Starting phenix.real_space_refine on Thu Mar 5 00:49:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uxf_26860/03_2026/7uxf_26860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uxf_26860/03_2026/7uxf_26860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uxf_26860/03_2026/7uxf_26860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uxf_26860/03_2026/7uxf_26860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uxf_26860/03_2026/7uxf_26860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uxf_26860/03_2026/7uxf_26860.map" } resolution = 2.7 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= 0.049 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 126 5.16 5 C 11028 2.51 5 N 2958 2.21 5 O 3426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17556 Number of models: 1 Model: "" Number of chains: 18 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: "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: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 3.88, per 1000 atoms: 0.22 Number of scatterers: 17556 At special positions: 0 Unit cell: (89.134, 97.83, 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 126 16.00 P 12 15.00 Mg 6 11.99 O 3426 8.00 N 2958 7.00 C 11028 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: 1.49 Conformation dependent library (CDL) restraints added in 758.3 milliseconds 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 36 sheets defined 52.8% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.639A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.835A 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 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.787A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.262A 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 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.741A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.638A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.834A 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 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.787A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 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 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.740A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.639A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.835A 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 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.786A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 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 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.740A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.638A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.835A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.787A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 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 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.741A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.639A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.835A 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 Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.787A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 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 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.740A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.638A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.835A 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 Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.787A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 301 through 305 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 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.740A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 366 through 368 No H-bonds generated for 'chain 'F' and resid 366 through 368' Processing helix chain 'F' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.696A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.304A 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 removed outlier: 3.799A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.799A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (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 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: 6.697A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.305A 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 removed outlier: 3.795A pdb=" N GLN B 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.795A pdb=" N GLN B 41 " --> pdb=" O ALA D 170 " (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 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: 6.696A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.304A 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 removed outlier: 3.795A pdb=" N GLN C 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.795A pdb=" N GLN C 41 " --> pdb=" O ALA E 170 " (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: 6.696A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.305A 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 removed outlier: 3.799A pdb=" N GLN D 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.799A pdb=" N GLN D 41 " --> pdb=" O ALA F 170 " (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: 6.696A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.305A 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: 6.696A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.304A 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 241 915 hydrogen bonds defined for protein. 2331 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5483 1.33 - 1.46: 3158 1.46 - 1.58: 8993 1.58 - 1.70: 18 1.70 - 1.82: 222 Bond restraints: 17874 Sorted by residual: bond pdb=" N VAL F 159 " pdb=" CA VAL F 159 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.14e-02 7.69e+03 1.44e+01 bond pdb=" N VAL D 159 " pdb=" CA VAL D 159 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.41e+01 bond pdb=" N VAL E 159 " pdb=" CA VAL E 159 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.14e-02 7.69e+03 1.30e+01 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.18e-02 7.18e+03 1.15e+01 ... (remaining 17869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 23379 1.90 - 3.79: 696 3.79 - 5.69: 127 5.69 - 7.58: 49 7.58 - 9.48: 7 Bond angle restraints: 24258 Sorted by residual: angle pdb=" C THR A 303 " pdb=" CA THR A 303 " pdb=" CB THR A 303 " ideal model delta sigma weight residual 109.99 119.47 -9.48 2.09e+00 2.29e-01 2.06e+01 angle pdb=" N ILE D 151 " pdb=" CA ILE D 151 " pdb=" C ILE D 151 " ideal model delta sigma weight residual 107.80 101.81 5.99 1.45e+00 4.76e-01 1.70e+01 angle pdb=" C ILE D 151 " pdb=" N VAL D 152 " pdb=" CA VAL D 152 " ideal model delta sigma weight residual 123.19 118.35 4.84 1.24e+00 6.50e-01 1.52e+01 angle pdb=" N THR A 303 " pdb=" CA THR A 303 " pdb=" C THR A 303 " ideal model delta sigma weight residual 112.89 108.06 4.83 1.24e+00 6.50e-01 1.52e+01 angle pdb=" CA GLY D 150 " pdb=" C GLY D 150 " pdb=" O GLY D 150 " ideal model delta sigma weight residual 121.37 117.70 3.67 1.09e+00 8.42e-01 1.14e+01 ... (remaining 24253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.59: 9920 20.59 - 41.18: 683 41.18 - 61.77: 125 61.77 - 82.36: 24 82.36 - 102.95: 6 Dihedral angle restraints: 10758 sinusoidal: 4344 harmonic: 6414 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 42.95 -102.95 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 42.91 -102.91 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 42.90 -102.90 1 2.00e+01 2.50e-03 2.94e+01 ... (remaining 10755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1939 0.054 - 0.108: 643 0.108 - 0.161: 97 0.161 - 0.215: 13 0.215 - 0.269: 8 Chirality restraints: 2700 Sorted by residual: chirality pdb=" CB VAL F 159 " pdb=" CA VAL F 159 " pdb=" CG1 VAL F 159 " pdb=" CG2 VAL F 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB VAL D 159 " pdb=" CA VAL D 159 " pdb=" CG1 VAL D 159 " pdb=" CG2 VAL D 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL B 159 " pdb=" CA VAL B 159 " pdb=" CG1 VAL B 159 " pdb=" CG2 VAL B 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2697 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 156 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C GLY A 156 " -0.070 2.00e-02 2.50e+03 pdb=" O GLY A 156 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP A 157 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 156 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C GLY F 156 " 0.070 2.00e-02 2.50e+03 pdb=" O GLY F 156 " -0.026 2.00e-02 2.50e+03 pdb=" N ASP F 157 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 156 " 0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C GLY E 156 " -0.068 2.00e-02 2.50e+03 pdb=" O GLY E 156 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP E 157 " 0.024 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 86 2.57 - 3.15: 13646 3.15 - 3.73: 28005 3.73 - 4.32: 42552 4.32 - 4.90: 69765 Nonbonded interactions: 154054 Sorted by model distance: nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.983 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.990 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.997 2.170 nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.015 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.019 2.170 ... (remaining 154049 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.220 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:9.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 17874 Z= 0.350 Angle : 0.805 9.477 24258 Z= 0.442 Chirality : 0.054 0.269 2700 Planarity : 0.006 0.060 3096 Dihedral : 14.773 102.947 6654 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.71 % Allowed : 3.15 % Favored : 95.14 % Cbeta Deviations : 0.05 % 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: 0.24 (0.18), residues: 2190 helix: -0.00 (0.18), residues: 870 sheet: 0.38 (0.24), residues: 414 loop : 0.49 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 372 TYR 0.014 0.001 TYR D 143 PHE 0.006 0.001 PHE E 262 TRP 0.013 0.002 TRP B 340 HIS 0.009 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00771 (17874) covalent geometry : angle 0.80547 (24258) hydrogen bonds : bond 0.18523 ( 899) hydrogen bonds : angle 7.15194 ( 2331) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 0.656 Fit side-chains REVERT: A 299 MET cc_start: 0.8577 (mtm) cc_final: 0.8280 (mtm) REVERT: A 305 MET cc_start: 0.8891 (mmm) cc_final: 0.8659 (mmp) REVERT: B 25 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6920 (p0) REVERT: B 51 ASP cc_start: 0.7822 (p0) cc_final: 0.7584 (p0) REVERT: B 92 ASN cc_start: 0.9011 (m-40) cc_final: 0.8793 (m110) REVERT: B 119 MET cc_start: 0.8154 (mtm) cc_final: 0.7914 (mtp) REVERT: B 123 MET cc_start: 0.8806 (mmt) cc_final: 0.8329 (mmp) REVERT: B 283 MET cc_start: 0.9134 (mmm) cc_final: 0.8865 (mmm) REVERT: C 25 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7391 (p0) REVERT: C 116 ARG cc_start: 0.8393 (ttm170) cc_final: 0.8190 (ttm170) REVERT: C 123 MET cc_start: 0.9002 (mmt) cc_final: 0.8558 (mmt) REVERT: C 359 LYS cc_start: 0.7762 (tptp) cc_final: 0.7490 (tptt) REVERT: D 153 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8468 (tp) REVERT: E 83 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7223 (mt-10) REVERT: E 132 MET cc_start: 0.8395 (ppp) cc_final: 0.8178 (ppp) REVERT: E 325 MET cc_start: 0.8642 (mmp) cc_final: 0.8222 (mmp) REVERT: E 355 MET cc_start: 0.8294 (mtt) cc_final: 0.7980 (mtp) REVERT: F 153 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8794 (tt) outliers start: 32 outliers final: 6 residues processed: 305 average time/residue: 0.7801 time to fit residues: 258.3752 Evaluate side-chains 195 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 246 GLN B 41 GLN B 353 GLN C 41 GLN C 225 ASN C 246 GLN C 353 GLN C 354 GLN D 161 HIS D 225 ASN D 353 GLN E 225 ASN E 314 GLN E 353 GLN E 354 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.088314 restraints weight = 20762.085| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.30 r_work: 0.2852 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17874 Z= 0.139 Angle : 0.606 6.989 24258 Z= 0.300 Chirality : 0.045 0.161 2700 Planarity : 0.005 0.043 3096 Dihedral : 7.521 98.541 2505 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.71 % Allowed : 8.71 % Favored : 89.58 % 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: 0.79 (0.19), residues: 2190 helix: 0.52 (0.18), residues: 894 sheet: 0.37 (0.24), residues: 402 loop : 0.89 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 95 TYR 0.013 0.001 TYR D 143 PHE 0.007 0.001 PHE E 127 TRP 0.010 0.002 TRP C 340 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00310 (17874) covalent geometry : angle 0.60613 (24258) hydrogen bonds : bond 0.04053 ( 899) hydrogen bonds : angle 5.49066 ( 2331) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.626 Fit side-chains REVERT: A 72 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: A 99 GLU cc_start: 0.7862 (mp0) cc_final: 0.7543 (mp0) REVERT: B 25 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7273 (p0) REVERT: B 72 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: B 123 MET cc_start: 0.8758 (mmt) cc_final: 0.8224 (mmm) REVERT: B 237 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8168 (mm-30) REVERT: B 283 MET cc_start: 0.9153 (mmm) cc_final: 0.8933 (mmm) REVERT: C 72 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6827 (tm-30) REVERT: C 123 MET cc_start: 0.8821 (mmt) cc_final: 0.8482 (mmt) REVERT: C 372 ARG cc_start: 0.8318 (ptp90) cc_final: 0.7868 (ptp-170) REVERT: D 72 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: D 314 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: D 326 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7628 (tptp) REVERT: E 72 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: E 123 MET cc_start: 0.8891 (mmp) cc_final: 0.8651 (mmt) REVERT: E 132 MET cc_start: 0.8335 (ppp) cc_final: 0.8085 (ppp) REVERT: E 325 MET cc_start: 0.8972 (mmp) cc_final: 0.8733 (mmm) REVERT: E 355 MET cc_start: 0.8540 (mtt) cc_final: 0.8125 (mtp) REVERT: F 72 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7622 (mt-10) REVERT: F 122 ILE cc_start: 0.8144 (mt) cc_final: 0.7851 (mp) REVERT: F 326 LYS cc_start: 0.8323 (tppt) cc_final: 0.8061 (mptt) REVERT: F 354 GLN cc_start: 0.7919 (mm110) cc_final: 0.7648 (mm110) REVERT: F 364 GLU cc_start: 0.7629 (pp20) cc_final: 0.6984 (pt0) REVERT: F 372 ARG cc_start: 0.8099 (ptp90) cc_final: 0.7871 (ptt-90) outliers start: 32 outliers final: 10 residues processed: 241 average time/residue: 0.7030 time to fit residues: 185.6879 Evaluate side-chains 217 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE 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 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 148 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 41 GLN B 115 ASN B 296 ASN B 353 GLN C 41 GLN C 115 ASN C 225 ASN C 296 ASN D 115 ASN D 225 ASN D 296 ASN E 246 GLN F 115 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.102716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.084488 restraints weight = 21020.879| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.32 r_work: 0.2772 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17874 Z= 0.261 Angle : 0.670 7.887 24258 Z= 0.330 Chirality : 0.050 0.182 2700 Planarity : 0.005 0.041 3096 Dihedral : 7.550 103.970 2497 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.60 % Allowed : 10.47 % Favored : 87.93 % 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: 0.70 (0.18), residues: 2190 helix: 0.48 (0.18), residues: 894 sheet: 0.39 (0.24), residues: 402 loop : 0.76 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 95 TYR 0.016 0.002 TYR C 188 PHE 0.010 0.002 PHE F 127 TRP 0.017 0.002 TRP C 340 HIS 0.004 0.001 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00635 (17874) covalent geometry : angle 0.66965 (24258) hydrogen bonds : bond 0.04528 ( 899) hydrogen bonds : angle 5.38012 ( 2331) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.581 Fit side-chains REVERT: A 99 GLU cc_start: 0.7897 (mp0) cc_final: 0.7668 (mp0) REVERT: B 25 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7377 (p0) REVERT: B 72 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: B 82 MET cc_start: 0.8754 (tpt) cc_final: 0.8524 (tpt) REVERT: B 123 MET cc_start: 0.8753 (mmt) cc_final: 0.8253 (mmm) REVERT: C 72 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: C 123 MET cc_start: 0.8840 (mmt) cc_final: 0.8441 (mmt) REVERT: C 314 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: C 325 MET cc_start: 0.8638 (mmp) cc_final: 0.8367 (mmm) REVERT: D 72 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: D 314 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: D 372 ARG cc_start: 0.8141 (ptp90) cc_final: 0.7836 (ptt-90) REVERT: E 132 MET cc_start: 0.8377 (ppp) cc_final: 0.8101 (ppp) REVERT: E 355 MET cc_start: 0.8561 (mtt) cc_final: 0.8159 (mtp) REVERT: F 47 MET cc_start: 0.6490 (mtm) cc_final: 0.5970 (mtp) REVERT: F 72 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: F 354 GLN cc_start: 0.8115 (mm110) cc_final: 0.7771 (mm110) REVERT: F 364 GLU cc_start: 0.7556 (pp20) cc_final: 0.7156 (pt0) outliers start: 30 outliers final: 17 residues processed: 212 average time/residue: 0.7271 time to fit residues: 168.3757 Evaluate side-chains 216 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE 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 E residue 50 LYS Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 225 ASN E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.088379 restraints weight = 20801.890| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.30 r_work: 0.2845 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17874 Z= 0.124 Angle : 0.564 7.468 24258 Z= 0.275 Chirality : 0.044 0.164 2700 Planarity : 0.004 0.037 3096 Dihedral : 7.037 99.768 2497 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.44 % Allowed : 11.70 % Favored : 86.86 % 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: 0.99 (0.19), residues: 2190 helix: 0.77 (0.18), residues: 900 sheet: 0.58 (0.25), residues: 390 loop : 0.82 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 95 TYR 0.009 0.001 TYR D 143 PHE 0.008 0.001 PHE F 127 TRP 0.010 0.002 TRP E 79 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00284 (17874) covalent geometry : angle 0.56449 (24258) hydrogen bonds : bond 0.03360 ( 899) hydrogen bonds : angle 5.07266 ( 2331) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.642 Fit side-chains REVERT: A 100 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: A 328 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7452 (mtpp) REVERT: A 364 GLU cc_start: 0.8272 (pp20) cc_final: 0.7859 (tm-30) REVERT: B 25 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7343 (p0) REVERT: B 132 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7998 (ptm) REVERT: B 237 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8169 (mm-30) REVERT: B 276 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: C 72 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: C 123 MET cc_start: 0.8836 (mmt) cc_final: 0.8433 (mmt) REVERT: C 372 ARG cc_start: 0.8329 (ptp-170) cc_final: 0.7939 (ptp-170) REVERT: D 72 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: D 153 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8498 (tp) REVERT: D 227 MET cc_start: 0.8296 (mmm) cc_final: 0.7639 (mmm) REVERT: D 314 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: D 372 ARG cc_start: 0.8144 (ptp90) cc_final: 0.7830 (ptt-90) REVERT: E 72 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: E 132 MET cc_start: 0.8283 (ppp) cc_final: 0.7943 (ppp) REVERT: E 283 MET cc_start: 0.9120 (mmm) cc_final: 0.8901 (mmm) REVERT: E 325 MET cc_start: 0.8952 (mmp) cc_final: 0.8541 (mmm) REVERT: E 355 MET cc_start: 0.8562 (mtt) cc_final: 0.8188 (mtp) REVERT: E 364 GLU cc_start: 0.7804 (pp20) cc_final: 0.7410 (tm-30) REVERT: F 47 MET cc_start: 0.6489 (mtm) cc_final: 0.6063 (mtp) REVERT: F 72 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: F 122 ILE cc_start: 0.8195 (mt) cc_final: 0.7906 (mp) REVERT: F 354 GLN cc_start: 0.8200 (mm110) cc_final: 0.7866 (mm110) REVERT: F 364 GLU cc_start: 0.7605 (pp20) cc_final: 0.7226 (pt0) outliers start: 27 outliers final: 8 residues processed: 225 average time/residue: 0.7258 time to fit residues: 178.2980 Evaluate side-chains 218 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 153 LEU 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 E residue 72 GLU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 171 optimal weight: 2.9990 chunk 132 optimal weight: 0.0670 chunk 67 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 210 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 41 GLN C 41 GLN C 225 ASN D 225 ASN E 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.105143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.087056 restraints weight = 20807.798| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.30 r_work: 0.2829 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 17874 Z= 0.166 Angle : 0.589 9.520 24258 Z= 0.288 Chirality : 0.046 0.167 2700 Planarity : 0.004 0.036 3096 Dihedral : 6.971 99.288 2495 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.03 % Allowed : 11.75 % Favored : 86.22 % 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: 1.03 (0.19), residues: 2190 helix: 0.81 (0.18), residues: 900 sheet: 0.61 (0.25), residues: 390 loop : 0.84 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.011 0.001 TYR C 188 PHE 0.009 0.001 PHE F 127 TRP 0.013 0.002 TRP C 340 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00395 (17874) covalent geometry : angle 0.58919 (24258) hydrogen bonds : bond 0.03650 ( 899) hydrogen bonds : angle 5.04679 ( 2331) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.672 Fit side-chains REVERT: A 99 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: A 100 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: A 328 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7459 (mtpp) REVERT: A 364 GLU cc_start: 0.8213 (pp20) cc_final: 0.7820 (tm-30) REVERT: B 25 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7365 (p0) REVERT: B 72 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: B 132 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8066 (ptm) REVERT: B 237 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8164 (mm-30) REVERT: B 276 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: C 72 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6997 (tm-30) REVERT: C 123 MET cc_start: 0.8827 (mmt) cc_final: 0.8159 (mmt) REVERT: C 372 ARG cc_start: 0.8485 (ptp-170) cc_final: 0.8139 (ptp-170) REVERT: D 72 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: D 153 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8608 (tp) REVERT: D 314 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7377 (tm-30) REVERT: E 72 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: E 132 MET cc_start: 0.8321 (ppp) cc_final: 0.7960 (ppp) REVERT: E 283 MET cc_start: 0.9133 (mmm) cc_final: 0.8922 (mmm) REVERT: E 355 MET cc_start: 0.8541 (mtt) cc_final: 0.8165 (mtp) REVERT: E 364 GLU cc_start: 0.7671 (pp20) cc_final: 0.7433 (tm-30) REVERT: F 47 MET cc_start: 0.6271 (mtm) cc_final: 0.6057 (mtp) REVERT: F 72 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: F 314 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: F 354 GLN cc_start: 0.8250 (mm110) cc_final: 0.7905 (mm110) REVERT: F 364 GLU cc_start: 0.7445 (pp20) cc_final: 0.7094 (pt0) outliers start: 38 outliers final: 18 residues processed: 222 average time/residue: 0.7782 time to fit residues: 188.2168 Evaluate side-chains 228 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 153 LEU 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 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 314 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 196 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 353 GLN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.103976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.085925 restraints weight = 20688.098| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.29 r_work: 0.2806 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17874 Z= 0.210 Angle : 0.618 9.899 24258 Z= 0.302 Chirality : 0.048 0.175 2700 Planarity : 0.005 0.037 3096 Dihedral : 7.130 102.283 2495 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.35 % Allowed : 12.02 % Favored : 85.63 % 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: 0.93 (0.18), residues: 2190 helix: 0.71 (0.18), residues: 900 sheet: 0.56 (0.25), residues: 390 loop : 0.79 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 95 TYR 0.011 0.001 TYR C 188 PHE 0.009 0.001 PHE F 127 TRP 0.015 0.002 TRP C 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00507 (17874) covalent geometry : angle 0.61782 (24258) hydrogen bonds : bond 0.03937 ( 899) hydrogen bonds : angle 5.11212 ( 2331) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.682 Fit side-chains REVERT: A 99 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: A 100 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: A 328 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7492 (mtpp) REVERT: A 364 GLU cc_start: 0.8148 (pp20) cc_final: 0.7824 (tm-30) REVERT: B 25 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7392 (p0) REVERT: B 57 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: B 72 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7449 (tp30) REVERT: B 132 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8068 (ptm) REVERT: B 237 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8172 (mm-30) REVERT: B 276 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: B 364 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7584 (pp20) REVERT: C 72 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: C 123 MET cc_start: 0.8813 (mmt) cc_final: 0.8409 (mmt) REVERT: C 372 ARG cc_start: 0.8548 (ptp-170) cc_final: 0.8225 (ptp-170) REVERT: D 72 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7096 (mt-10) REVERT: D 153 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8593 (tp) REVERT: D 314 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: E 72 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: E 132 MET cc_start: 0.8318 (ppp) cc_final: 0.7960 (ppp) REVERT: E 222 ASP cc_start: 0.8489 (t70) cc_final: 0.8078 (t70) REVERT: E 283 MET cc_start: 0.9135 (mmm) cc_final: 0.8927 (mmm) REVERT: E 355 MET cc_start: 0.8554 (mtt) cc_final: 0.8156 (mtp) REVERT: F 50 LYS cc_start: 0.7624 (ptmt) cc_final: 0.7001 (ptmt) REVERT: F 72 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: F 95 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7630 (mtm-85) REVERT: F 364 GLU cc_start: 0.7403 (pp20) cc_final: 0.7066 (pt0) outliers start: 44 outliers final: 21 residues processed: 228 average time/residue: 0.7632 time to fit residues: 189.6254 Evaluate side-chains 231 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 153 LEU 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 349 LEU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 94 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 225 ASN E 353 GLN E 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.105735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.087702 restraints weight = 20834.934| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.31 r_work: 0.2831 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17874 Z= 0.132 Angle : 0.563 10.008 24258 Z= 0.273 Chirality : 0.045 0.166 2700 Planarity : 0.004 0.036 3096 Dihedral : 6.823 99.982 2495 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.03 % Allowed : 12.61 % Favored : 85.36 % 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: 1.09 (0.18), residues: 2190 helix: 0.91 (0.18), residues: 900 sheet: 0.57 (0.25), residues: 390 loop : 0.85 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 95 TYR 0.009 0.001 TYR D 69 PHE 0.008 0.001 PHE C 255 TRP 0.010 0.002 TRP E 79 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00307 (17874) covalent geometry : angle 0.56259 (24258) hydrogen bonds : bond 0.03351 ( 899) hydrogen bonds : angle 4.94374 ( 2331) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.722 Fit side-chains REVERT: A 328 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7468 (mtpp) REVERT: A 364 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: B 57 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: B 132 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7931 (ptm) REVERT: B 237 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8086 (mm-30) REVERT: B 276 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: C 72 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: C 123 MET cc_start: 0.8814 (mmt) cc_final: 0.8472 (mmt) REVERT: C 372 ARG cc_start: 0.8553 (ptp-170) cc_final: 0.8233 (ptp-170) REVERT: D 72 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: D 153 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8549 (tp) REVERT: D 314 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: E 72 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: E 132 MET cc_start: 0.8269 (ppp) cc_final: 0.7875 (ppp) REVERT: E 283 MET cc_start: 0.9136 (mmm) cc_final: 0.8880 (mmm) REVERT: E 355 MET cc_start: 0.8569 (mtt) cc_final: 0.8166 (mtp) REVERT: F 50 LYS cc_start: 0.7669 (ptmt) cc_final: 0.7440 (ptmt) REVERT: F 72 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: F 95 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7677 (mtm-85) REVERT: F 364 GLU cc_start: 0.7331 (pp20) cc_final: 0.7009 (pt0) outliers start: 38 outliers final: 16 residues processed: 228 average time/residue: 0.7675 time to fit residues: 190.9940 Evaluate side-chains 224 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 153 LEU 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 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 62 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 353 GLN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.085909 restraints weight = 20912.005| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.30 r_work: 0.2813 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17874 Z= 0.216 Angle : 0.621 11.858 24258 Z= 0.303 Chirality : 0.048 0.173 2700 Planarity : 0.005 0.037 3096 Dihedral : 7.030 102.431 2493 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.08 % Allowed : 12.98 % Favored : 84.94 % 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: 0.94 (0.18), residues: 2190 helix: 0.75 (0.18), residues: 900 sheet: 0.54 (0.26), residues: 390 loop : 0.79 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.012 0.001 TYR C 188 PHE 0.009 0.001 PHE F 127 TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00523 (17874) covalent geometry : angle 0.62052 (24258) hydrogen bonds : bond 0.03967 ( 899) hydrogen bonds : angle 5.07302 ( 2331) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.646 Fit side-chains REVERT: A 328 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7438 (mtpp) REVERT: A 364 GLU cc_start: 0.8082 (pp20) cc_final: 0.7736 (tm-30) REVERT: B 57 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: B 132 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8085 (ptm) REVERT: B 237 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8149 (mm-30) REVERT: B 276 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: C 72 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: C 123 MET cc_start: 0.8846 (mmt) cc_final: 0.8473 (mmt) REVERT: C 372 ARG cc_start: 0.8561 (ptp-170) cc_final: 0.8231 (ptp-170) REVERT: D 72 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: D 80 ASP cc_start: 0.8152 (m-30) cc_final: 0.7758 (m-30) REVERT: D 153 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8602 (tp) REVERT: D 314 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: E 72 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: E 132 MET cc_start: 0.8342 (ppp) cc_final: 0.7967 (ppp) REVERT: E 283 MET cc_start: 0.9154 (mmm) cc_final: 0.8932 (mmm) REVERT: E 355 MET cc_start: 0.8591 (mtt) cc_final: 0.8201 (mtp) REVERT: F 72 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: F 95 ARG cc_start: 0.7976 (mtt-85) cc_final: 0.7707 (mtm-85) REVERT: F 349 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7594 (mp) REVERT: F 364 GLU cc_start: 0.7348 (pp20) cc_final: 0.6934 (pt0) outliers start: 39 outliers final: 22 residues processed: 224 average time/residue: 0.7449 time to fit residues: 182.1235 Evaluate side-chains 228 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 153 LEU 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 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 152 optimal weight: 0.4980 chunk 202 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 26 optimal weight: 0.0970 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 225 ASN E 353 GLN E 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.106853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.088910 restraints weight = 20746.633| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.30 r_work: 0.2861 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17874 Z= 0.107 Angle : 0.545 11.127 24258 Z= 0.264 Chirality : 0.044 0.157 2700 Planarity : 0.004 0.039 3096 Dihedral : 6.588 97.755 2493 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.50 % Allowed : 13.51 % Favored : 84.99 % 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: 1.21 (0.19), residues: 2190 helix: 1.03 (0.18), residues: 900 sheet: 0.55 (0.25), residues: 390 loop : 0.93 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.009 0.001 TYR E 294 PHE 0.008 0.001 PHE C 255 TRP 0.011 0.002 TRP E 79 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00236 (17874) covalent geometry : angle 0.54496 (24258) hydrogen bonds : bond 0.03111 ( 899) hydrogen bonds : angle 4.85678 ( 2331) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.653 Fit side-chains REVERT: A 328 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7385 (mtpp) REVERT: A 364 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: B 57 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: B 123 MET cc_start: 0.8683 (mmt) cc_final: 0.8055 (mmp) REVERT: B 132 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7914 (ptm) REVERT: B 237 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8094 (mm-30) REVERT: B 276 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: C 72 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: C 123 MET cc_start: 0.8796 (mmt) cc_final: 0.8459 (mmt) REVERT: C 372 ARG cc_start: 0.8547 (ptp-170) cc_final: 0.8222 (ptp-170) REVERT: D 72 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: D 80 ASP cc_start: 0.8107 (m-30) cc_final: 0.7725 (m-30) REVERT: D 153 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8623 (tp) REVERT: E 72 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7210 (mt-10) REVERT: E 132 MET cc_start: 0.8260 (ppp) cc_final: 0.7957 (ppp) REVERT: E 355 MET cc_start: 0.8572 (mtt) cc_final: 0.8180 (mtp) REVERT: F 50 LYS cc_start: 0.7648 (ptmt) cc_final: 0.6914 (ptmt) REVERT: F 72 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: F 95 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7646 (mtt90) REVERT: F 190 MET cc_start: 0.8036 (mtp) cc_final: 0.7569 (ttm) REVERT: F 314 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: F 355 MET cc_start: 0.8512 (mtt) cc_final: 0.8293 (mtp) REVERT: F 364 GLU cc_start: 0.7258 (pp20) cc_final: 0.6871 (pt0) REVERT: F 372 ARG cc_start: 0.8014 (ptt-90) cc_final: 0.7751 (ptt-90) outliers start: 28 outliers final: 14 residues processed: 227 average time/residue: 0.7532 time to fit residues: 186.5656 Evaluate side-chains 227 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 141 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 95 optimal weight: 0.0020 chunk 136 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 chunk 122 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.090073 restraints weight = 20520.765| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.47 r_work: 0.2886 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17874 Z= 0.092 Angle : 0.529 10.323 24258 Z= 0.255 Chirality : 0.043 0.137 2700 Planarity : 0.004 0.036 3096 Dihedral : 6.112 86.957 2493 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.34 % Allowed : 13.84 % Favored : 84.83 % 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: 1.48 (0.19), residues: 2190 helix: 1.29 (0.18), residues: 900 sheet: 0.62 (0.26), residues: 390 loop : 1.06 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.008 0.001 TYR D 143 PHE 0.007 0.001 PHE C 31 TRP 0.012 0.002 TRP E 79 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00198 (17874) covalent geometry : angle 0.52867 (24258) hydrogen bonds : bond 0.02846 ( 899) hydrogen bonds : angle 4.71310 ( 2331) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.643 Fit side-chains REVERT: A 328 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7419 (mtpp) REVERT: A 364 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: B 57 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: B 132 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7952 (ptm) REVERT: B 237 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8102 (mm-30) REVERT: B 276 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: C 123 MET cc_start: 0.8759 (mmt) cc_final: 0.8415 (mmt) REVERT: C 372 ARG cc_start: 0.8531 (ptp-170) cc_final: 0.8198 (ptp-170) REVERT: D 72 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: D 80 ASP cc_start: 0.8095 (m-30) cc_final: 0.7718 (m-30) REVERT: D 153 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8522 (tp) REVERT: E 50 LYS cc_start: 0.7676 (ptmt) cc_final: 0.7452 (ptmm) REVERT: E 72 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: E 132 MET cc_start: 0.8273 (ppp) cc_final: 0.7959 (ppp) REVERT: E 355 MET cc_start: 0.8569 (mtt) cc_final: 0.8181 (mtp) REVERT: F 50 LYS cc_start: 0.7617 (ptmt) cc_final: 0.6866 (ptmt) REVERT: F 72 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: F 95 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7667 (mtt90) REVERT: F 190 MET cc_start: 0.7988 (mtp) cc_final: 0.7517 (ttm) REVERT: F 364 GLU cc_start: 0.7262 (pp20) cc_final: 0.6879 (pt0) REVERT: F 372 ARG cc_start: 0.8048 (ptt-90) cc_final: 0.7791 (ptt-90) outliers start: 25 outliers final: 9 residues processed: 224 average time/residue: 0.7179 time to fit residues: 175.7596 Evaluate side-chains 219 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 198 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 353 GLN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.085214 restraints weight = 20986.501| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.31 r_work: 0.2774 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 17874 Z= 0.282 Angle : 0.668 13.220 24258 Z= 0.328 Chirality : 0.051 0.170 2700 Planarity : 0.005 0.041 3096 Dihedral : 7.041 101.139 2493 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.28 % Allowed : 14.26 % Favored : 84.46 % 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: 0.99 (0.18), residues: 2190 helix: 0.76 (0.18), residues: 900 sheet: 0.58 (0.26), residues: 390 loop : 0.85 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 95 TYR 0.013 0.002 TYR D 133 PHE 0.012 0.002 PHE F 127 TRP 0.018 0.002 TRP C 340 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00692 (17874) covalent geometry : angle 0.66762 (24258) hydrogen bonds : bond 0.04368 ( 899) hydrogen bonds : angle 5.08971 ( 2331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5604.31 seconds wall clock time: 96 minutes 22.20 seconds (5782.20 seconds total)