Starting phenix.real_space_refine on Mon Jan 20 10:01:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v30_42939/01_2025/8v30_42939_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v30_42939/01_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_42939/01_2025/8v30_42939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v30_42939/01_2025/8v30_42939.map" model { file = "/net/cci-nas-00/data/ceres_data/8v30_42939/01_2025/8v30_42939_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v30_42939/01_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.04, per 1000 atoms: 0.61 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: 3.67 Conformation dependent library (CDL) restraints added in 1.6 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: 2.21 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: 5.22 Time building geometry restraints manager: 4.25 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: 0.950 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.920 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.880 ------------------------------------------------------------------------------- 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 : 0.008 0.161 15240 Z= 0.550 Angle : 0.938 16.151 20695 Z= 0.485 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 *********************** 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 : 1.686 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: 1.6891 time to fit residues: 196.2532 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 : 1.589 ------------------------------------------------------------------------------- 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 = 0.051088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.039911 restraints weight = 35918.714| |-----------------------------------------------------------------------------| r_work (start): 0.2412 rms_B_bonded: 2.63 r_work: 0.2273 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2144 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2144 ------------------------------------------------------------------------------- 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 15240 Z= 0.298 Angle : 0.684 9.665 20695 Z= 0.319 Chirality : 0.049 0.286 2300 Planarity : 0.004 0.034 2630 Dihedral : 8.753 116.794 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 *********************** 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 : 1.647 Fit side-chains REVERT: A 41 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8901 (mp10) REVERT: A 44 MET cc_start: 0.0049 (OUTLIER) cc_final: -0.1000 (pmt) REVERT: A 49 GLN cc_start: 0.8575 (mt0) cc_final: 0.7578 (mt0) REVERT: A 305 MET cc_start: 0.9343 (mmm) cc_final: 0.9132 (mmm) REVERT: B 50 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8772 (mtmm) REVERT: B 325 MET cc_start: 0.9127 (mmp) cc_final: 0.8775 (mmm) REVERT: D 355 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8916 (ptm) REVERT: E 314 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8185 (tt0) outliers start: 16 outliers final: 4 residues processed: 103 average time/residue: 1.7933 time to fit residues: 199.6947 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 : 1.699 ------------------------------------------------------------------------------- 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: 6.9990 chunk 47 optimal weight: 0.0270 chunk 31 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.3844 ------------------------------------------------------------------------------- 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 = 0.2725 r_free = 0.2725 target = 0.051298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.040174 restraints weight = 35605.307| |-----------------------------------------------------------------------------| r_work (start): 0.2400 rms_B_bonded: 2.61 r_work: 0.2259 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2129 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15240 Z= 0.298 Angle : 0.655 8.066 20695 Z= 0.307 Chirality : 0.049 0.267 2300 Planarity : 0.003 0.032 2630 Dihedral : 7.619 95.073 2170 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.95 % Allowed : 7.85 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1835 helix: 0.71 (0.20), residues: 795 sheet: 0.70 (0.28), residues: 360 loop : 0.24 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 79 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE A 127 TYR 0.007 0.001 TYR B 188 ARG 0.002 0.000 ARG B 254 *********************** 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 : 1.647 Fit side-chains REVERT: A 41 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8920 (mp10) REVERT: A 49 GLN cc_start: 0.8659 (mt0) cc_final: 0.8230 (mt0) REVERT: A 305 MET cc_start: 0.9362 (mmm) cc_final: 0.9123 (mmm) REVERT: A 314 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: B 49 GLN cc_start: 0.8779 (mt0) cc_final: 0.8498 (mt0) REVERT: E 314 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8222 (tt0) outliers start: 15 outliers final: 4 residues processed: 107 average time/residue: 1.7805 time to fit residues: 205.7153 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 : 1.615 ------------------------------------------------------------------------------- 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: 0.9980 chunk 158 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 114 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.2702 r_free = 0.2702 target = 0.051082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.039778 restraints weight = 35819.753| |-----------------------------------------------------------------------------| r_work (start): 0.2409 rms_B_bonded: 2.66 r_work: 0.2267 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2136 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15240 Z= 0.246 Angle : 0.624 7.638 20695 Z= 0.290 Chirality : 0.047 0.279 2300 Planarity : 0.003 0.032 2630 Dihedral : 7.003 80.643 2170 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.95 % Allowed : 8.10 % 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: 0.96 (0.21), residues: 1835 helix: 1.00 (0.20), residues: 795 sheet: 0.72 (0.28), residues: 360 loop : 0.35 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.004 0.001 HIS B 161 PHE 0.008 0.001 PHE A 127 TYR 0.006 0.001 TYR D 69 ARG 0.001 0.000 ARG A 177 *********************** 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: 15 poor density : 100 time to evaluate : 1.687 Fit side-chains REVERT: A 41 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8931 (mp10) REVERT: A 44 MET cc_start: -0.0287 (OUTLIER) cc_final: -0.1414 (pmt) REVERT: A 49 GLN cc_start: 0.8715 (mt0) cc_final: 0.8001 (mt0) REVERT: A 305 MET cc_start: 0.9328 (mmm) cc_final: 0.9089 (mmm) REVERT: A 314 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: B 49 GLN cc_start: 0.8801 (mt0) cc_final: 0.8594 (mt0) REVERT: B 246 GLN cc_start: 0.8804 (mt0) cc_final: 0.8597 (mt0) REVERT: B 314 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7795 (tp40) REVERT: B 325 MET cc_start: 0.9128 (mmp) cc_final: 0.8897 (mmm) REVERT: C 314 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: E 47 MET cc_start: 0.8067 (pmm) cc_final: 0.7849 (pmm) REVERT: E 314 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8151 (tt0) outliers start: 15 outliers final: 3 residues processed: 106 average time/residue: 1.7841 time to fit residues: 204.0940 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 : 1.679 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET 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: 1.9990 chunk 152 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.2716 r_free = 0.2716 target = 0.050885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.039801 restraints weight = 35939.858| |-----------------------------------------------------------------------------| r_work (start): 0.2389 rms_B_bonded: 2.61 r_work: 0.2247 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2116 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15240 Z= 0.316 Angle : 0.646 7.709 20695 Z= 0.302 Chirality : 0.049 0.284 2300 Planarity : 0.003 0.033 2630 Dihedral : 6.847 81.590 2170 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.95 % Allowed : 8.48 % 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 (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: 1.29 (0.21), residues: 1835 helix: 1.33 (0.20), residues: 765 sheet: 0.72 (0.28), residues: 360 loop : 0.60 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 79 HIS 0.005 0.001 HIS B 161 PHE 0.012 0.001 PHE A 127 TYR 0.007 0.001 TYR A 188 ARG 0.002 0.000 ARG C 254 *********************** 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: 15 poor density : 98 time to evaluate : 1.707 Fit side-chains REVERT: A 41 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8920 (mp10) REVERT: A 305 MET cc_start: 0.9377 (mmm) cc_final: 0.9152 (mmm) REVERT: A 314 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: B 314 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7857 (tp40) REVERT: C 314 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: D 314 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8293 (tp40) REVERT: E 47 MET cc_start: 0.8093 (pmm) cc_final: 0.7879 (pmm) REVERT: E 314 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8216 (tt0) outliers start: 15 outliers final: 2 residues processed: 105 average time/residue: 1.7810 time to fit residues: 202.3992 Evaluate side-chains 104 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.050804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.039536 restraints weight = 35945.606| |-----------------------------------------------------------------------------| r_work (start): 0.2406 rms_B_bonded: 2.65 r_work: 0.2265 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2135 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15240 Z= 0.245 Angle : 0.616 7.367 20695 Z= 0.286 Chirality : 0.047 0.277 2300 Planarity : 0.003 0.034 2630 Dihedral : 6.582 78.764 2170 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.76 % Allowed : 8.86 % 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: 0.74 (0.28), residues: 360 loop : 0.67 (0.25), residues: 710 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 D 127 TYR 0.006 0.001 TYR E 69 ARG 0.001 0.000 ARG E 206 *********************** 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 110 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.675 Fit side-chains REVERT: A 41 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8908 (mp10) REVERT: A 305 MET cc_start: 0.9354 (mmm) cc_final: 0.9121 (mmm) REVERT: A 314 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: B 314 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7778 (tp40) REVERT: C 107 GLU cc_start: 0.9366 (OUTLIER) cc_final: 0.8868 (tt0) REVERT: C 314 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: E 47 MET cc_start: 0.8133 (pmm) cc_final: 0.7910 (pmm) REVERT: E 314 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8141 (tt0) outliers start: 12 outliers final: 3 residues processed: 104 average time/residue: 1.8188 time to fit residues: 204.5789 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 : 1.846 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 111 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.2644 r_free = 0.2644 target = 0.048568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.037514 restraints weight = 36713.751| |-----------------------------------------------------------------------------| r_work (start): 0.2348 rms_B_bonded: 2.62 r_work: 0.2205 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2074 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 15240 Z= 0.483 Angle : 0.710 8.258 20695 Z= 0.335 Chirality : 0.052 0.310 2300 Planarity : 0.004 0.037 2630 Dihedral : 6.896 85.677 2170 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.01 % Allowed : 8.54 % 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 (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: 1.27 (0.21), residues: 1835 helix: 1.33 (0.20), residues: 760 sheet: 0.77 (0.28), residues: 355 loop : 0.53 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 1 HIS 0.006 0.001 HIS B 161 PHE 0.014 0.001 PHE A 127 TYR 0.009 0.001 TYR A 188 ARG 0.003 0.000 ARG C 116 *********************** 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 112 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.614 Fit side-chains REVERT: A 176 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8813 (mtp) REVERT: A 305 MET cc_start: 0.9349 (mmm) cc_final: 0.9118 (mmm) REVERT: A 314 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: B 314 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7869 (tp40) REVERT: C 107 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.9030 (tt0) REVERT: C 314 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: D 82 MET cc_start: 0.9331 (tpt) cc_final: 0.9010 (tpp) REVERT: D 314 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8225 (tp40) REVERT: E 314 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8203 (tt0) outliers start: 16 outliers final: 3 residues processed: 107 average time/residue: 1.6888 time to fit residues: 196.2345 Evaluate side-chains 105 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 119 optimal weight: 0.0770 chunk 88 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 32 optimal weight: 0.0570 chunk 22 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 174 optimal weight: 0.1980 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.2769 r_free = 0.2769 target = 0.053236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.042211 restraints weight = 35110.213| |-----------------------------------------------------------------------------| r_work (start): 0.2451 rms_B_bonded: 2.59 r_work: 0.2313 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2183 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15240 Z= 0.144 Angle : 0.591 8.253 20695 Z= 0.273 Chirality : 0.045 0.253 2300 Planarity : 0.003 0.033 2630 Dihedral : 6.237 73.908 2170 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.70 % Allowed : 8.86 % 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 (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: 1.52 (0.20), residues: 765 sheet: 1.02 (0.30), residues: 320 loop : 0.71 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 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 B 312 *********************** 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 112 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.620 Fit side-chains REVERT: A 44 MET cc_start: -0.0598 (OUTLIER) cc_final: -0.1346 (pmt) REVERT: A 49 GLN cc_start: 0.8438 (mt0) cc_final: 0.7629 (mt0) REVERT: A 305 MET cc_start: 0.9377 (mmm) cc_final: 0.9168 (mmm) REVERT: B 314 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7839 (tp40) REVERT: B 325 MET cc_start: 0.9195 (mmp) cc_final: 0.8916 (mmm) REVERT: C 107 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.8862 (tt0) REVERT: C 246 GLN cc_start: 0.8782 (mt0) cc_final: 0.8384 (mt0) REVERT: C 314 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: E 314 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8107 (tt0) outliers start: 11 outliers final: 1 residues processed: 107 average time/residue: 1.7918 time to fit residues: 207.0289 Evaluate side-chains 105 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.667 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 108 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.2730 r_free = 0.2730 target = 0.051590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.040609 restraints weight = 35458.024| |-----------------------------------------------------------------------------| r_work (start): 0.2409 rms_B_bonded: 2.58 r_work: 0.2270 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2139 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15240 Z= 0.252 Angle : 0.618 9.023 20695 Z= 0.285 Chirality : 0.047 0.275 2300 Planarity : 0.003 0.033 2630 Dihedral : 6.185 75.520 2170 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.51 % Allowed : 9.18 % Favored : 90.32 % 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: 1.52 (0.21), residues: 1835 helix: 1.53 (0.20), residues: 765 sheet: 0.76 (0.28), residues: 360 loop : 0.76 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE D 127 TYR 0.006 0.001 TYR B 188 ARG 0.002 0.000 ARG C 254 *********************** 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 109 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 1.700 Fit side-chains REVERT: A 44 MET cc_start: -0.0090 (OUTLIER) cc_final: -0.0881 (pmt) REVERT: A 49 GLN cc_start: 0.8511 (mt0) cc_final: 0.7790 (mt0) REVERT: A 305 MET cc_start: 0.9383 (mmm) cc_final: 0.9155 (mmm) REVERT: B 314 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.7863 (tp40) REVERT: B 325 MET cc_start: 0.9229 (mmp) cc_final: 0.8926 (mmm) REVERT: C 51 ASP cc_start: 0.9331 (m-30) cc_final: 0.8926 (p0) REVERT: C 107 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.8909 (tt0) REVERT: C 314 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: D 314 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8224 (tp40) REVERT: E 314 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8162 (tt0) outliers start: 8 outliers final: 1 residues processed: 106 average time/residue: 1.7607 time to fit residues: 201.7430 Evaluate side-chains 107 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 107 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D 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 138 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 158 optimal weight: 0.0980 chunk 132 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.052108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.041107 restraints weight = 35787.007| |-----------------------------------------------------------------------------| r_work (start): 0.2426 rms_B_bonded: 2.59 r_work: 0.2288 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2157 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15240 Z= 0.214 Angle : 0.603 10.460 20695 Z= 0.277 Chirality : 0.046 0.257 2300 Planarity : 0.003 0.034 2630 Dihedral : 5.996 72.874 2170 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.51 % Allowed : 9.30 % Favored : 90.19 % 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: 1.54 (0.20), residues: 765 sheet: 0.78 (0.28), residues: 360 loop : 0.80 (0.26), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS A 161 PHE 0.008 0.001 PHE A 127 TYR 0.006 0.001 TYR E 69 ARG 0.002 0.000 ARG B 290 ********************** 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 107 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.693 Fit side-chains REVERT: A 305 MET cc_start: 0.9379 (mmm) cc_final: 0.9160 (mmm) REVERT: B 314 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7860 (tp40) REVERT: B 325 MET cc_start: 0.9231 (mmp) cc_final: 0.8923 (mmm) REVERT: C 51 ASP cc_start: 0.9326 (m-30) cc_final: 0.8933 (p0) REVERT: C 107 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.9063 (tt0) REVERT: C 314 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: D 51 ASP cc_start: 0.9339 (m-30) cc_final: 0.9025 (OUTLIER) REVERT: E 314 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8119 (tt0) outliers start: 8 outliers final: 3 residues processed: 104 average time/residue: 1.8049 time to fit residues: 204.0492 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 : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 147 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.2674 r_free = 0.2674 target = 0.049816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.038767 restraints weight = 36093.025| |-----------------------------------------------------------------------------| r_work (start): 0.2382 rms_B_bonded: 2.61 r_work: 0.2240 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2110 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15240 Z= 0.333 Angle : 0.644 9.410 20695 Z= 0.300 Chirality : 0.049 0.285 2300 Planarity : 0.003 0.033 2630 Dihedral : 6.286 78.437 2170 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: 1.47 (0.21), residues: 1835 helix: 1.47 (0.20), residues: 765 sheet: 0.76 (0.28), residues: 360 loop : 0.75 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 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 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8578.11 seconds wall clock time: 152 minutes 44.95 seconds (9164.95 seconds total)