sat Aug 23 22:20:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v30_42939/08_2025/8v30_42939_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v30_42939/08_2025/8v30_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_42939/08_2025/8v30_42939_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v30_42939/08_2025/8v30_42939_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v30_42939/08_2025/8v30_42939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v30_42939/08_2025/8v30_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-2.0-5787/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: 4.32, 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: 1.29 Conformation dependent library (CDL) restraints added in 648.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.91 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: 3.13 Time building geometry restraints manager: 1.74 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: 20396 3.23 - 6.46: 237 6.46 - 9.69: 41 9.69 - 12.92: 12 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: 8742 27.39 - 54.79: 417 54.79 - 82.18: 23 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 - 0.046: 1641 0.046 - 0.092: 443 0.092 - 0.138: 197 0.138 - 0.185: 13 0.185 - 0.231: 6 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 2.44 2.21 0.23 2.00e-01 2.50e+01 1.33e+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 2.44 2.23 0.22 2.00e-01 2.50e+01 1.19e+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 2.44 2.23 0.22 2.00e-01 2.50e+01 1.16e+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: 1.530 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.710 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- 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= 0.566 Angle : 0.945 16.151 20725 Z= 0.490 Chirality : 0.050 0.231 2300 Planarity : 0.006 0.051 2630 Dihedral : 14.972 136.963 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 aren 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 0.00823 (15240) covalent geometry : angle 0.93780 (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 : 0.617 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: 0.8420 time to fit residues: 97.6622 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 : 0.630 ------------------------------------------------------------------------------- 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: D 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.052327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.041164 restraints weight = 35818.635| |-----------------------------------------------------------------------------| r_work (start): 0.2451 rms_B_bonded: 2.63 r_work: 0.2312 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2184 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0855 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 : 0.653 9.284 20725 Z= 0.303 Chirality : 0.047 0.257 2300 Planarity : 0.004 0.034 2630 Dihedral : 8.766 117.413 2175 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.89 % Allowed : 8.48 % Favored : 90.63 % 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 aren not related in a simple way. whole: 0.21 (0.20), residues: 1835 helix: 0.11 (0.19), residues: 795 sheet: 0.69 (0.29), residues: 365 loop : 0.11 (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 255 TRP 0.008 0.001 TRP C 340 HIS 0.003 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00313 (15240) covalent geometry : angle 0.65260 (20695) hydrogen bonds : bond 0.03303 ( 695) hydrogen bonds : angle 4.57587 ( 1809) Misc. bond : bond 0.00067 ( 4) link_TRANS : bond 0.00066 ( 10) link_TRANS : angle 1.04853 ( 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 : 0.577 Fit side-chains REVERT: A 41 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8891 (mp10) REVERT: A 44 MET cc_start: 0.0042 (OUTLIER) cc_final: -0.0993 (pmt) REVERT: A 49 GLN cc_start: 0.8584 (mt0) cc_final: 0.7598 (mt0) REVERT: A 305 MET cc_start: 0.9331 (mmm) cc_final: 0.9115 (mmm) REVERT: B 325 MET cc_start: 0.9127 (mmp) cc_final: 0.8791 (mmm) REVERT: D 355 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8911 (ptm) outliers start: 14 outliers final: 3 residues processed: 103 average time/residue: 0.8874 time to fit residues: 98.6908 Evaluate side-chains 102 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 355 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: 1.9990 chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.050301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.039168 restraints weight = 36257.990| |-----------------------------------------------------------------------------| r_work (start): 0.2379 rms_B_bonded: 2.62 r_work: 0.2236 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2105 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15254 Z= 0.230 Angle : 0.688 8.640 20725 Z= 0.324 Chirality : 0.050 0.274 2300 Planarity : 0.004 0.033 2630 Dihedral : 7.546 94.695 2170 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.01 % Allowed : 7.91 % Favored : 91.08 % 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 aren not related in a simple way. whole: 0.67 (0.21), residues: 1835 helix: 0.69 (0.20), residues: 795 sheet: 0.73 (0.28), residues: 360 loop : 0.20 (0.25), 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 0.013 0.001 PHE A 127 TRP 0.011 0.002 TRP D 79 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00541 (15240) covalent geometry : angle 0.68605 (20695) hydrogen bonds : bond 0.03954 ( 695) hydrogen bonds : angle 4.38368 ( 1809) Misc. bond : bond 0.00102 ( 4) link_TRANS : bond 0.00230 ( 10) link_TRANS : angle 1.59482 ( 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 117 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.628 Fit side-chains REVERT: A 41 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8907 (mp10) REVERT: A 305 MET cc_start: 0.9364 (mmm) cc_final: 0.9116 (mmm) REVERT: A 314 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: B 49 GLN cc_start: 0.8793 (mt0) cc_final: 0.8559 (mt0) REVERT: B 50 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8758 (mtmm) REVERT: B 283 MET cc_start: 0.9153 (mmm) cc_final: 0.8898 (mmm) outliers start: 16 outliers final: 3 residues processed: 109 average time/residue: 0.8607 time to fit residues: 101.2237 Evaluate side-chains 102 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 120 optimal weight: 0.0030 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 92 optimal weight: 0.0060 chunk 155 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 7 optimal weight: 0.0030 chunk 154 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 = 0.2756 r_free = 0.2756 target = 0.053349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.042060 restraints weight = 35586.352| |-----------------------------------------------------------------------------| r_work (start): 0.2471 rms_B_bonded: 2.65 r_work: 0.2332 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2203 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1297 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= 0.090 Angle : 0.585 8.102 20725 Z= 0.270 Chirality : 0.045 0.244 2300 Planarity : 0.003 0.030 2630 Dihedral : 6.895 74.651 2170 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.76 % Allowed : 8.80 % Favored : 90.44 % 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 aren not related in a simple way. whole: 1.01 (0.21), residues: 1835 helix: 1.06 (0.20), residues: 795 sheet: 0.72 (0.28), residues: 360 loop : 0.37 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 206 TYR 0.006 0.001 TYR E 69 PHE 0.007 0.001 PHE B 255 TRP 0.010 0.001 TRP G 1 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00205 (15240) covalent geometry : angle 0.58379 (20695) hydrogen bonds : bond 0.02370 ( 695) hydrogen bonds : angle 4.16985 ( 1809) Misc. bond : bond 0.00024 ( 4) link_TRANS : bond 0.00112 ( 10) link_TRANS : angle 1.28356 ( 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 115 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.604 Fit side-chains REVERT: A 41 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8915 (mp10) REVERT: A 44 MET cc_start: 0.0017 (OUTLIER) cc_final: -0.1040 (pmt) REVERT: A 49 GLN cc_start: 0.8456 (mt0) cc_final: 0.7296 (mt0) REVERT: A 305 MET cc_start: 0.9293 (mmm) cc_final: 0.9073 (mmm) REVERT: B 246 GLN cc_start: 0.8901 (mt0) cc_final: 0.8695 (mt0) REVERT: B 314 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.7784 (tp40) REVERT: B 325 MET cc_start: 0.9060 (mmp) cc_final: 0.8827 (mmm) outliers start: 12 outliers final: 1 residues processed: 106 average time/residue: 0.8920 time to fit residues: 102.0180 Evaluate side-chains 101 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 355 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.2666 r_free = 0.2666 target = 0.049413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.038174 restraints weight = 36463.435| |-----------------------------------------------------------------------------| r_work (start): 0.2368 rms_B_bonded: 2.64 r_work: 0.2227 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2097 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 15254 Z= 0.277 Angle : 0.685 8.561 20725 Z= 0.322 Chirality : 0.051 0.300 2300 Planarity : 0.004 0.032 2630 Dihedral : 6.912 82.895 2170 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.14 % Allowed : 8.29 % Favored : 90.57 % 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 aren not related in a simple way. whole: 1.25 (0.21), residues: 1835 helix: 1.29 (0.20), residues: 765 sheet: 0.74 (0.28), residues: 360 loop : 0.56 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 335 TYR 0.008 0.001 TYR A 188 PHE 0.012 0.001 PHE A 127 TRP 0.012 0.002 TRP G 1 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00651 (15240) covalent geometry : angle 0.68316 (20695) hydrogen bonds : bond 0.03801 ( 695) hydrogen bonds : angle 4.27767 ( 1809) Misc. bond : bond 0.00103 ( 4) link_TRANS : bond 0.00238 ( 10) link_TRANS : angle 1.47016 ( 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 117 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.643 Fit side-chains REVERT: A 305 MET cc_start: 0.9346 (mmm) cc_final: 0.9102 (mmm) REVERT: A 314 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: B 314 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.7850 (tp40) REVERT: C 314 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: E 314 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8109 (tt0) outliers start: 18 outliers final: 5 residues processed: 105 average time/residue: 0.8859 time to fit residues: 100.3244 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 : 0.641 ------------------------------------------------------------------------------- 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 C residue 355 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 E 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.053077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.041937 restraints weight = 35232.330| |-----------------------------------------------------------------------------| r_work (start): 0.2446 rms_B_bonded: 2.61 r_work: 0.2307 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2177 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15254 Z= 0.106 Angle : 0.594 7.665 20725 Z= 0.274 Chirality : 0.045 0.247 2300 Planarity : 0.003 0.029 2630 Dihedral : 6.486 74.298 2170 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.63 % Allowed : 9.37 % 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 aren not related in a simple way. whole: 1.46 (0.21), residues: 1835 helix: 1.46 (0.20), residues: 765 sheet: 0.74 (0.28), residues: 360 loop : 0.73 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 206 TYR 0.007 0.001 TYR E 69 PHE 0.007 0.001 PHE B 255 TRP 0.011 0.001 TRP C 79 HIS 0.003 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00249 (15240) covalent geometry : angle 0.59227 (20695) hydrogen bonds : bond 0.02548 ( 695) hydrogen bonds : angle 4.10493 ( 1809) Misc. bond : bond 0.00044 ( 4) link_TRANS : bond 0.00097 ( 10) link_TRANS : angle 1.24312 ( 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 109 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.625 Fit side-chains REVERT: A 44 MET cc_start: -0.0035 (OUTLIER) cc_final: -0.1075 (pmt) REVERT: A 49 GLN cc_start: 0.8469 (mt0) cc_final: 0.7528 (mt0) REVERT: A 305 MET cc_start: 0.9359 (mmm) cc_final: 0.9131 (mmm) REVERT: B 314 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.7857 (tp40) REVERT: B 325 MET cc_start: 0.9158 (mmp) cc_final: 0.8869 (mmm) REVERT: C 314 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8095 (tt0) outliers start: 10 outliers final: 2 residues processed: 103 average time/residue: 0.8315 time to fit residues: 92.3348 Evaluate side-chains 104 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET 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 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: 6.9990 chunk 154 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 246 GLN D 354 GLN E 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.051546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.040434 restraints weight = 35573.952| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 2.60 r_work: 0.2266 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2135 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1500 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 : 0.627 7.606 20725 Z= 0.291 Chirality : 0.048 0.272 2300 Planarity : 0.003 0.029 2630 Dihedral : 6.408 76.759 2170 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.63 % Allowed : 9.24 % 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 aren not related in a simple way. whole: 1.46 (0.21), residues: 1835 helix: 1.47 (0.20), residues: 765 sheet: 0.75 (0.28), residues: 360 loop : 0.71 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 335 TYR 0.007 0.001 TYR B 188 PHE 0.009 0.001 PHE A 127 TRP 0.010 0.001 TRP C 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00426 (15240) covalent geometry : angle 0.62524 (20695) hydrogen bonds : bond 0.03155 ( 695) hydrogen bonds : angle 4.13592 ( 1809) Misc. bond : bond 0.00064 ( 4) link_TRANS : bond 0.00137 ( 10) link_TRANS : angle 1.31557 ( 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 108 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.583 Fit side-chains REVERT: A 44 MET cc_start: -0.0154 (OUTLIER) cc_final: -0.1170 (pmt) REVERT: A 49 GLN cc_start: 0.8466 (mt0) cc_final: 0.7583 (mt0) REVERT: A 176 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8763 (mtp) REVERT: A 305 MET cc_start: 0.9393 (mmm) cc_final: 0.9165 (mmm) REVERT: A 314 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: B 314 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.7843 (tp40) REVERT: C 314 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: D 314 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8278 (tp40) outliers start: 10 outliers final: 3 residues processed: 103 average time/residue: 0.8118 time to fit residues: 90.1966 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 : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 176 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 C residue 355 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 180 LEU 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: 10.0000 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN C 354 GLN D 49 GLN E 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.053077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.041951 restraints weight = 35387.173| |-----------------------------------------------------------------------------| r_work (start): 0.2445 rms_B_bonded: 2.61 r_work: 0.2306 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2177 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15254 Z= 0.112 Angle : 0.592 8.512 20725 Z= 0.272 Chirality : 0.046 0.237 2300 Planarity : 0.003 0.031 2630 Dihedral : 6.091 71.485 2170 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.70 % Allowed : 9.18 % 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 aren not related in a simple way. whole: 1.56 (0.21), residues: 1835 helix: 1.60 (0.20), residues: 760 sheet: 0.74 (0.28), residues: 360 loop : 0.76 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 335 TYR 0.006 0.001 TYR E 69 PHE 0.007 0.001 PHE C 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 0.00267 (15240) covalent geometry : angle 0.59090 (20695) hydrogen bonds : bond 0.02588 ( 695) hydrogen bonds : angle 4.05768 ( 1809) Misc. bond : bond 0.00038 ( 4) link_TRANS : bond 0.00111 ( 10) link_TRANS : angle 1.17872 ( 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 111 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.389 Fit side-chains REVERT: A 305 MET cc_start: 0.9358 (mmm) cc_final: 0.9136 (mmm) REVERT: A 314 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: B 314 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.7858 (tp40) REVERT: B 325 MET cc_start: 0.9173 (mmp) cc_final: 0.8870 (mmm) REVERT: C 314 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: D 314 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8290 (tp40) outliers start: 11 outliers final: 3 residues processed: 107 average time/residue: 0.8057 time to fit residues: 93.0340 Evaluate side-chains 106 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 C residue 355 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 180 LEU 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: 0.7980 chunk 128 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 137 GLN C 49 GLN D 49 GLN D 354 GLN E 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.049511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.038403 restraints weight = 36361.919| |-----------------------------------------------------------------------------| r_work (start): 0.2373 rms_B_bonded: 2.62 r_work: 0.2232 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2101 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1614 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= 0.255 Angle : 0.673 8.261 20725 Z= 0.315 Chirality : 0.050 0.284 2300 Planarity : 0.003 0.029 2630 Dihedral : 6.452 80.019 2170 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.44 % Allowed : 9.49 % Favored : 90.06 % 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 aren not related in a simple way. whole: 1.39 (0.21), residues: 1835 helix: 1.41 (0.20), residues: 765 sheet: 0.73 (0.28), residues: 360 loop : 0.67 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 335 TYR 0.008 0.001 TYR A 188 PHE 0.013 0.001 PHE A 127 TRP 0.011 0.002 TRP G 1 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00603 (15240) covalent geometry : angle 0.67139 (20695) hydrogen bonds : bond 0.03692 ( 695) hydrogen bonds : angle 4.21852 ( 1809) Misc. bond : bond 0.00084 ( 4) link_TRANS : bond 0.00183 ( 10) link_TRANS : angle 1.22614 ( 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 105 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.735 Fit side-chains REVERT: A 305 MET cc_start: 0.9362 (mmm) cc_final: 0.9128 (mmm) REVERT: A 314 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: B 314 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7860 (tp40) REVERT: B 325 MET cc_start: 0.9175 (mmp) cc_final: 0.8911 (mmm) REVERT: C 314 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: D 314 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8210 (tp40) outliers start: 7 outliers final: 2 residues processed: 104 average time/residue: 0.8779 time to fit residues: 98.5501 Evaluate side-chains 104 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 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 = 0.2731 r_free = 0.2731 target = 0.052293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.041125 restraints weight = 35777.377| |-----------------------------------------------------------------------------| r_work (start): 0.2447 rms_B_bonded: 2.62 r_work: 0.2308 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2179 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15254 Z= 0.104 Angle : 0.594 10.662 20725 Z= 0.272 Chirality : 0.045 0.239 2300 Planarity : 0.003 0.030 2630 Dihedral : 5.971 71.757 2170 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.32 % Allowed : 9.56 % 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 aren not related in a simple way. whole: 1.61 (0.21), residues: 1835 helix: 1.54 (0.20), residues: 765 sheet: 1.04 (0.30), residues: 320 loop : 0.76 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 206 TYR 0.007 0.001 TYR E 69 PHE 0.007 0.001 PHE C 255 TRP 0.013 0.001 TRP E 79 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00245 (15240) covalent geometry : angle 0.59303 (20695) hydrogen bonds : bond 0.02499 ( 695) hydrogen bonds : angle 4.06893 ( 1809) Misc. bond : bond 0.00033 ( 4) link_TRANS : bond 0.00090 ( 10) link_TRANS : angle 1.11380 ( 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 105 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.633 Fit side-chains REVERT: A 305 MET cc_start: 0.9332 (mmm) cc_final: 0.9107 (mmm) REVERT: B 314 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.7814 (tp40) REVERT: B 325 MET cc_start: 0.9154 (mmp) cc_final: 0.8883 (mmm) REVERT: C 51 ASP cc_start: 0.9321 (m-30) cc_final: 0.8892 (p0) REVERT: C 314 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: D 314 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8227 (tp40) outliers start: 5 outliers final: 2 residues processed: 104 average time/residue: 0.8569 time to fit residues: 96.1443 Evaluate side-chains 105 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 76 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 143 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 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: 0.8980 chunk 147 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 137 GLN C 49 GLN D 49 GLN D 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.054116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.043001 restraints weight = 35155.115| |-----------------------------------------------------------------------------| r_work (start): 0.2476 rms_B_bonded: 2.61 r_work: 0.2341 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2212 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1633 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= 0.096 Angle : 0.574 10.736 20725 Z= 0.260 Chirality : 0.044 0.212 2300 Planarity : 0.003 0.029 2630 Dihedral : 5.510 61.775 2170 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.32 % Allowed : 9.87 % 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 aren not related in a simple way. whole: 1.74 (0.21), residues: 1835 helix: 1.77 (0.21), residues: 760 sheet: 0.82 (0.29), residues: 360 loop : 0.84 (0.26), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 206 TYR 0.006 0.001 TYR D 69 PHE 0.006 0.001 PHE B 255 TRP 0.013 0.001 TRP C 356 HIS 0.003 0.000 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00230 (15240) covalent geometry : angle 0.57345 (20695) hydrogen bonds : bond 0.02369 ( 695) hydrogen bonds : angle 3.98513 ( 1809) Misc. bond : bond 0.00007 ( 4) link_TRANS : bond 0.00102 ( 10) link_TRANS : angle 0.87690 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4799.87 seconds wall clock time: 82 minutes 55.89 seconds (4975.89 seconds total)