Starting phenix.real_space_refine on Sun Jun 15 21:21:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uxf_26860/06_2025/7uxf_26860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uxf_26860/06_2025/7uxf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uxf_26860/06_2025/7uxf_26860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uxf_26860/06_2025/7uxf_26860.map" model { file = "/net/cci-nas-00/data/ceres_data/7uxf_26860/06_2025/7uxf_26860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uxf_26860/06_2025/7uxf_26860.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.15, per 1000 atoms: 0.75 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: 5.44 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 3.18 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: 9.14 Time building geometry restraints manager: 5.97 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 3.810 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: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 51.400 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.180 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:18.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.330 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), 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 TRP 0.013 0.002 TRP B 340 HIS 0.009 0.001 HIS D 161 PHE 0.006 0.001 PHE E 262 TYR 0.014 0.001 TYR D 143 ARG 0.009 0.001 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.18523 ( 899) hydrogen bonds : angle 7.15194 ( 2331) covalent geometry : bond 0.00771 (17874) covalent geometry : angle 0.80547 (24258) *********************** 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 : 1.995 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: 2.1725 time to fit residues: 723.0923 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 : 2.677 ------------------------------------------------------------------------------- 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 187 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.088366 restraints weight = 20720.906| |-----------------------------------------------------------------------------| 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: 0.2746 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1242 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= 0.137 Angle : 0.604 6.802 24258 Z= 0.299 Chirality : 0.045 0.157 2700 Planarity : 0.005 0.045 3096 Dihedral : 7.516 98.399 2505 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.71 % Allowed : 8.55 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 2190 helix: 0.53 (0.18), residues: 894 sheet: 0.37 (0.24), residues: 402 loop : 0.90 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 340 HIS 0.003 0.001 HIS D 161 PHE 0.007 0.001 PHE E 127 TYR 0.016 0.001 TYR D 143 ARG 0.006 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 899) hydrogen bonds : angle 5.49722 ( 2331) covalent geometry : bond 0.00306 (17874) covalent geometry : angle 0.60442 (24258) *********************** 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 258 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 1.876 Fit side-chains REVERT: A 72 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7726 (mm-30) REVERT: A 99 GLU cc_start: 0.7867 (mp0) cc_final: 0.7548 (mp0) REVERT: B 25 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7284 (p0) REVERT: B 72 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: B 123 MET cc_start: 0.8762 (mmt) cc_final: 0.8228 (mmm) REVERT: B 237 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8170 (mm-30) REVERT: B 283 MET cc_start: 0.9155 (mmm) cc_final: 0.8938 (mmm) REVERT: C 72 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: C 123 MET cc_start: 0.8824 (mmt) cc_final: 0.8480 (mmt) REVERT: C 176 MET cc_start: 0.9114 (mmm) cc_final: 0.8892 (mmm) REVERT: C 372 ARG cc_start: 0.8324 (ptp90) cc_final: 0.7872 (ptp-170) REVERT: D 72 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: D 314 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: D 326 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7640 (tptp) REVERT: E 72 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: E 123 MET cc_start: 0.8890 (mmp) cc_final: 0.8645 (mmt) REVERT: E 132 MET cc_start: 0.8347 (ppp) cc_final: 0.8097 (ppp) REVERT: E 325 MET cc_start: 0.8968 (mmp) cc_final: 0.8732 (mmm) REVERT: E 355 MET cc_start: 0.8551 (mtt) cc_final: 0.8140 (mtp) REVERT: F 72 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: F 122 ILE cc_start: 0.8117 (mt) cc_final: 0.7822 (mp) REVERT: F 326 LYS cc_start: 0.8324 (tppt) cc_final: 0.8059 (mptt) REVERT: F 354 GLN cc_start: 0.7879 (mm110) cc_final: 0.7604 (mm110) REVERT: F 372 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7862 (ptt-90) outliers start: 32 outliers final: 10 residues processed: 242 average time/residue: 1.5336 time to fit residues: 408.3098 Evaluate side-chains 215 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 1.989 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3147 r_free = 0.3147 target = 0.104541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.086438 restraints weight = 20691.116| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.30 r_work: 0.2805 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 17874 Z= 0.203 Angle : 0.628 7.384 24258 Z= 0.308 Chirality : 0.047 0.196 2700 Planarity : 0.005 0.038 3096 Dihedral : 7.327 99.983 2497 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.66 % Allowed : 10.36 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 2190 helix: 0.62 (0.18), residues: 894 sheet: 0.43 (0.24), residues: 402 loop : 0.82 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS D 161 PHE 0.009 0.001 PHE F 127 TYR 0.014 0.001 TYR C 188 ARG 0.009 0.001 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 899) hydrogen bonds : angle 5.28533 ( 2331) covalent geometry : bond 0.00487 (17874) covalent geometry : angle 0.62778 (24258) *********************** 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 233 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 2.203 Fit side-chains REVERT: A 99 GLU cc_start: 0.7928 (mp0) cc_final: 0.7664 (mp0) REVERT: B 25 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7369 (p0) REVERT: B 72 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: B 82 MET cc_start: 0.8737 (tpt) cc_final: 0.8522 (tpt) REVERT: B 123 MET cc_start: 0.8735 (mmt) cc_final: 0.8249 (mmm) REVERT: C 72 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: C 123 MET cc_start: 0.8837 (mmt) cc_final: 0.8441 (mmt) REVERT: D 72 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7033 (mt-10) REVERT: D 153 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8520 (tp) REVERT: D 314 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: D 326 LYS cc_start: 0.8418 (mmtt) cc_final: 0.7625 (tptp) REVERT: D 372 ARG cc_start: 0.8140 (ptp90) cc_final: 0.7907 (ptt-90) REVERT: E 132 MET cc_start: 0.8348 (ppp) cc_final: 0.8065 (ppp) REVERT: E 325 MET cc_start: 0.8991 (mmp) cc_final: 0.8632 (mmm) REVERT: E 355 MET cc_start: 0.8552 (mtt) cc_final: 0.8145 (mtp) REVERT: F 47 MET cc_start: 0.6517 (mtm) cc_final: 0.6014 (mtp) REVERT: F 72 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: F 354 GLN cc_start: 0.8104 (mm110) cc_final: 0.7797 (mm110) REVERT: F 364 GLU cc_start: 0.7437 (pp20) cc_final: 0.7076 (pt0) outliers start: 31 outliers final: 13 residues processed: 221 average time/residue: 2.0259 time to fit residues: 493.8876 Evaluate side-chains 212 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 2.313 ------------------------------------------------------------------------------- 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 72 GLU 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 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 F residue 72 GLU 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 102 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.106011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.087933 restraints weight = 20630.639| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.30 r_work: 0.2846 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1659 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= 0.146 Angle : 0.575 7.990 24258 Z= 0.281 Chirality : 0.045 0.160 2700 Planarity : 0.004 0.040 3096 Dihedral : 6.981 98.203 2497 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.60 % Allowed : 11.43 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2190 helix: 0.78 (0.18), residues: 900 sheet: 0.60 (0.25), residues: 390 loop : 0.81 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.003 0.001 HIS B 371 PHE 0.009 0.001 PHE F 127 TYR 0.010 0.001 TYR C 188 ARG 0.008 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 899) hydrogen bonds : angle 5.06482 ( 2331) covalent geometry : bond 0.00343 (17874) covalent geometry : angle 0.57514 (24258) *********************** 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 232 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 1.931 Fit side-chains REVERT: A 326 LYS cc_start: 0.7756 (tptt) cc_final: 0.7535 (tptm) REVERT: A 364 GLU cc_start: 0.8335 (pp20) cc_final: 0.7939 (tm-30) REVERT: B 25 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7332 (p0) REVERT: B 72 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: B 132 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8017 (ptm) REVERT: B 237 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8186 (mm-30) REVERT: B 276 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: C 72 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: C 123 MET cc_start: 0.8813 (mmt) cc_final: 0.8388 (mmt) REVERT: C 372 ARG cc_start: 0.8395 (ptp-170) cc_final: 0.7991 (ptp-170) REVERT: D 72 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7092 (mt-10) REVERT: D 153 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8628 (tp) REVERT: D 227 MET cc_start: 0.8328 (mmm) cc_final: 0.7682 (mmm) REVERT: D 314 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: D 372 ARG cc_start: 0.8142 (ptp90) cc_final: 0.7826 (ptt-90) REVERT: E 72 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: E 132 MET cc_start: 0.8306 (ppp) cc_final: 0.7976 (ppp) REVERT: E 325 MET cc_start: 0.8965 (mmp) cc_final: 0.8559 (mmm) REVERT: E 355 MET cc_start: 0.8556 (mtt) cc_final: 0.8179 (mtp) REVERT: E 364 GLU cc_start: 0.7821 (pp20) cc_final: 0.7434 (tm-30) REVERT: F 47 MET cc_start: 0.6451 (mtm) cc_final: 0.6041 (mtp) REVERT: F 50 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7499 (ptmt) REVERT: F 72 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: F 314 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: F 354 GLN cc_start: 0.8203 (mm110) cc_final: 0.7866 (mm110) REVERT: F 364 GLU cc_start: 0.7453 (pp20) cc_final: 0.7212 (pt0) outliers start: 30 outliers final: 12 residues processed: 222 average time/residue: 1.6653 time to fit residues: 405.5777 Evaluate side-chains 220 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL 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 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 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 F residue 50 LYS Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 314 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 D 225 ASN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.102942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.084937 restraints weight = 21070.007| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.30 r_work: 0.2778 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1703 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 : 0.678 8.773 24258 Z= 0.334 Chirality : 0.051 0.193 2700 Planarity : 0.005 0.039 3096 Dihedral : 7.448 105.332 2495 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.51 % Allowed : 11.00 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2190 helix: 0.51 (0.18), residues: 900 sheet: 0.51 (0.25), residues: 390 loop : 0.69 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.011 0.002 PHE F 127 TYR 0.013 0.002 TYR C 188 ARG 0.007 0.001 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 899) hydrogen bonds : angle 5.29049 ( 2331) covalent geometry : bond 0.00687 (17874) covalent geometry : angle 0.67788 (24258) *********************** 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 244 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 1.977 Fit side-chains REVERT: A 99 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 100 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7622 (pm20) REVERT: A 328 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7444 (mtpp) REVERT: A 364 GLU cc_start: 0.8172 (pp20) cc_final: 0.7822 (tm-30) REVERT: B 72 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: B 276 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: B 364 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7484 (pp20) REVERT: C 72 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7138 (tm-30) REVERT: C 123 MET cc_start: 0.8826 (mmt) cc_final: 0.8200 (mmt) REVERT: C 372 ARG cc_start: 0.8570 (ptp-170) cc_final: 0.8221 (ptp-170) REVERT: D 72 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: D 153 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8643 (tp) REVERT: D 314 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: D 372 ARG cc_start: 0.8165 (ptp90) cc_final: 0.7877 (ptt-90) REVERT: E 72 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: E 132 MET cc_start: 0.8347 (ppp) cc_final: 0.7922 (ppp) REVERT: E 355 MET cc_start: 0.8558 (mtt) cc_final: 0.8171 (mtp) REVERT: E 364 GLU cc_start: 0.7686 (pp20) cc_final: 0.7468 (tm-30) REVERT: F 47 MET cc_start: 0.6064 (mtm) cc_final: 0.5841 (mtp) REVERT: F 72 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: F 95 ARG cc_start: 0.7892 (mtt-85) cc_final: 0.7597 (mtm-85) REVERT: F 354 GLN cc_start: 0.8238 (mm110) cc_final: 0.7886 (mm110) REVERT: F 364 GLU cc_start: 0.7318 (pp20) cc_final: 0.7044 (pt0) outliers start: 47 outliers final: 23 residues processed: 223 average time/residue: 1.7593 time to fit residues: 427.3444 Evaluate side-chains 231 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 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 122 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 E 353 GLN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.106172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.088142 restraints weight = 20833.945| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.31 r_work: 0.2852 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1835 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= 0.115 Angle : 0.556 9.449 24258 Z= 0.270 Chirality : 0.044 0.167 2700 Planarity : 0.004 0.035 3096 Dihedral : 6.889 100.866 2495 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.82 % Allowed : 12.29 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2190 helix: 0.86 (0.18), residues: 900 sheet: 0.58 (0.25), residues: 390 loop : 0.82 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 79 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 255 TYR 0.009 0.001 TYR D 69 ARG 0.008 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 899) hydrogen bonds : angle 4.96823 ( 2331) covalent geometry : bond 0.00258 (17874) covalent geometry : angle 0.55565 (24258) *********************** 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 246 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 1.893 Fit side-chains REVERT: A 99 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 100 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: A 328 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7415 (mtpp) REVERT: A 364 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: B 25 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7401 (p0) REVERT: B 57 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: B 123 MET cc_start: 0.8749 (mmt) cc_final: 0.8147 (mmp) REVERT: B 132 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8011 (ptm) REVERT: B 237 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8154 (mm-30) REVERT: B 276 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7838 (mt-10) REVERT: C 72 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: C 123 MET cc_start: 0.8832 (mmt) cc_final: 0.8479 (mmt) REVERT: C 372 ARG cc_start: 0.8567 (ptp-170) cc_final: 0.8246 (ptp-170) REVERT: D 72 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: D 80 ASP cc_start: 0.8145 (m-30) cc_final: 0.7761 (m-30) REVERT: D 153 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8552 (tp) REVERT: E 72 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: E 132 MET cc_start: 0.8280 (ppp) cc_final: 0.7906 (ppp) REVERT: E 355 MET cc_start: 0.8593 (mtt) cc_final: 0.8213 (mtp) REVERT: F 50 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7044 (ptmt) REVERT: F 72 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: F 364 GLU cc_start: 0.7299 (pp20) cc_final: 0.7087 (pt0) outliers start: 34 outliers final: 12 residues processed: 232 average time/residue: 1.7080 time to fit residues: 433.1863 Evaluate side-chains 225 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 2.005 ------------------------------------------------------------------------------- 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 328 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 25 ASP 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 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 211 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 72 GLU 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 97 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 246 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 = 0.3156 r_free = 0.3156 target = 0.105482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.087471 restraints weight = 20744.418| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.30 r_work: 0.2839 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1856 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= 0.143 Angle : 0.570 10.317 24258 Z= 0.277 Chirality : 0.045 0.166 2700 Planarity : 0.004 0.036 3096 Dihedral : 6.795 98.859 2495 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.92 % Allowed : 12.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 2190 helix: 0.94 (0.18), residues: 900 sheet: 0.61 (0.26), residues: 390 loop : 0.85 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE F 127 TYR 0.009 0.001 TYR C 188 ARG 0.007 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 899) hydrogen bonds : angle 4.94825 ( 2331) covalent geometry : bond 0.00336 (17874) covalent geometry : angle 0.57008 (24258) *********************** 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 239 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 1.997 Fit side-chains REVERT: A 72 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: A 99 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: A 100 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: A 364 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: B 57 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: B 132 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8019 (ptm) REVERT: B 237 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8144 (mm-30) REVERT: B 276 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: C 72 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: C 99 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: C 123 MET cc_start: 0.8831 (mmt) cc_final: 0.8463 (mmt) REVERT: C 372 ARG cc_start: 0.8568 (ptp-170) cc_final: 0.8244 (ptp-170) REVERT: D 72 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: D 80 ASP cc_start: 0.8129 (m-30) cc_final: 0.7735 (m-30) REVERT: D 153 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8561 (tp) REVERT: E 72 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: E 132 MET cc_start: 0.8299 (ppp) cc_final: 0.7909 (ppp) REVERT: E 355 MET cc_start: 0.8580 (mtt) cc_final: 0.8179 (mtp) REVERT: F 50 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7073 (ptmt) REVERT: F 72 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: F 95 ARG cc_start: 0.7942 (mtt-85) cc_final: 0.7668 (mtm-85) REVERT: F 364 GLU cc_start: 0.7297 (pp20) cc_final: 0.6904 (pt0) outliers start: 36 outliers final: 14 residues processed: 224 average time/residue: 1.7214 time to fit residues: 421.2227 Evaluate side-chains 226 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 100 GLU 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 99 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 241 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F 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 Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 180 optimal weight: 0.7980 chunk 121 optimal weight: 0.0980 chunk 118 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 36 optimal weight: 0.0020 chunk 85 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- 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 41 GLN 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 = 0.3162 r_free = 0.3162 target = 0.105979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.087993 restraints weight = 20707.278| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.30 r_work: 0.2848 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1910 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= 0.133 Angle : 0.562 11.392 24258 Z= 0.273 Chirality : 0.045 0.158 2700 Planarity : 0.004 0.035 3096 Dihedral : 6.637 97.495 2493 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.08 % Allowed : 12.87 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.19), residues: 2190 helix: 1.01 (0.18), residues: 900 sheet: 0.60 (0.26), residues: 390 loop : 0.89 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 255 TYR 0.009 0.001 TYR C 188 ARG 0.007 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 899) hydrogen bonds : angle 4.89618 ( 2331) covalent geometry : bond 0.00310 (17874) covalent geometry : angle 0.56164 (24258) *********************** 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 238 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 1.870 Fit side-chains REVERT: A 99 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: A 100 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: A 328 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7106 (mtpp) REVERT: A 364 GLU cc_start: 0.8138 (pp20) cc_final: 0.7855 (tm-30) REVERT: B 57 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: B 72 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: B 123 MET cc_start: 0.8682 (mmt) cc_final: 0.8042 (mmp) REVERT: B 132 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7949 (ptm) REVERT: B 237 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8120 (mm-30) REVERT: B 276 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: C 72 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6936 (tm-30) REVERT: C 99 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: C 123 MET cc_start: 0.8837 (mmt) cc_final: 0.8491 (mmt) REVERT: C 372 ARG cc_start: 0.8573 (ptp-170) cc_final: 0.8244 (ptp-170) REVERT: D 72 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: D 80 ASP cc_start: 0.8135 (m-30) cc_final: 0.7745 (m-30) REVERT: D 153 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8561 (tp) REVERT: E 72 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: E 132 MET cc_start: 0.8301 (ppp) cc_final: 0.7997 (ppp) REVERT: E 355 MET cc_start: 0.8589 (mtt) cc_final: 0.8196 (mtp) REVERT: F 50 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7030 (ptmt) REVERT: F 72 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: F 95 ARG cc_start: 0.7967 (mtt-85) cc_final: 0.7700 (mtm-85) REVERT: F 190 MET cc_start: 0.8053 (mtp) cc_final: 0.7660 (ttm) REVERT: F 364 GLU cc_start: 0.7224 (pp20) cc_final: 0.6846 (pt0) REVERT: F 372 ARG cc_start: 0.8032 (ptt-90) cc_final: 0.7767 (ptt-90) outliers start: 39 outliers final: 18 residues processed: 225 average time/residue: 1.6607 time to fit residues: 409.5504 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 : 1.952 ------------------------------------------------------------------------------- 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 328 LYS Chi-restraints excluded: chain A residue 349 LEU 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 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 99 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 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 50 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 186 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 214 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 164 optimal weight: 0.2980 chunk 215 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 41 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 = 0.3149 r_free = 0.3149 target = 0.105055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.087011 restraints weight = 20853.068| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.31 r_work: 0.2833 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17874 Z= 0.168 Angle : 0.588 12.093 24258 Z= 0.286 Chirality : 0.046 0.164 2700 Planarity : 0.004 0.036 3096 Dihedral : 6.752 98.779 2493 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.08 % Allowed : 12.82 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2190 helix: 0.93 (0.18), residues: 900 sheet: 0.56 (0.26), residues: 390 loop : 0.88 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.003 0.001 HIS C 161 PHE 0.009 0.001 PHE F 127 TYR 0.010 0.001 TYR C 188 ARG 0.007 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 899) hydrogen bonds : angle 4.95993 ( 2331) covalent geometry : bond 0.00402 (17874) covalent geometry : angle 0.58808 (24258) *********************** 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 234 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 2.118 Fit side-chains REVERT: A 72 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: A 99 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: A 100 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: A 328 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7086 (mtpp) REVERT: A 364 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: B 57 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: B 72 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7454 (tp30) REVERT: B 132 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8028 (ptm) REVERT: B 237 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8173 (mm-30) REVERT: B 276 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: C 72 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: C 99 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: C 123 MET cc_start: 0.8831 (mmt) cc_final: 0.8479 (mmt) REVERT: C 372 ARG cc_start: 0.8560 (ptp-170) cc_final: 0.8232 (ptp-170) REVERT: D 72 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: D 80 ASP cc_start: 0.8136 (m-30) cc_final: 0.7750 (m-30) REVERT: D 153 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8562 (tp) REVERT: E 72 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: E 132 MET cc_start: 0.8345 (ppp) cc_final: 0.7951 (ppp) REVERT: E 355 MET cc_start: 0.8597 (mtt) cc_final: 0.8199 (mtp) REVERT: F 50 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7084 (ptmt) REVERT: F 72 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: F 95 ARG cc_start: 0.7973 (mtt-85) cc_final: 0.7707 (mtm-85) REVERT: F 364 GLU cc_start: 0.7250 (pp20) cc_final: 0.6866 (pt0) REVERT: F 372 ARG cc_start: 0.8013 (ptt-90) cc_final: 0.7748 (ptt-90) outliers start: 39 outliers final: 18 residues processed: 218 average time/residue: 1.7161 time to fit residues: 408.5934 Evaluate side-chains 230 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 GLU 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 A residue 364 GLU 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 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 99 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 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F 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 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 45 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 74 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 41 GLN 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 = 0.3189 r_free = 0.3189 target = 0.107856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.090044 restraints weight = 20660.860| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.30 r_work: 0.2874 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17874 Z= 0.103 Angle : 0.538 11.772 24258 Z= 0.260 Chirality : 0.044 0.147 2700 Planarity : 0.004 0.038 3096 Dihedral : 6.349 93.750 2493 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.44 % Allowed : 13.78 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.19), residues: 2190 helix: 1.17 (0.18), residues: 900 sheet: 0.62 (0.26), residues: 390 loop : 0.98 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 79 HIS 0.003 0.001 HIS D 161 PHE 0.007 0.001 PHE C 31 TYR 0.008 0.001 TYR D 69 ARG 0.007 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 899) hydrogen bonds : angle 4.79409 ( 2331) covalent geometry : bond 0.00227 (17874) covalent geometry : angle 0.53753 (24258) ********************** 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 236 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 2.180 Fit side-chains REVERT: A 364 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: B 57 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: B 72 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: B 132 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7914 (ptm) REVERT: B 237 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8111 (mm-30) REVERT: B 276 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: B 364 GLU cc_start: 0.7714 (pt0) cc_final: 0.7500 (pt0) REVERT: C 72 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6880 (tm-30) REVERT: C 99 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: C 123 MET cc_start: 0.8778 (mmt) cc_final: 0.8450 (mmt) REVERT: C 372 ARG cc_start: 0.8581 (ptp-170) cc_final: 0.8243 (ptp-170) REVERT: D 72 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: D 80 ASP cc_start: 0.8103 (m-30) cc_final: 0.7719 (m-30) REVERT: E 72 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: E 132 MET cc_start: 0.8266 (ppp) cc_final: 0.7946 (ppp) REVERT: E 355 MET cc_start: 0.8594 (mtt) cc_final: 0.8190 (mtp) REVERT: F 50 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7080 (ptmt) REVERT: F 72 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: F 95 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.7668 (mtt90) REVERT: F 190 MET cc_start: 0.7987 (mtp) cc_final: 0.7567 (ttm) REVERT: F 364 GLU cc_start: 0.7224 (pp20) cc_final: 0.6855 (pt0) REVERT: F 372 ARG cc_start: 0.8053 (ptt-90) cc_final: 0.7798 (ptt-90) outliers start: 27 outliers final: 10 residues processed: 224 average time/residue: 1.6451 time to fit residues: 402.4283 Evaluate side-chains 223 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET 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 72 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL 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 159 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 174 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 41 GLN E 246 GLN E 353 GLN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.105885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.087958 restraints weight = 20721.869| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.30 r_work: 0.2842 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17874 Z= 0.154 Angle : 0.576 12.354 24258 Z= 0.280 Chirality : 0.046 0.155 2700 Planarity : 0.004 0.038 3096 Dihedral : 6.543 95.647 2493 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.66 % Allowed : 13.57 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 2190 helix: 1.10 (0.18), residues: 900 sheet: 0.63 (0.26), residues: 390 loop : 0.96 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.003 0.001 HIS D 161 PHE 0.009 0.001 PHE F 127 TYR 0.010 0.001 TYR C 188 ARG 0.007 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 899) hydrogen bonds : angle 4.88994 ( 2331) covalent geometry : bond 0.00365 (17874) covalent geometry : angle 0.57579 (24258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13374.10 seconds wall clock time: 232 minutes 31.44 seconds (13951.44 seconds total)