Starting phenix.real_space_refine on Fri Feb 6 09:54:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7utj_26772/02_2026/7utj_26772.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utj_26772/02_2026/7utj_26772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7utj_26772/02_2026/7utj_26772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utj_26772/02_2026/7utj_26772.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7utj_26772/02_2026/7utj_26772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utj_26772/02_2026/7utj_26772.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 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 12 5.49 5 Mg 6 5.21 5 S 216 5.16 5 C 15462 2.51 5 N 4200 2.21 5 O 4695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24591 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "H" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "I" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "K" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "L" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "Z" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 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} Chain: "F" 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.48, per 1000 atoms: 0.22 Number of scatterers: 24591 At special positions: 0 Unit cell: (122.831, 101.091, 219.574, 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 216 16.00 P 12 15.00 Mg 6 11.99 O 4695 8.00 N 4200 7.00 C 15462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5892 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 36 sheets defined 57.9% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.531A 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 197 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 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.185A 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 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.531A 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 194 through 197 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 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.185A 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 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 127 removed outlier: 3.840A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.530A 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 194 through 197 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 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.512A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.185A 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 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 127 removed outlier: 3.840A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.530A 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 194 through 197 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 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.186A 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 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.531A 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 194 through 197 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 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.512A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.185A 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 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'F' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.531A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 260 Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 261 through 262 No H-bonds generated for 'chain 'F' and resid 261 through 262' Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'G' and resid 711 through 731 Processing helix chain 'G' and resid 738 through 766 Processing helix chain 'G' and resid 772 through 804 Processing helix chain 'G' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER G 817 " --> pdb=" O ASP G 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU G 818 " --> pdb=" O SER G 814 " (cutoff:3.500A) Processing helix chain 'G' and resid 848 through 853 Processing helix chain 'H' and resid 711 through 731 Processing helix chain 'H' and resid 738 through 766 Processing helix chain 'H' and resid 772 through 804 Processing helix chain 'H' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER H 817 " --> pdb=" O ASP H 813 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU H 818 " --> pdb=" O SER H 814 " (cutoff:3.500A) Processing helix chain 'H' and resid 848 through 853 Processing helix chain 'I' and resid 711 through 731 Processing helix chain 'I' and resid 738 through 766 Processing helix chain 'I' and resid 772 through 804 Processing helix chain 'I' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER I 817 " --> pdb=" O ASP I 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU I 818 " --> pdb=" O SER I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 848 through 853 Processing helix chain 'K' and resid 711 through 731 Processing helix chain 'K' and resid 738 through 766 Processing helix chain 'K' and resid 772 through 804 Processing helix chain 'K' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER K 817 " --> pdb=" O ASP K 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU K 818 " --> pdb=" O SER K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 848 through 853 Processing helix chain 'L' and resid 711 through 731 Processing helix chain 'L' and resid 738 through 766 Processing helix chain 'L' and resid 772 through 804 Processing helix chain 'L' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER L 817 " --> pdb=" O ASP L 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU L 818 " --> pdb=" O SER L 814 " (cutoff:3.500A) Processing helix chain 'L' and resid 848 through 853 Processing helix chain 'Z' and resid 711 through 731 Processing helix chain 'Z' and resid 738 through 766 Processing helix chain 'Z' and resid 772 through 804 Processing helix chain 'Z' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER Z 817 " --> pdb=" O ASP Z 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU Z 818 " --> pdb=" O SER Z 814 " (cutoff:3.500A) Processing helix chain 'Z' and resid 848 through 853 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.552A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (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 41 through 42 Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 6.041A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.043A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AB3, first strand: chain 'B' and resid 41 through 42 removed outlier: 6.042A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.043A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AC2, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.043A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC5, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AC8, first strand: chain 'D' and resid 41 through 42 removed outlier: 6.042A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD6, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD8, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 1478 hydrogen bonds defined for protein. 4068 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: 5.47 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4558 1.32 - 1.45: 5837 1.45 - 1.57: 14235 1.57 - 1.69: 18 1.69 - 1.82: 372 Bond restraints: 25020 Sorted by residual: bond pdb=" N VAL B 159 " pdb=" CA VAL B 159 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.42e+01 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.14e-02 7.69e+03 1.35e+01 bond pdb=" N VAL F 159 " pdb=" CA VAL F 159 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" N VAL E 159 " pdb=" CA VAL E 159 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.458 1.498 -0.041 1.18e-02 7.18e+03 1.20e+01 ... (remaining 25015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 31043 1.42 - 2.85: 2041 2.85 - 4.27: 540 4.27 - 5.70: 138 5.70 - 7.12: 78 Bond angle restraints: 33840 Sorted by residual: angle pdb=" CA LEU Z 790 " pdb=" C LEU Z 790 " pdb=" O LEU Z 790 " ideal model delta sigma weight residual 120.55 115.33 5.22 1.06e+00 8.90e-01 2.43e+01 angle pdb=" N GLN I 789 " pdb=" CA GLN I 789 " pdb=" C GLN I 789 " ideal model delta sigma weight residual 111.28 107.19 4.09 1.09e+00 8.42e-01 1.41e+01 angle pdb=" CA ASP E 157 " pdb=" CB ASP E 157 " pdb=" CG ASP E 157 " ideal model delta sigma weight residual 112.60 116.24 -3.64 1.00e+00 1.00e+00 1.32e+01 angle pdb=" N GLN Z 789 " pdb=" CA GLN Z 789 " pdb=" C GLN Z 789 " ideal model delta sigma weight residual 111.28 107.40 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N GLN K 789 " pdb=" CA GLN K 789 " pdb=" C GLN K 789 " ideal model delta sigma weight residual 111.28 107.50 3.78 1.09e+00 8.42e-01 1.20e+01 ... (remaining 33835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.20: 14441 27.20 - 54.39: 717 54.39 - 81.59: 124 81.59 - 108.78: 6 108.78 - 135.98: 18 Dihedral angle restraints: 15306 sinusoidal: 6156 harmonic: 9150 Sorted by residual: dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.98 -135.98 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.98 -135.98 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.97 -135.97 1 2.00e+01 2.50e-03 4.13e+01 ... (remaining 15303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2586 0.052 - 0.104: 970 0.104 - 0.156: 203 0.156 - 0.208: 62 0.208 - 0.260: 13 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CA LEU A 153 " pdb=" N LEU A 153 " pdb=" C LEU A 153 " pdb=" CB LEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA LEU D 153 " pdb=" N LEU D 153 " pdb=" C LEU D 153 " pdb=" CB LEU D 153 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU C 153 " pdb=" N LEU C 153 " pdb=" C LEU C 153 " pdb=" CB LEU C 153 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3831 not shown) Planarity restraints: 4290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Z 790 " -0.022 2.00e-02 2.50e+03 4.57e-02 2.08e+01 pdb=" C LEU Z 790 " 0.079 2.00e-02 2.50e+03 pdb=" O LEU Z 790 " -0.029 2.00e-02 2.50e+03 pdb=" N ASN Z 791 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 156 " -0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C GLY D 156 " 0.079 2.00e-02 2.50e+03 pdb=" O GLY D 156 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP D 157 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 156 " 0.022 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C GLY A 156 " -0.078 2.00e-02 2.50e+03 pdb=" O GLY A 156 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP A 157 " 0.027 2.00e-02 2.50e+03 ... (remaining 4287 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 118 2.52 - 3.12: 18285 3.12 - 3.71: 38677 3.71 - 4.31: 59255 4.31 - 4.90: 97350 Nonbonded interactions: 213685 Sorted by model distance: nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 1.927 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.955 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.957 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 1.973 2.170 ... (remaining 213680 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'Z' } 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: 3.270 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.390 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 0.065 25020 Z= 0.422 Angle : 0.915 7.122 33840 Z= 0.525 Chirality : 0.059 0.260 3834 Planarity : 0.005 0.046 4290 Dihedral : 16.795 135.978 9414 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.88 % Allowed : 4.15 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3102 helix: 0.43 (0.12), residues: 1626 sheet: -0.11 (0.25), residues: 408 loop : -0.34 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 28 TYR 0.009 0.001 TYR F 53 PHE 0.007 0.001 PHE B 127 TRP 0.016 0.003 TRP K 859 HIS 0.008 0.002 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00927 (25020) covalent geometry : angle 0.91478 (33840) hydrogen bonds : bond 0.15212 ( 1458) hydrogen bonds : angle 6.35337 ( 4068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 432 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7964 (mm110) cc_final: 0.7312 (mm110) REVERT: A 325 MET cc_start: 0.8575 (mmp) cc_final: 0.7939 (mmp) REVERT: B 206 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7759 (ttp-170) REVERT: B 211 ASP cc_start: 0.7587 (t0) cc_final: 0.7337 (t0) REVERT: B 305 MET cc_start: 0.9020 (mmm) cc_final: 0.8503 (mmm) REVERT: B 325 MET cc_start: 0.8799 (mmp) cc_final: 0.8182 (mmp) REVERT: C 82 MET cc_start: 0.8755 (tpt) cc_final: 0.8466 (tpp) REVERT: C 211 ASP cc_start: 0.7858 (t0) cc_final: 0.7596 (t0) REVERT: C 325 MET cc_start: 0.9009 (mmp) cc_final: 0.8751 (mmp) REVERT: D 305 MET cc_start: 0.8913 (mmm) cc_final: 0.8547 (mmm) REVERT: D 326 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.6052 (ptpt) REVERT: E 325 MET cc_start: 0.8817 (mmp) cc_final: 0.8524 (mmp) REVERT: E 326 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5637 (ptmm) REVERT: F 12 ASN cc_start: 0.7886 (m110) cc_final: 0.7566 (m110) REVERT: F 47 MET cc_start: 0.6726 (mmm) cc_final: 0.6338 (mmp) REVERT: F 206 ARG cc_start: 0.7488 (ttm170) cc_final: 0.6688 (ttp80) REVERT: F 269 MET cc_start: 0.8846 (mtp) cc_final: 0.8547 (mtm) REVERT: G 717 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6527 (ttmt) REVERT: G 719 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7353 (mtm) REVERT: G 816 MET cc_start: 0.7436 (tpt) cc_final: 0.7187 (tpt) REVERT: G 834 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6838 (tptt) REVERT: H 715 LEU cc_start: 0.7340 (tp) cc_final: 0.7116 (tt) REVERT: I 826 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.7010 (mmm) REVERT: K 721 MET cc_start: 0.6388 (mmp) cc_final: 0.5343 (ptt) REVERT: L 744 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7636 (m) REVERT: L 795 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6486 (tmtt) REVERT: Z 719 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7695 (mtp) REVERT: Z 792 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7797 (mt) outliers start: 103 outliers final: 12 residues processed: 481 average time/residue: 0.7695 time to fit residues: 415.0290 Evaluate side-chains 321 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 299 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 717 LYS Chi-restraints excluded: chain G residue 719 MET Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 834 LYS Chi-restraints excluded: chain I residue 792 ILE Chi-restraints excluded: chain I residue 826 MET Chi-restraints excluded: chain L residue 744 SER Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 719 MET Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain Z residue 792 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 314 GLN D 353 GLN E 92 ASN I 824 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102727 restraints weight = 25794.072| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.46 r_work: 0.2818 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25020 Z= 0.181 Angle : 0.622 7.836 33840 Z= 0.317 Chirality : 0.044 0.173 3834 Planarity : 0.005 0.043 4290 Dihedral : 10.599 145.562 3516 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.64 % Allowed : 9.99 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.15), residues: 3102 helix: 1.08 (0.12), residues: 1602 sheet: 0.15 (0.24), residues: 402 loop : 0.23 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 210 TYR 0.011 0.001 TYR C 188 PHE 0.011 0.001 PHE G 729 TRP 0.011 0.002 TRP D 340 HIS 0.008 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00409 (25020) covalent geometry : angle 0.62158 (33840) hydrogen bonds : bond 0.05212 ( 1458) hydrogen bonds : angle 4.89187 ( 4068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 326 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7972 (mm110) cc_final: 0.7085 (mm110) REVERT: A 314 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8617 (tt0) REVERT: A 325 MET cc_start: 0.8526 (mmp) cc_final: 0.7888 (mmp) REVERT: A 326 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6520 (tppp) REVERT: A 364 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: B 57 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8176 (tp30) REVERT: B 211 ASP cc_start: 0.8646 (t0) cc_final: 0.8444 (t70) REVERT: B 225 ASN cc_start: 0.8330 (m110) cc_final: 0.8111 (m110) REVERT: B 229 THR cc_start: 0.8260 (m) cc_final: 0.8022 (m) REVERT: B 252 ASN cc_start: 0.8777 (p0) cc_final: 0.8553 (p0) REVERT: B 328 LYS cc_start: 0.8546 (mttt) cc_final: 0.8067 (tttp) REVERT: B 372 ARG cc_start: 0.8259 (ptp90) cc_final: 0.8007 (ptt-90) REVERT: C 72 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: C 206 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7859 (ttp-110) REVERT: C 246 GLN cc_start: 0.8967 (mt0) cc_final: 0.8686 (mt0) REVERT: C 328 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8334 (tttp) REVERT: C 372 ARG cc_start: 0.8653 (ptp-170) cc_final: 0.8235 (ptt180) REVERT: D 57 GLU cc_start: 0.7803 (tt0) cc_final: 0.7509 (mm-30) REVERT: D 121 GLN cc_start: 0.8758 (tt0) cc_final: 0.8486 (tt0) REVERT: D 305 MET cc_start: 0.9201 (mmm) cc_final: 0.8861 (mmm) REVERT: D 325 MET cc_start: 0.8832 (mmp) cc_final: 0.8482 (mmp) REVERT: D 326 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7277 (mmmt) REVERT: D 328 LYS cc_start: 0.8571 (tttp) cc_final: 0.8220 (tmtt) REVERT: E 84 LYS cc_start: 0.8475 (mttp) cc_final: 0.8080 (mtpm) REVERT: E 314 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: E 326 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7082 (tmtt) REVERT: E 328 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7755 (mtpp) REVERT: E 355 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7919 (mtt) REVERT: F 47 MET cc_start: 0.6988 (mmm) cc_final: 0.6607 (mmp) REVERT: F 125 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7549 (mt-10) REVERT: F 206 ARG cc_start: 0.7560 (ttm170) cc_final: 0.6952 (ttp80) REVERT: F 269 MET cc_start: 0.9176 (mtp) cc_final: 0.8830 (mtm) REVERT: G 723 MET cc_start: 0.6105 (tmm) cc_final: 0.5814 (tpp) REVERT: G 816 MET cc_start: 0.7554 (tpt) cc_final: 0.6814 (tpt) REVERT: H 715 LEU cc_start: 0.6352 (tp) cc_final: 0.5930 (tp) REVERT: H 719 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6516 (mtp) REVERT: H 756 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.6788 (tpp) REVERT: I 826 MET cc_start: 0.6768 (tpt) cc_final: 0.6427 (mmm) REVERT: K 721 MET cc_start: 0.6097 (mmp) cc_final: 0.4976 (ptt) REVERT: L 773 LYS cc_start: 0.5377 (ptmt) cc_final: 0.4907 (ptpp) REVERT: L 795 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5334 (tmtt) REVERT: Z 721 MET cc_start: 0.5971 (tpp) cc_final: 0.5751 (tpt) REVERT: Z 792 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6938 (mt) outliers start: 70 outliers final: 17 residues processed: 367 average time/residue: 0.7789 time to fit residues: 321.3198 Evaluate side-chains 320 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain H residue 719 MET Chi-restraints excluded: chain H residue 756 MET Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 792 ILE Chi-restraints excluded: chain Z residue 840 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 268 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 213 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 174 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 263 GLN B 296 ASN C 92 ASN D 225 ASN D 354 GLN E 162 ASN I 824 ASN L 718 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.152143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.103931 restraints weight = 25672.035| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.43 r_work: 0.2829 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25020 Z= 0.142 Angle : 0.561 8.543 33840 Z= 0.282 Chirality : 0.042 0.177 3834 Planarity : 0.004 0.042 4290 Dihedral : 10.069 156.878 3487 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.41 % Allowed : 11.43 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.15), residues: 3102 helix: 1.36 (0.13), residues: 1644 sheet: 0.35 (0.25), residues: 402 loop : 0.48 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 28 TYR 0.008 0.001 TYR C 188 PHE 0.009 0.001 PHE L 729 TRP 0.010 0.002 TRP C 340 HIS 0.006 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00316 (25020) covalent geometry : angle 0.56112 (33840) hydrogen bonds : bond 0.04552 ( 1458) hydrogen bonds : angle 4.57265 ( 4068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 306 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8002 (mm110) cc_final: 0.7084 (mm110) REVERT: A 57 GLU cc_start: 0.8158 (tp30) cc_final: 0.7873 (tt0) REVERT: A 206 ARG cc_start: 0.8493 (ttm110) cc_final: 0.8091 (ttp-170) REVERT: A 314 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8612 (tt0) REVERT: A 364 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: B 57 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8110 (tp30) REVERT: B 225 ASN cc_start: 0.8364 (m110) cc_final: 0.8105 (m110) REVERT: B 229 THR cc_start: 0.8287 (m) cc_final: 0.8056 (m) REVERT: B 252 ASN cc_start: 0.8654 (p0) cc_final: 0.8446 (p0) REVERT: B 299 MET cc_start: 0.9051 (mtm) cc_final: 0.8806 (mtm) REVERT: B 328 LYS cc_start: 0.8539 (mttt) cc_final: 0.7951 (tptp) REVERT: B 372 ARG cc_start: 0.8304 (ptp90) cc_final: 0.7991 (ptt-90) REVERT: C 12 ASN cc_start: 0.8373 (m110) cc_final: 0.8055 (m-40) REVERT: C 72 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: C 83 GLU cc_start: 0.8351 (tt0) cc_final: 0.8138 (mt-10) REVERT: C 206 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7841 (ttp-110) REVERT: C 246 GLN cc_start: 0.8940 (mt0) cc_final: 0.8677 (mt0) REVERT: C 328 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8307 (tttp) REVERT: C 372 ARG cc_start: 0.8669 (ptp-170) cc_final: 0.8206 (ptt180) REVERT: D 57 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7542 (mm-30) REVERT: D 121 GLN cc_start: 0.8701 (tt0) cc_final: 0.8448 (tm-30) REVERT: D 305 MET cc_start: 0.9171 (mmm) cc_final: 0.8841 (mmm) REVERT: D 314 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8762 (tp40) REVERT: D 325 MET cc_start: 0.8881 (mmp) cc_final: 0.8536 (mmp) REVERT: D 328 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8304 (tmtt) REVERT: E 84 LYS cc_start: 0.8432 (mttp) cc_final: 0.8153 (mtpm) REVERT: E 107 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: E 314 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8685 (tt0) REVERT: F 11 ASP cc_start: 0.8388 (t0) cc_final: 0.8167 (t70) REVERT: F 47 MET cc_start: 0.7057 (mmm) cc_final: 0.6634 (mmp) REVERT: F 206 ARG cc_start: 0.7485 (ttm170) cc_final: 0.6942 (ttp80) REVERT: F 269 MET cc_start: 0.9191 (mtp) cc_final: 0.8935 (mtm) REVERT: F 328 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8542 (tttm) REVERT: G 816 MET cc_start: 0.7594 (tpt) cc_final: 0.6888 (tpt) REVERT: H 756 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7956 (tpt) REVERT: I 826 MET cc_start: 0.6734 (tpt) cc_final: 0.6481 (mmm) REVERT: K 721 MET cc_start: 0.5823 (mmt) cc_final: 0.5154 (ptt) REVERT: L 795 LYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5320 (tmtt) outliers start: 64 outliers final: 17 residues processed: 340 average time/residue: 0.8394 time to fit residues: 319.7193 Evaluate side-chains 318 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain G residue 724 MET Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain H residue 756 MET Chi-restraints excluded: chain H residue 816 MET Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 190 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 310 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 296 ASN D 225 ASN F 162 ASN G 718 GLN I 824 ASN Z 718 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.150121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.101284 restraints weight = 25713.812| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.49 r_work: 0.2805 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25020 Z= 0.221 Angle : 0.608 9.910 33840 Z= 0.305 Chirality : 0.045 0.169 3834 Planarity : 0.005 0.044 4290 Dihedral : 10.036 157.740 3471 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.53 % Allowed : 11.54 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.15), residues: 3102 helix: 1.33 (0.13), residues: 1650 sheet: 0.38 (0.25), residues: 402 loop : 0.49 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 28 TYR 0.011 0.001 TYR E 133 PHE 0.010 0.002 PHE G 729 TRP 0.013 0.002 TRP B 340 HIS 0.008 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00528 (25020) covalent geometry : angle 0.60832 (33840) hydrogen bonds : bond 0.04750 ( 1458) hydrogen bonds : angle 4.62388 ( 4068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 293 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7986 (mm110) cc_final: 0.7037 (mm110) REVERT: A 57 GLU cc_start: 0.8191 (tp30) cc_final: 0.7862 (tt0) REVERT: A 364 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: B 72 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7606 (tp30) REVERT: B 225 ASN cc_start: 0.8414 (m110) cc_final: 0.8129 (m110) REVERT: B 252 ASN cc_start: 0.8900 (p0) cc_final: 0.8646 (p0) REVERT: B 305 MET cc_start: 0.9199 (mmm) cc_final: 0.8848 (mmm) REVERT: B 355 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8611 (mtm) REVERT: B 372 ARG cc_start: 0.8294 (ptp90) cc_final: 0.7998 (ptt-90) REVERT: C 72 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: C 83 GLU cc_start: 0.8441 (tt0) cc_final: 0.8240 (mt-10) REVERT: C 206 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7925 (ttp-110) REVERT: C 241 GLU cc_start: 0.8909 (tt0) cc_final: 0.8680 (tt0) REVERT: C 246 GLN cc_start: 0.8944 (mt0) cc_final: 0.8643 (mt0) REVERT: C 328 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8351 (tttp) REVERT: C 372 ARG cc_start: 0.8710 (ptp-170) cc_final: 0.8184 (ptt180) REVERT: D 57 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: D 121 GLN cc_start: 0.8775 (tt0) cc_final: 0.8506 (tt0) REVERT: D 284 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8856 (mttp) REVERT: D 305 MET cc_start: 0.9200 (mmm) cc_final: 0.8836 (mmm) REVERT: D 325 MET cc_start: 0.8907 (mmp) cc_final: 0.8357 (mmp) REVERT: D 328 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8330 (tmtt) REVERT: E 84 LYS cc_start: 0.8494 (mttp) cc_final: 0.8205 (mtpm) REVERT: E 107 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: E 314 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: F 47 MET cc_start: 0.7096 (mmm) cc_final: 0.6702 (mmp) REVERT: F 206 ARG cc_start: 0.7594 (ttm170) cc_final: 0.7025 (ttp-170) REVERT: F 269 MET cc_start: 0.9191 (mtp) cc_final: 0.8911 (mtm) REVERT: F 314 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: G 723 MET cc_start: 0.6764 (tmm) cc_final: 0.6301 (tpt) REVERT: G 816 MET cc_start: 0.7562 (tpt) cc_final: 0.6792 (tpt) REVERT: H 845 LYS cc_start: 0.5359 (OUTLIER) cc_final: 0.5122 (ptpp) REVERT: K 721 MET cc_start: 0.5934 (mmt) cc_final: 0.5162 (ptt) REVERT: K 845 LYS cc_start: 0.4851 (OUTLIER) cc_final: 0.4649 (pttm) REVERT: L 795 LYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5367 (tmtt) REVERT: Z 845 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5582 (pmmt) outliers start: 67 outliers final: 23 residues processed: 335 average time/residue: 0.8376 time to fit residues: 313.5262 Evaluate side-chains 323 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 724 MET Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain H residue 845 LYS Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain K residue 845 LYS Chi-restraints excluded: chain L residue 721 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 845 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 124 optimal weight: 0.5980 chunk 189 optimal weight: 9.9990 chunk 174 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 282 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 106 optimal weight: 0.0060 chunk 80 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 162 ASN B 296 ASN C 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.152375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.104110 restraints weight = 25661.340| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.44 r_work: 0.2851 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 25020 Z= 0.110 Angle : 0.539 8.887 33840 Z= 0.268 Chirality : 0.041 0.163 3834 Planarity : 0.004 0.042 4290 Dihedral : 9.863 161.309 3471 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.34 % Allowed : 12.82 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.15), residues: 3102 helix: 1.60 (0.13), residues: 1650 sheet: 0.43 (0.26), residues: 390 loop : 0.65 (0.21), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 28 TYR 0.008 0.001 TYR E 294 PHE 0.007 0.001 PHE G 729 TRP 0.010 0.001 TRP C 340 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00231 (25020) covalent geometry : angle 0.53933 (33840) hydrogen bonds : bond 0.04144 ( 1458) hydrogen bonds : angle 4.43433 ( 4068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 305 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7895 (mm110) cc_final: 0.6953 (mm110) REVERT: A 57 GLU cc_start: 0.8167 (tp30) cc_final: 0.7824 (tt0) REVERT: A 314 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: A 364 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: B 225 ASN cc_start: 0.8384 (m110) cc_final: 0.8020 (m110) REVERT: B 229 THR cc_start: 0.8163 (m) cc_final: 0.7947 (m) REVERT: B 252 ASN cc_start: 0.8677 (p0) cc_final: 0.8430 (p0) REVERT: B 372 ARG cc_start: 0.8271 (ptp90) cc_final: 0.7941 (ptt-90) REVERT: C 72 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: C 206 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7872 (ttp-110) REVERT: C 241 GLU cc_start: 0.8794 (tt0) cc_final: 0.8541 (tt0) REVERT: C 246 GLN cc_start: 0.8877 (mt0) cc_final: 0.8577 (mt0) REVERT: C 328 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8411 (tttp) REVERT: C 372 ARG cc_start: 0.8740 (ptp-170) cc_final: 0.8232 (ptt180) REVERT: D 57 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: D 121 GLN cc_start: 0.8686 (tt0) cc_final: 0.8364 (tt0) REVERT: D 305 MET cc_start: 0.9163 (mmm) cc_final: 0.8780 (mmm) REVERT: D 314 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8539 (tp40) REVERT: D 325 MET cc_start: 0.8861 (mmp) cc_final: 0.8351 (mmp) REVERT: D 328 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8334 (tmtt) REVERT: E 84 LYS cc_start: 0.8478 (mttp) cc_final: 0.8194 (mtpm) REVERT: E 314 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8662 (tt0) REVERT: E 328 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7777 (mtpp) REVERT: E 364 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: F 11 ASP cc_start: 0.8271 (t0) cc_final: 0.8017 (t70) REVERT: F 47 MET cc_start: 0.7221 (mmm) cc_final: 0.6874 (mmp) REVERT: F 206 ARG cc_start: 0.7557 (ttm170) cc_final: 0.6969 (ttp-170) REVERT: F 269 MET cc_start: 0.9169 (mtp) cc_final: 0.8882 (mtm) REVERT: G 723 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6275 (tpt) REVERT: G 816 MET cc_start: 0.7394 (tpt) cc_final: 0.6697 (tpt) REVERT: G 845 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5785 (pptt) REVERT: I 816 MET cc_start: 0.6279 (OUTLIER) cc_final: 0.5592 (tmm) REVERT: K 721 MET cc_start: 0.5773 (mmt) cc_final: 0.5140 (ptt) REVERT: L 776 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6715 (tt) REVERT: L 795 LYS cc_start: 0.5974 (OUTLIER) cc_final: 0.5366 (tmtt) REVERT: L 834 LYS cc_start: 0.6859 (tppt) cc_final: 0.6003 (ttmm) REVERT: L 862 LYS cc_start: 0.5044 (mppt) cc_final: 0.4659 (tptt) REVERT: Z 845 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5611 (pmmt) outliers start: 62 outliers final: 22 residues processed: 338 average time/residue: 0.7766 time to fit residues: 294.8610 Evaluate side-chains 327 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 288 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 723 MET Chi-restraints excluded: chain G residue 845 LYS Chi-restraints excluded: chain H residue 724 MET Chi-restraints excluded: chain I residue 816 MET Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 721 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 845 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 297 optimal weight: 0.9990 chunk 228 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 296 ASN C 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.150946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.102375 restraints weight = 25706.450| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.54 r_work: 0.2840 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25020 Z= 0.172 Angle : 0.570 9.393 33840 Z= 0.283 Chirality : 0.043 0.175 3834 Planarity : 0.004 0.042 4290 Dihedral : 9.861 159.285 3469 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.53 % Allowed : 13.27 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.15), residues: 3102 helix: 1.58 (0.13), residues: 1650 sheet: 0.43 (0.26), residues: 390 loop : 0.65 (0.21), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 28 TYR 0.009 0.001 TYR L 837 PHE 0.009 0.001 PHE C 31 TRP 0.011 0.002 TRP B 340 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00404 (25020) covalent geometry : angle 0.57026 (33840) hydrogen bonds : bond 0.04321 ( 1458) hydrogen bonds : angle 4.46294 ( 4068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 299 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7905 (mm110) cc_final: 0.6960 (mm110) REVERT: A 57 GLU cc_start: 0.8155 (tp30) cc_final: 0.7863 (tt0) REVERT: A 364 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: B 57 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8060 (mt-10) REVERT: B 225 ASN cc_start: 0.8433 (m110) cc_final: 0.8085 (m110) REVERT: B 252 ASN cc_start: 0.8857 (p0) cc_final: 0.8586 (p0) REVERT: B 355 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8607 (mtm) REVERT: B 372 ARG cc_start: 0.8290 (ptp90) cc_final: 0.7973 (ptt-90) REVERT: C 72 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: C 206 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7924 (ttp-110) REVERT: C 246 GLN cc_start: 0.8888 (mt0) cc_final: 0.8640 (mt0) REVERT: D 57 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: D 121 GLN cc_start: 0.8683 (tt0) cc_final: 0.8426 (tt0) REVERT: D 305 MET cc_start: 0.9190 (mmm) cc_final: 0.8824 (mmm) REVERT: D 314 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8543 (tp40) REVERT: D 325 MET cc_start: 0.8873 (mmp) cc_final: 0.8524 (mmp) REVERT: D 328 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8372 (tmtt) REVERT: E 84 LYS cc_start: 0.8512 (mttp) cc_final: 0.8240 (mtpm) REVERT: E 107 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: E 314 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8683 (tt0) REVERT: E 328 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.7875 (mtpp) REVERT: E 364 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: F 11 ASP cc_start: 0.8580 (t0) cc_final: 0.8348 (t70) REVERT: F 47 MET cc_start: 0.7230 (mmm) cc_final: 0.6936 (mmp) REVERT: F 206 ARG cc_start: 0.7574 (ttm170) cc_final: 0.6991 (ttp-170) REVERT: F 269 MET cc_start: 0.9170 (mtp) cc_final: 0.8872 (mtm) REVERT: G 723 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6283 (tpt) REVERT: G 816 MET cc_start: 0.7579 (tpt) cc_final: 0.6773 (tpt) REVERT: G 845 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5827 (pptt) REVERT: K 721 MET cc_start: 0.5777 (mmt) cc_final: 0.5145 (ptt) REVERT: K 792 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6482 (mm) REVERT: L 776 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6533 (tt) REVERT: L 795 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5364 (tmtt) REVERT: L 834 LYS cc_start: 0.6832 (tppt) cc_final: 0.5963 (ttmm) REVERT: L 862 LYS cc_start: 0.4990 (mppt) cc_final: 0.4715 (tptt) REVERT: Z 845 LYS cc_start: 0.5905 (OUTLIER) cc_final: 0.5618 (pmmt) REVERT: Z 849 MET cc_start: 0.4599 (mmt) cc_final: 0.4343 (mmt) outliers start: 67 outliers final: 25 residues processed: 340 average time/residue: 0.7373 time to fit residues: 282.4468 Evaluate side-chains 334 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 723 MET Chi-restraints excluded: chain G residue 845 LYS Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 756 MET Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 792 ILE Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 721 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 845 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 38 optimal weight: 0.6980 chunk 252 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 287 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 217 optimal weight: 0.6980 chunk 270 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 296 ASN C 12 ASN E 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.101911 restraints weight = 25755.764| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.59 r_work: 0.2799 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25020 Z= 0.180 Angle : 0.581 11.452 33840 Z= 0.287 Chirality : 0.043 0.178 3834 Planarity : 0.004 0.042 4290 Dihedral : 9.891 162.409 3469 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.45 % Allowed : 13.69 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.15), residues: 3102 helix: 1.55 (0.13), residues: 1656 sheet: 0.57 (0.26), residues: 384 loop : 0.70 (0.21), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 206 TYR 0.009 0.001 TYR L 837 PHE 0.009 0.001 PHE C 31 TRP 0.012 0.002 TRP B 340 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00425 (25020) covalent geometry : angle 0.58110 (33840) hydrogen bonds : bond 0.04335 ( 1458) hydrogen bonds : angle 4.47947 ( 4068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7760 (mm110) cc_final: 0.6830 (mm110) REVERT: A 57 GLU cc_start: 0.8236 (tp30) cc_final: 0.7981 (tt0) REVERT: A 364 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: B 57 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8026 (mt-10) REVERT: B 72 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: B 225 ASN cc_start: 0.8435 (m110) cc_final: 0.8069 (m110) REVERT: B 252 ASN cc_start: 0.8844 (p0) cc_final: 0.8555 (p0) REVERT: B 328 LYS cc_start: 0.8496 (mttt) cc_final: 0.7912 (tptp) REVERT: B 355 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8606 (mtm) REVERT: B 372 ARG cc_start: 0.8308 (ptp90) cc_final: 0.7987 (ptt-90) REVERT: C 72 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: C 206 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7933 (ttp-110) REVERT: C 246 GLN cc_start: 0.8882 (mt0) cc_final: 0.8539 (mt0) REVERT: D 57 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: D 121 GLN cc_start: 0.8688 (tt0) cc_final: 0.8419 (tt0) REVERT: D 305 MET cc_start: 0.9201 (mmm) cc_final: 0.8825 (mmm) REVERT: D 314 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8575 (tp40) REVERT: D 325 MET cc_start: 0.8834 (mmp) cc_final: 0.8471 (mmp) REVERT: D 328 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8273 (tmtt) REVERT: E 84 LYS cc_start: 0.8545 (mttp) cc_final: 0.8218 (mtpm) REVERT: E 95 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7739 (mtp180) REVERT: E 107 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: E 314 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: E 328 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7845 (mtpp) REVERT: F 11 ASP cc_start: 0.8585 (t0) cc_final: 0.8329 (t70) REVERT: F 47 MET cc_start: 0.7175 (mmm) cc_final: 0.6881 (mmp) REVERT: F 206 ARG cc_start: 0.7592 (ttm170) cc_final: 0.7004 (ttp-170) REVERT: F 269 MET cc_start: 0.9183 (mtp) cc_final: 0.8896 (mtm) REVERT: F 364 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: G 723 MET cc_start: 0.6738 (tmm) cc_final: 0.6329 (tpt) REVERT: G 816 MET cc_start: 0.7508 (tpt) cc_final: 0.6768 (tpt) REVERT: G 836 SER cc_start: 0.7543 (m) cc_final: 0.7339 (p) REVERT: G 845 LYS cc_start: 0.6145 (OUTLIER) cc_final: 0.5885 (pptt) REVERT: K 712 ILE cc_start: 0.5989 (OUTLIER) cc_final: 0.5694 (pt) REVERT: K 721 MET cc_start: 0.5787 (mmt) cc_final: 0.5153 (ptt) REVERT: K 792 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6502 (mm) REVERT: L 776 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6657 (tt) REVERT: L 795 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5375 (tmtt) REVERT: L 862 LYS cc_start: 0.5081 (mppt) cc_final: 0.4435 (tmtt) REVERT: Z 845 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5719 (pmmt) REVERT: Z 849 MET cc_start: 0.4665 (mmt) cc_final: 0.4382 (mmt) outliers start: 65 outliers final: 23 residues processed: 345 average time/residue: 0.7674 time to fit residues: 298.4200 Evaluate side-chains 338 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 296 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 845 LYS Chi-restraints excluded: chain H residue 724 MET Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 792 ILE Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 845 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 287 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 176 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.103389 restraints weight = 25945.341| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.59 r_work: 0.2842 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25020 Z= 0.135 Angle : 0.553 10.948 33840 Z= 0.271 Chirality : 0.042 0.200 3834 Planarity : 0.004 0.042 4290 Dihedral : 9.816 167.653 3469 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.96 % Allowed : 14.74 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.15), residues: 3102 helix: 1.69 (0.13), residues: 1656 sheet: 0.50 (0.27), residues: 378 loop : 0.79 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 206 TYR 0.008 0.001 TYR E 294 PHE 0.008 0.001 PHE C 31 TRP 0.011 0.001 TRP C 340 HIS 0.005 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00307 (25020) covalent geometry : angle 0.55302 (33840) hydrogen bonds : bond 0.04040 ( 1458) hydrogen bonds : angle 4.38752 ( 4068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7645 (mm110) cc_final: 0.6752 (mm110) REVERT: A 57 GLU cc_start: 0.8253 (tp30) cc_final: 0.8006 (tt0) REVERT: A 364 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: B 57 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8018 (mt-10) REVERT: B 225 ASN cc_start: 0.8375 (m110) cc_final: 0.7971 (m110) REVERT: B 229 THR cc_start: 0.8214 (m) cc_final: 0.7982 (m) REVERT: B 252 ASN cc_start: 0.8739 (p0) cc_final: 0.8443 (p0) REVERT: B 328 LYS cc_start: 0.8451 (mttt) cc_final: 0.7848 (tptp) REVERT: B 372 ARG cc_start: 0.8297 (ptp90) cc_final: 0.7974 (ptt-90) REVERT: C 72 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: C 206 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7887 (ttp-110) REVERT: C 246 GLN cc_start: 0.8880 (mt0) cc_final: 0.8510 (mt0) REVERT: D 57 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: D 121 GLN cc_start: 0.8633 (tt0) cc_final: 0.8389 (tt0) REVERT: D 305 MET cc_start: 0.9175 (mmm) cc_final: 0.8791 (mmm) REVERT: D 314 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8571 (tp40) REVERT: D 325 MET cc_start: 0.8825 (mmp) cc_final: 0.8478 (mmp) REVERT: D 328 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8316 (tmtt) REVERT: E 84 LYS cc_start: 0.8543 (mttp) cc_final: 0.8219 (mtpm) REVERT: E 107 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: E 314 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8643 (tt0) REVERT: E 328 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.7868 (mtpp) REVERT: E 364 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: F 11 ASP cc_start: 0.8571 (t0) cc_final: 0.8293 (t70) REVERT: F 47 MET cc_start: 0.7181 (mmm) cc_final: 0.6890 (mmp) REVERT: F 206 ARG cc_start: 0.7571 (ttm170) cc_final: 0.6985 (ttp-170) REVERT: F 269 MET cc_start: 0.9142 (mtp) cc_final: 0.8915 (mtm) REVERT: F 364 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: G 723 MET cc_start: 0.6717 (tmm) cc_final: 0.6309 (tpt) REVERT: G 816 MET cc_start: 0.7508 (tpt) cc_final: 0.6791 (tpt) REVERT: G 836 SER cc_start: 0.7546 (m) cc_final: 0.7335 (p) REVERT: K 712 ILE cc_start: 0.5953 (OUTLIER) cc_final: 0.5676 (pt) REVERT: K 721 MET cc_start: 0.5728 (mmt) cc_final: 0.5159 (ptt) REVERT: L 776 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6299 (tt) REVERT: L 795 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5413 (tmtt) REVERT: L 834 LYS cc_start: 0.6804 (tppt) cc_final: 0.5932 (ttmm) REVERT: L 862 LYS cc_start: 0.5055 (mppt) cc_final: 0.4830 (tmtt) REVERT: Z 845 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5668 (pmmt) outliers start: 52 outliers final: 21 residues processed: 334 average time/residue: 0.7415 time to fit residues: 278.9296 Evaluate side-chains 331 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 295 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 845 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 192 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 201 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 chunk 276 optimal weight: 20.0000 chunk 32 optimal weight: 0.4980 chunk 262 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.153180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.106206 restraints weight = 25801.361| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.41 r_work: 0.2870 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25020 Z= 0.117 Angle : 0.540 11.380 33840 Z= 0.264 Chirality : 0.041 0.206 3834 Planarity : 0.004 0.040 4290 Dihedral : 9.765 179.617 3469 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.85 % Allowed : 14.71 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.16), residues: 3102 helix: 1.80 (0.13), residues: 1656 sheet: 0.55 (0.27), residues: 378 loop : 0.86 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 28 TYR 0.008 0.001 TYR D 143 PHE 0.008 0.001 PHE B 31 TRP 0.010 0.001 TRP C 340 HIS 0.005 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00259 (25020) covalent geometry : angle 0.54025 (33840) hydrogen bonds : bond 0.03860 ( 1458) hydrogen bonds : angle 4.31873 ( 4068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 311 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7677 (mm110) cc_final: 0.6801 (mm110) REVERT: A 57 GLU cc_start: 0.8228 (tp30) cc_final: 0.8010 (tt0) REVERT: A 314 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: A 364 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: B 57 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8098 (mt-10) REVERT: B 72 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7545 (tp30) REVERT: B 225 ASN cc_start: 0.8370 (m110) cc_final: 0.7971 (m110) REVERT: B 229 THR cc_start: 0.8180 (m) cc_final: 0.7964 (m) REVERT: B 328 LYS cc_start: 0.8422 (mttt) cc_final: 0.7837 (tptp) REVERT: B 372 ARG cc_start: 0.8239 (ptp90) cc_final: 0.7918 (ptt-90) REVERT: C 72 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7480 (mm-30) REVERT: C 206 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7878 (ttp-110) REVERT: C 246 GLN cc_start: 0.8848 (mt0) cc_final: 0.8455 (mt0) REVERT: D 121 GLN cc_start: 0.8623 (tt0) cc_final: 0.8358 (tm-30) REVERT: D 305 MET cc_start: 0.9153 (mmm) cc_final: 0.8780 (mmm) REVERT: D 314 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8577 (tp40) REVERT: D 325 MET cc_start: 0.8763 (mmp) cc_final: 0.8392 (mmp) REVERT: D 328 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8335 (tmtt) REVERT: E 84 LYS cc_start: 0.8494 (mttp) cc_final: 0.8222 (mtpm) REVERT: E 107 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8510 (tt0) REVERT: E 314 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: E 364 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: F 11 ASP cc_start: 0.8445 (t0) cc_final: 0.8179 (t70) REVERT: F 47 MET cc_start: 0.7163 (mmm) cc_final: 0.6881 (mmp) REVERT: F 206 ARG cc_start: 0.7510 (ttm170) cc_final: 0.6935 (ttp-170) REVERT: F 364 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: G 723 MET cc_start: 0.6698 (tmm) cc_final: 0.6314 (tpt) REVERT: G 816 MET cc_start: 0.7506 (tpt) cc_final: 0.6779 (tpt) REVERT: H 723 MET cc_start: 0.6407 (tpt) cc_final: 0.5961 (tpt) REVERT: I 724 MET cc_start: 0.6416 (tpp) cc_final: 0.6125 (tpt) REVERT: K 712 ILE cc_start: 0.5967 (OUTLIER) cc_final: 0.5678 (pt) REVERT: K 721 MET cc_start: 0.5691 (mmt) cc_final: 0.5164 (ptt) REVERT: L 795 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.5414 (tmtt) REVERT: L 814 SER cc_start: 0.5389 (p) cc_final: 0.5174 (m) REVERT: Z 845 LYS cc_start: 0.5961 (OUTLIER) cc_final: 0.5631 (pmmt) outliers start: 49 outliers final: 21 residues processed: 341 average time/residue: 0.7200 time to fit residues: 277.5767 Evaluate side-chains 336 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 301 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 845 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 93 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 295 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 201 optimal weight: 0.0570 chunk 123 optimal weight: 0.9990 chunk 293 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.106047 restraints weight = 25651.451| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.41 r_work: 0.2913 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25020 Z= 0.113 Angle : 0.543 11.680 33840 Z= 0.264 Chirality : 0.041 0.205 3834 Planarity : 0.004 0.041 4290 Dihedral : 9.621 172.477 3469 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.66 % Allowed : 15.20 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.16), residues: 3102 helix: 1.86 (0.13), residues: 1656 sheet: 0.59 (0.27), residues: 378 loop : 0.92 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 206 TYR 0.008 0.001 TYR B 69 PHE 0.008 0.001 PHE E 127 TRP 0.010 0.001 TRP C 340 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00251 (25020) covalent geometry : angle 0.54303 (33840) hydrogen bonds : bond 0.03779 ( 1458) hydrogen bonds : angle 4.28487 ( 4068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 312 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7698 (mm110) cc_final: 0.6873 (mm110) REVERT: A 57 GLU cc_start: 0.8226 (tp30) cc_final: 0.8025 (tt0) REVERT: A 224 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7357 (mp0) REVERT: A 314 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: A 364 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: B 57 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8132 (mt-10) REVERT: B 72 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7518 (tp30) REVERT: B 225 ASN cc_start: 0.8350 (m110) cc_final: 0.7944 (m110) REVERT: B 328 LYS cc_start: 0.8480 (mttt) cc_final: 0.7926 (tptp) REVERT: B 372 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7912 (ptt-90) REVERT: C 72 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: C 206 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7829 (ttp-110) REVERT: C 246 GLN cc_start: 0.8842 (mt0) cc_final: 0.8458 (mt0) REVERT: D 57 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7745 (mt-10) REVERT: D 121 GLN cc_start: 0.8636 (tt0) cc_final: 0.8386 (tm-30) REVERT: D 305 MET cc_start: 0.9154 (mmm) cc_final: 0.8780 (mmm) REVERT: D 314 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8586 (tp40) REVERT: D 325 MET cc_start: 0.8742 (mmp) cc_final: 0.8372 (mmp) REVERT: D 326 LYS cc_start: 0.8637 (ttpp) cc_final: 0.7794 (mptt) REVERT: D 328 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8350 (tmtt) REVERT: E 84 LYS cc_start: 0.8519 (mttp) cc_final: 0.8252 (mtpm) REVERT: E 107 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: E 314 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8486 (tm-30) REVERT: F 11 ASP cc_start: 0.8444 (t0) cc_final: 0.8178 (t70) REVERT: F 47 MET cc_start: 0.7226 (mmm) cc_final: 0.6959 (mmp) REVERT: F 199 SER cc_start: 0.8681 (p) cc_final: 0.8443 (t) REVERT: F 206 ARG cc_start: 0.7604 (ttm170) cc_final: 0.7018 (ttp-170) REVERT: G 723 MET cc_start: 0.6594 (tmm) cc_final: 0.6217 (tpt) REVERT: G 816 MET cc_start: 0.7494 (tpt) cc_final: 0.6783 (tpt) REVERT: I 724 MET cc_start: 0.6312 (tpp) cc_final: 0.6008 (tpt) REVERT: K 712 ILE cc_start: 0.5908 (OUTLIER) cc_final: 0.5612 (pt) REVERT: K 721 MET cc_start: 0.5645 (mmt) cc_final: 0.5147 (ptt) REVERT: L 719 MET cc_start: 0.6774 (mtm) cc_final: 0.6517 (mtp) REVERT: L 795 LYS cc_start: 0.5943 (OUTLIER) cc_final: 0.5440 (tmtt) REVERT: Z 717 LYS cc_start: 0.6845 (ttmt) cc_final: 0.6481 (mmtp) REVERT: Z 845 LYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5694 (pmmt) outliers start: 44 outliers final: 23 residues processed: 341 average time/residue: 0.7418 time to fit residues: 285.9846 Evaluate side-chains 329 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 294 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 845 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 115 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 296 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 284 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 162 ASN C 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.152700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.103797 restraints weight = 25726.641| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.51 r_work: 0.2856 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25020 Z= 0.137 Angle : 0.554 13.171 33840 Z= 0.271 Chirality : 0.042 0.203 3834 Planarity : 0.004 0.041 4290 Dihedral : 9.618 174.948 3469 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.58 % Allowed : 15.54 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.16), residues: 3102 helix: 1.82 (0.13), residues: 1656 sheet: 0.55 (0.27), residues: 378 loop : 0.88 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 206 TYR 0.008 0.001 TYR D 143 PHE 0.008 0.001 PHE E 127 TRP 0.010 0.001 TRP C 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00315 (25020) covalent geometry : angle 0.55372 (33840) hydrogen bonds : bond 0.03902 ( 1458) hydrogen bonds : angle 4.32201 ( 4068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9232.16 seconds wall clock time: 158 minutes 5.08 seconds (9485.08 seconds total)