Starting phenix.real_space_refine on Fri Jun 13 13:49:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v30_42939/06_2025/8v30_42939_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v30_42939/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v30_42939/06_2025/8v30_42939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v30_42939/06_2025/8v30_42939.map" model { file = "/net/cci-nas-00/data/ceres_data/8v30_42939/06_2025/8v30_42939_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v30_42939/06_2025/8v30_42939_neut.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.98, per 1000 atoms: 0.67 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: 4.28 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.25 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: 7.15 Time building geometry restraints manager: 5.03 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: 0.00 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: 1.210 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 40.300 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 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:15.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (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 TRP 0.012 0.002 TRP B 356 HIS 0.003 0.001 HIS A 161 PHE 0.017 0.002 PHE C 255 TYR 0.008 0.001 TYR E 306 ARG 0.005 0.000 ARG E 290 Details of bonding type rmsd link_TRANS : bond 0.14368 ( 10) link_TRANS : angle 3.27791 ( 30) hydrogen bonds : bond 0.17373 ( 695) hydrogen bonds : angle 6.63065 ( 1809) covalent geometry : bond 0.00823 (15240) covalent geometry : angle 0.93780 (20695) Misc. bond : bond 0.00114 ( 4) *********************** 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 : 1.873 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: 1.6694 time to fit residues: 193.8069 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 : 1.808 ------------------------------------------------------------------------------- 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 156 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.2704 r_free = 0.2704 target = 0.051087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.039912 restraints weight = 35917.584| |-----------------------------------------------------------------------------| r_work (start): 0.2412 rms_B_bonded: 2.63 r_work: 0.2272 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2143 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15254 Z= 0.195 Angle : 0.684 9.667 20725 Z= 0.320 Chirality : 0.049 0.287 2300 Planarity : 0.004 0.034 2630 Dihedral : 8.753 116.787 2175 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.01 % Allowed : 7.97 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1835 helix: 0.16 (0.19), residues: 795 sheet: 0.65 (0.28), residues: 365 loop : 0.14 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE D 127 TYR 0.006 0.001 TYR B 188 ARG 0.003 0.000 ARG B 116 Details of bonding type rmsd link_TRANS : bond 0.00056 ( 10) link_TRANS : angle 1.06780 ( 30) hydrogen bonds : bond 0.03685 ( 695) hydrogen bonds : angle 4.56537 ( 1809) covalent geometry : bond 0.00453 (15240) covalent geometry : angle 0.68370 (20695) Misc. bond : bond 0.00080 ( 4) *********************** 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 115 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 1.683 Fit side-chains REVERT: A 41 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8905 (mp10) REVERT: A 44 MET cc_start: 0.0013 (OUTLIER) cc_final: -0.1022 (pmt) REVERT: A 49 GLN cc_start: 0.8572 (mt0) cc_final: 0.7573 (mt0) REVERT: A 305 MET cc_start: 0.9343 (mmm) cc_final: 0.9132 (mmm) REVERT: B 50 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8766 (mtmm) REVERT: B 325 MET cc_start: 0.9128 (mmp) cc_final: 0.8775 (mmm) REVERT: D 355 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8915 (ptm) REVERT: E 314 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8187 (tt0) outliers start: 16 outliers final: 4 residues processed: 103 average time/residue: 1.7256 time to fit residues: 192.5498 Evaluate side-chains 105 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 176 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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 E 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.050675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.039576 restraints weight = 35736.835| |-----------------------------------------------------------------------------| r_work (start): 0.2385 rms_B_bonded: 2.61 r_work: 0.2243 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2112 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15254 Z= 0.222 Angle : 0.676 8.253 20725 Z= 0.318 Chirality : 0.049 0.275 2300 Planarity : 0.004 0.033 2630 Dihedral : 7.735 97.902 2170 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.95 % Allowed : 7.78 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1835 helix: 0.71 (0.20), residues: 795 sheet: 0.69 (0.28), residues: 360 loop : 0.22 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.005 0.001 HIS B 161 PHE 0.011 0.001 PHE A 127 TYR 0.007 0.001 TYR A 188 ARG 0.002 0.000 ARG C 254 Details of bonding type rmsd link_TRANS : bond 0.00217 ( 10) link_TRANS : angle 1.49092 ( 30) hydrogen bonds : bond 0.03705 ( 695) hydrogen bonds : angle 4.37636 ( 1809) covalent geometry : bond 0.00524 (15240) covalent geometry : angle 0.67427 (20695) Misc. bond : bond 0.00091 ( 4) *********************** 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 : 1.774 Fit side-chains REVERT: A 41 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8924 (mp10) REVERT: A 305 MET cc_start: 0.9363 (mmm) cc_final: 0.9121 (mmm) REVERT: A 314 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: B 49 GLN cc_start: 0.8799 (mt0) cc_final: 0.8520 (mt0) REVERT: E 314 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8244 (tt0) outliers start: 15 outliers final: 4 residues processed: 107 average time/residue: 1.7942 time to fit residues: 207.6669 Evaluate side-chains 103 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain E residue 176 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 105 optimal weight: 2.9990 chunk 153 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.2766 r_free = 0.2766 target = 0.053025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.041955 restraints weight = 35268.106| |-----------------------------------------------------------------------------| r_work (start): 0.2446 rms_B_bonded: 2.59 r_work: 0.2307 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2178 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15254 Z= 0.111 Angle : 0.599 7.859 20725 Z= 0.277 Chirality : 0.046 0.265 2300 Planarity : 0.003 0.030 2630 Dihedral : 6.968 77.779 2170 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.89 % Allowed : 8.16 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1835 helix: 1.03 (0.20), residues: 795 sheet: 0.73 (0.28), residues: 360 loop : 0.37 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.003 0.000 HIS A 161 PHE 0.007 0.001 PHE C 255 TYR 0.006 0.001 TYR E 69 ARG 0.001 0.000 ARG D 206 Details of bonding type rmsd link_TRANS : bond 0.00127 ( 10) link_TRANS : angle 1.38282 ( 30) hydrogen bonds : bond 0.02603 ( 695) hydrogen bonds : angle 4.17367 ( 1809) covalent geometry : bond 0.00261 (15240) covalent geometry : angle 0.59688 (20695) Misc. bond : bond 0.00041 ( 4) *********************** 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: 14 poor density : 104 time to evaluate : 1.688 Fit side-chains REVERT: A 44 MET cc_start: 0.0072 (OUTLIER) cc_final: -0.0978 (pmt) REVERT: A 49 GLN cc_start: 0.8471 (mt0) cc_final: 0.7456 (mt0) REVERT: A 305 MET cc_start: 0.9345 (mmm) cc_final: 0.9118 (mmm) REVERT: A 314 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: B 314 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.7833 (tp40) REVERT: B 325 MET cc_start: 0.9137 (mmp) cc_final: 0.8879 (mmm) REVERT: C 314 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: E 314 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8137 (tt0) outliers start: 14 outliers final: 1 residues processed: 110 average time/residue: 1.7867 time to fit residues: 211.9992 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 : 1.657 ------------------------------------------------------------------------------- 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 123 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 67 optimal weight: 0.4980 chunk 147 optimal weight: 0.0570 chunk 139 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.5104 ------------------------------------------------------------------------------- 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 = 0.2717 r_free = 0.2717 target = 0.051606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.040290 restraints weight = 35979.397| |-----------------------------------------------------------------------------| r_work (start): 0.2427 rms_B_bonded: 2.65 r_work: 0.2286 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2157 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1377 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= 0.137 Angle : 0.606 7.430 20725 Z= 0.280 Chirality : 0.046 0.268 2300 Planarity : 0.003 0.030 2630 Dihedral : 6.591 75.304 2170 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.89 % Allowed : 8.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1835 helix: 1.41 (0.20), residues: 765 sheet: 0.66 (0.28), residues: 365 loop : 0.72 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.003 0.001 HIS B 161 PHE 0.008 0.001 PHE A 127 TYR 0.006 0.001 TYR B 188 ARG 0.001 0.000 ARG E 254 Details of bonding type rmsd link_TRANS : bond 0.00148 ( 10) link_TRANS : angle 1.33148 ( 30) hydrogen bonds : bond 0.02859 ( 695) hydrogen bonds : angle 4.12060 ( 1809) covalent geometry : bond 0.00323 (15240) covalent geometry : angle 0.60462 (20695) Misc. bond : bond 0.00050 ( 4) *********************** 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 113 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.642 Fit side-chains REVERT: A 123 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.9086 (mmt) REVERT: A 305 MET cc_start: 0.9328 (mmm) cc_final: 0.9088 (mmm) REVERT: A 314 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: B 314 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7778 (tp40) REVERT: C 314 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: E 314 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8101 (tt0) outliers start: 14 outliers final: 2 residues processed: 104 average time/residue: 1.7599 time to fit residues: 198.0393 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 : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 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 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 21 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 113 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 246 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 = 0.2710 r_free = 0.2710 target = 0.051311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.039999 restraints weight = 35884.332| |-----------------------------------------------------------------------------| r_work (start): 0.2419 rms_B_bonded: 2.65 r_work: 0.2278 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2147 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1454 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= 0.152 Angle : 0.610 6.990 20725 Z= 0.283 Chirality : 0.047 0.260 2300 Planarity : 0.003 0.030 2630 Dihedral : 6.398 74.600 2170 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.89 % Allowed : 8.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1835 helix: 1.46 (0.20), residues: 765 sheet: 0.67 (0.28), residues: 365 loop : 0.78 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.004 0.001 HIS E 161 PHE 0.008 0.001 PHE B 127 TYR 0.006 0.001 TYR B 188 ARG 0.001 0.000 ARG C 116 Details of bonding type rmsd link_TRANS : bond 0.00123 ( 10) link_TRANS : angle 1.28854 ( 30) hydrogen bonds : bond 0.02935 ( 695) hydrogen bonds : angle 4.10880 ( 1809) covalent geometry : bond 0.00361 (15240) covalent geometry : angle 0.60845 (20695) Misc. bond : bond 0.00060 ( 4) *********************** 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 114 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.722 Fit side-chains REVERT: A 44 MET cc_start: -0.0272 (OUTLIER) cc_final: -0.1332 (pmt) REVERT: A 49 GLN cc_start: 0.8690 (mt0) cc_final: 0.7906 (mt0) REVERT: A 305 MET cc_start: 0.9339 (mmm) cc_final: 0.9103 (mmm) REVERT: A 314 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: B 314 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7799 (tp40) REVERT: B 325 MET cc_start: 0.9139 (mmp) cc_final: 0.8843 (mmm) REVERT: C 107 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8875 (tt0) REVERT: C 314 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: D 314 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8268 (tp40) REVERT: E 314 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8127 (tt0) outliers start: 14 outliers final: 3 residues processed: 107 average time/residue: 1.7072 time to fit residues: 198.0215 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 : 1.763 ------------------------------------------------------------------------------- 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 92 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.2739 r_free = 0.2739 target = 0.051827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.040728 restraints weight = 35737.387| |-----------------------------------------------------------------------------| r_work (start): 0.2420 rms_B_bonded: 2.62 r_work: 0.2280 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2149 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15254 Z= 0.151 Angle : 0.608 7.651 20725 Z= 0.282 Chirality : 0.047 0.255 2300 Planarity : 0.003 0.029 2630 Dihedral : 6.208 74.130 2170 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.89 % Allowed : 8.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.21), residues: 1835 helix: 1.48 (0.20), residues: 765 sheet: 0.65 (0.28), residues: 365 loop : 0.79 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.004 0.001 HIS E 161 PHE 0.008 0.001 PHE A 127 TYR 0.005 0.001 TYR B 188 ARG 0.001 0.000 ARG C 116 Details of bonding type rmsd link_TRANS : bond 0.00120 ( 10) link_TRANS : angle 1.24443 ( 30) hydrogen bonds : bond 0.02929 ( 695) hydrogen bonds : angle 4.08958 ( 1809) covalent geometry : bond 0.00360 (15240) covalent geometry : angle 0.60689 (20695) Misc. bond : bond 0.00057 ( 4) *********************** 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 115 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 1.631 Fit side-chains REVERT: A 305 MET cc_start: 0.9391 (mmm) cc_final: 0.9165 (mmm) REVERT: A 314 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: B 314 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.7838 (tp40) REVERT: B 325 MET cc_start: 0.9173 (mmp) cc_final: 0.8868 (mmm) REVERT: C 107 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.8881 (tt0) REVERT: C 314 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: D 314 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8301 (tp40) REVERT: E 314 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8158 (tt0) outliers start: 14 outliers final: 3 residues processed: 110 average time/residue: 1.6167 time to fit residues: 192.4378 Evaluate side-chains 109 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 53 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 C 354 GLN D 49 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 = 0.2652 r_free = 0.2652 target = 0.048868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.037765 restraints weight = 36375.455| |-----------------------------------------------------------------------------| r_work (start): 0.2355 rms_B_bonded: 2.61 r_work: 0.2214 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2084 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 15254 Z= 0.310 Angle : 0.702 7.969 20725 Z= 0.332 Chirality : 0.052 0.296 2300 Planarity : 0.004 0.036 2630 Dihedral : 6.647 83.202 2170 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.82 % Allowed : 8.92 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.21), residues: 1835 helix: 1.38 (0.20), residues: 760 sheet: 0.61 (0.28), residues: 370 loop : 0.64 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 1 HIS 0.006 0.001 HIS B 161 PHE 0.013 0.001 PHE A 127 TYR 0.009 0.001 TYR C 169 ARG 0.004 0.000 ARG C 177 Details of bonding type rmsd link_TRANS : bond 0.00240 ( 10) link_TRANS : angle 1.30827 ( 30) hydrogen bonds : bond 0.03982 ( 695) hydrogen bonds : angle 4.30698 ( 1809) covalent geometry : bond 0.00730 (15240) covalent geometry : angle 0.70070 (20695) Misc. bond : bond 0.00099 ( 4) *********************** 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: 13 poor density : 98 time to evaluate : 1.667 Fit side-chains REVERT: A 123 MET cc_start: 0.9284 (tpt) cc_final: 0.9083 (mmt) REVERT: A 176 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8764 (mtp) REVERT: A 305 MET cc_start: 0.9352 (mmm) cc_final: 0.9120 (mmm) REVERT: A 314 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: B 314 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7858 (tp40) REVERT: C 107 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.9008 (tt0) REVERT: C 314 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: D 314 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8184 (tp40) REVERT: E 314 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8208 (tt0) outliers start: 13 outliers final: 4 residues processed: 107 average time/residue: 1.6996 time to fit residues: 196.6444 Evaluate side-chains 107 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 107 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 271 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 108 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.053302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.042243 restraints weight = 35087.489| |-----------------------------------------------------------------------------| r_work (start): 0.2452 rms_B_bonded: 2.60 r_work: 0.2314 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2183 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1571 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= 0.099 Angle : 0.591 9.279 20725 Z= 0.273 Chirality : 0.045 0.244 2300 Planarity : 0.003 0.030 2630 Dihedral : 6.089 72.827 2170 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.63 % Allowed : 9.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.21), residues: 1835 helix: 1.50 (0.20), residues: 765 sheet: 1.05 (0.30), residues: 320 loop : 0.73 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.002 0.000 HIS A 161 PHE 0.007 0.001 PHE B 255 TYR 0.007 0.001 TYR E 69 ARG 0.002 0.000 ARG C 177 Details of bonding type rmsd link_TRANS : bond 0.00097 ( 10) link_TRANS : angle 1.13224 ( 30) hydrogen bonds : bond 0.02461 ( 695) hydrogen bonds : angle 4.07639 ( 1809) covalent geometry : bond 0.00234 (15240) covalent geometry : angle 0.59034 (20695) Misc. bond : bond 0.00032 ( 4) *********************** 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 : 1.649 Fit side-chains REVERT: A 305 MET cc_start: 0.9382 (mmm) cc_final: 0.9167 (mmm) REVERT: A 314 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: B 314 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7824 (tp40) REVERT: B 325 MET cc_start: 0.9177 (mmp) cc_final: 0.8898 (mmm) REVERT: C 51 ASP cc_start: 0.9316 (m-30) cc_final: 0.8924 (p0) REVERT: C 107 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.8841 (tt0) REVERT: C 314 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: E 314 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8110 (tt0) outliers start: 10 outliers final: 2 residues processed: 107 average time/residue: 1.7397 time to fit residues: 201.4962 Evaluate side-chains 108 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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 355 MET 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 138 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 105 optimal weight: 0.0470 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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 C 354 GLN D 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.053303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.042274 restraints weight = 35548.758| |-----------------------------------------------------------------------------| r_work (start): 0.2453 rms_B_bonded: 2.61 r_work: 0.2316 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2188 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15254 Z= 0.106 Angle : 0.583 10.284 20725 Z= 0.266 Chirality : 0.045 0.240 2300 Planarity : 0.003 0.031 2630 Dihedral : 5.745 67.267 2170 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.44 % Allowed : 9.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.21), residues: 1835 helix: 1.69 (0.21), residues: 760 sheet: 0.80 (0.28), residues: 360 loop : 0.81 (0.26), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.003 0.000 HIS E 161 PHE 0.007 0.001 PHE C 255 TYR 0.006 0.001 TYR E 69 ARG 0.002 0.000 ARG E 335 Details of bonding type rmsd link_TRANS : bond 0.00097 ( 10) link_TRANS : angle 0.91484 ( 30) hydrogen bonds : bond 0.02567 ( 695) hydrogen bonds : angle 4.01526 ( 1809) covalent geometry : bond 0.00252 (15240) covalent geometry : angle 0.58284 (20695) Misc. bond : bond 0.00018 ( 4) ********************** 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: 7 poor density : 101 time to evaluate : 1.814 Fit side-chains REVERT: A 305 MET cc_start: 0.9381 (mmm) cc_final: 0.9173 (mmm) REVERT: A 314 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: B 314 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7834 (tp40) REVERT: B 325 MET cc_start: 0.9182 (mmp) cc_final: 0.8846 (mmm) REVERT: C 51 ASP cc_start: 0.9322 (m-30) cc_final: 0.8929 (p0) REVERT: C 314 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: D 51 ASP cc_start: 0.9336 (m-30) cc_final: 0.9028 (OUTLIER) REVERT: E 314 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8068 (tt0) outliers start: 7 outliers final: 2 residues processed: 106 average time/residue: 1.8507 time to fit residues: 214.0011 Evaluate side-chains 106 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 1.850 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 147 optimal weight: 0.0980 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.2718 r_free = 0.2718 target = 0.051030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.040052 restraints weight = 35687.013| |-----------------------------------------------------------------------------| r_work (start): 0.2394 rms_B_bonded: 2.59 r_work: 0.2254 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2123 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15254 Z= 0.207 Angle : 0.640 10.035 20725 Z= 0.298 Chirality : 0.048 0.256 2300 Planarity : 0.003 0.031 2630 Dihedral : 6.118 74.754 2170 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.44 % Allowed : 9.87 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1835 helix: 1.51 (0.21), residues: 765 sheet: 0.78 (0.28), residues: 360 loop : 0.79 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.005 0.001 HIS B 161 PHE 0.011 0.001 PHE B 127 TYR 0.007 0.001 TYR A 188 ARG 0.005 0.000 ARG E 335 Details of bonding type rmsd link_TRANS : bond 0.00076 ( 10) link_TRANS : angle 0.89746 ( 30) hydrogen bonds : bond 0.03371 ( 695) hydrogen bonds : angle 4.13783 ( 1809) covalent geometry : bond 0.00493 (15240) covalent geometry : angle 0.63905 (20695) Misc. bond : bond 0.00064 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9509.54 seconds wall clock time: 163 minutes 10.33 seconds (9790.33 seconds total)