Starting phenix.real_space_refine on Thu Mar 5 19:47:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wvt_21925/03_2026/6wvt_21925.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wvt_21925/03_2026/6wvt_21925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wvt_21925/03_2026/6wvt_21925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wvt_21925/03_2026/6wvt_21925.map" model { file = "/net/cci-nas-00/data/ceres_data/6wvt_21925/03_2026/6wvt_21925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wvt_21925/03_2026/6wvt_21925.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 216 5.16 5 C 15882 2.51 5 N 4296 2.21 5 O 4836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 210 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25248 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "H" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "I" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "K" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "L" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "N" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "O" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "Q" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "X" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 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: "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: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.12, per 1000 atoms: 0.20 Number of scatterers: 25248 At special positions: 0 Unit cell: (122.13, 104.535, 219.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 216 16.00 P 12 15.00 Mg 6 11.99 O 4836 8.00 N 4296 7.00 C 15882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.1 seconds 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6048 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 30 sheets defined 51.1% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.654A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.825A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.562A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.739A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 145 removed outlier: 3.900A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.734A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 204 through 216 removed outlier: 4.100A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.712A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.861A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 275 through 283 removed outlier: 3.604A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) 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 318 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 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 6.384A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 365 through 369 removed outlier: 4.063A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.549A pdb=" N CYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 375 " --> pdb=" O HIS B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 375' Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.654A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.825A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.563A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.738A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 removed outlier: 3.901A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.734A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 204 through 216 removed outlier: 4.100A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 removed outlier: 3.713A pdb=" N GLU D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.861A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 275 through 283 removed outlier: 3.604A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) 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 318 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 347 Processing helix chain 'D' and resid 348 through 353 removed outlier: 6.384A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 365 through 369 removed outlier: 4.062A pdb=" N SER D 368 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 369' Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.548A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE D 375 " --> pdb=" O HIS D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 375' Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.654A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 91 removed outlier: 3.825A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.563A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.738A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 145 removed outlier: 3.900A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.733A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 204 through 216 removed outlier: 4.101A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 removed outlier: 3.713A pdb=" N GLU E 226 " --> pdb=" O ASP E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.861A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 275 through 283 removed outlier: 3.604A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) 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 318 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 347 Processing helix chain 'E' and resid 348 through 353 removed outlier: 6.384A pdb=" N THR E 351 " --> pdb=" O SER E 348 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 365 through 369 removed outlier: 4.062A pdb=" N SER E 368 " --> pdb=" O ALA E 365 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE E 369 " --> pdb=" O GLY E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 369' Processing helix chain 'E' and resid 370 through 375 removed outlier: 3.549A pdb=" N CYS E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE E 375 " --> pdb=" O HIS E 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 370 through 375' Processing helix chain 'F' and resid 55 through 61 removed outlier: 3.654A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 91 removed outlier: 3.825A pdb=" N LYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.562A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.739A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 145 removed outlier: 3.901A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 175 removed outlier: 3.733A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 204 through 216 removed outlier: 4.100A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 230 removed outlier: 3.713A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.860A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 275 through 283 removed outlier: 3.604A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) 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 318 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 347 Processing helix chain 'F' and resid 348 through 353 removed outlier: 6.384A pdb=" N THR F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 363 Processing helix chain 'F' and resid 365 through 369 removed outlier: 4.062A pdb=" N SER F 368 " --> pdb=" O ALA F 365 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE F 369 " --> pdb=" O GLY F 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 365 through 369' Processing helix chain 'F' and resid 370 through 375 removed outlier: 3.549A pdb=" N CYS F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE F 375 " --> pdb=" O HIS F 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 370 through 375' Processing helix chain 'H' and resid 55 through 61 removed outlier: 3.654A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 91 removed outlier: 3.824A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 removed outlier: 3.561A pdb=" N GLU H 100 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.739A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 145 removed outlier: 3.901A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 175 removed outlier: 3.733A pdb=" N ILE H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 204 through 216 removed outlier: 4.101A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 230 removed outlier: 3.713A pdb=" N GLU H 226 " --> pdb=" O ASP H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 257 removed outlier: 3.860A pdb=" N CYS H 257 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 262 Processing helix chain 'H' and resid 275 through 283 removed outlier: 3.605A pdb=" N TYR H 279 " --> pdb=" O HIS H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 295 Processing helix chain 'H' and resid 301 through 305 Processing helix chain 'H' and resid 308 through 318 Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 347 Processing helix chain 'H' and resid 348 through 353 removed outlier: 6.384A pdb=" N THR H 351 " --> pdb=" O SER H 348 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN H 353 " --> pdb=" O SER H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 363 Processing helix chain 'H' and resid 365 through 369 removed outlier: 4.062A pdb=" N SER H 368 " --> pdb=" O ALA H 365 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE H 369 " --> pdb=" O GLY H 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 365 through 369' Processing helix chain 'H' and resid 370 through 375 removed outlier: 3.549A pdb=" N CYS H 374 " --> pdb=" O VAL H 370 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE H 375 " --> pdb=" O HIS H 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 370 through 375' Processing helix chain 'I' and resid 55 through 61 removed outlier: 3.654A pdb=" N LYS I 61 " --> pdb=" O GLU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 91 removed outlier: 3.824A pdb=" N LYS I 84 " --> pdb=" O ASP I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.562A pdb=" N GLU I 100 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.738A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 145 removed outlier: 3.901A pdb=" N LEU I 142 " --> pdb=" O ALA I 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR I 143 " --> pdb=" O VAL I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 175 removed outlier: 3.733A pdb=" N ILE I 175 " --> pdb=" O PRO I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 193 Processing helix chain 'I' and resid 204 through 216 removed outlier: 4.100A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 230 removed outlier: 3.713A pdb=" N GLU I 226 " --> pdb=" O ASP I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 257 removed outlier: 3.861A pdb=" N CYS I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 262 Processing helix chain 'I' and resid 275 through 283 removed outlier: 3.605A pdb=" N TYR I 279 " --> pdb=" O HIS I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 295 Processing helix chain 'I' and resid 301 through 305 Processing helix chain 'I' and resid 308 through 318 Processing helix chain 'I' and resid 334 through 336 No H-bonds generated for 'chain 'I' and resid 334 through 336' Processing helix chain 'I' and resid 337 through 347 Processing helix chain 'I' and resid 348 through 353 removed outlier: 6.384A pdb=" N THR I 351 " --> pdb=" O SER I 348 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN I 353 " --> pdb=" O SER I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 363 Processing helix chain 'I' and resid 365 through 369 removed outlier: 4.061A pdb=" N SER I 368 " --> pdb=" O ALA I 365 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE I 369 " --> pdb=" O GLY I 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 365 through 369' Processing helix chain 'I' and resid 370 through 375 removed outlier: 3.549A pdb=" N CYS I 374 " --> pdb=" O VAL I 370 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE I 375 " --> pdb=" O HIS I 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 370 through 375' Processing helix chain 'K' and resid 712 through 727 Processing helix chain 'K' and resid 739 through 764 Processing helix chain 'K' and resid 769 through 802 removed outlier: 3.806A pdb=" N LYS K 773 " --> pdb=" O ASP K 769 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE K 792 " --> pdb=" O HIS K 788 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS K 795 " --> pdb=" O ASN K 791 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL K 796 " --> pdb=" O ILE K 792 " (cutoff:3.500A) Processing helix chain 'K' and resid 812 through 843 removed outlier: 4.097A pdb=" N LEU K 818 " --> pdb=" O SER K 814 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR K 843 " --> pdb=" O ALA K 839 " (cutoff:3.500A) Processing helix chain 'L' and resid 712 through 727 Processing helix chain 'L' and resid 739 through 764 Processing helix chain 'L' and resid 769 through 802 removed outlier: 3.806A pdb=" N LYS L 773 " --> pdb=" O ASP L 769 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP L 775 " --> pdb=" O ALA L 771 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE L 792 " --> pdb=" O HIS L 788 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS L 795 " --> pdb=" O ASN L 791 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL L 796 " --> pdb=" O ILE L 792 " (cutoff:3.500A) Processing helix chain 'L' and resid 812 through 843 removed outlier: 4.098A pdb=" N LEU L 818 " --> pdb=" O SER L 814 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR L 843 " --> pdb=" O ALA L 839 " (cutoff:3.500A) Processing helix chain 'N' and resid 712 through 727 Processing helix chain 'N' and resid 739 through 764 Processing helix chain 'N' and resid 769 through 802 removed outlier: 3.807A pdb=" N LYS N 773 " --> pdb=" O ASP N 769 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP N 775 " --> pdb=" O ALA N 771 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE N 792 " --> pdb=" O HIS N 788 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS N 795 " --> pdb=" O ASN N 791 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL N 796 " --> pdb=" O ILE N 792 " (cutoff:3.500A) Processing helix chain 'N' and resid 812 through 843 removed outlier: 4.098A pdb=" N LEU N 818 " --> pdb=" O SER N 814 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR N 843 " --> pdb=" O ALA N 839 " (cutoff:3.500A) Processing helix chain 'O' and resid 712 through 727 Processing helix chain 'O' and resid 739 through 764 Processing helix chain 'O' and resid 769 through 802 removed outlier: 3.806A pdb=" N LYS O 773 " --> pdb=" O ASP O 769 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP O 775 " --> pdb=" O ALA O 771 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE O 792 " --> pdb=" O HIS O 788 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS O 795 " --> pdb=" O ASN O 791 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL O 796 " --> pdb=" O ILE O 792 " (cutoff:3.500A) Processing helix chain 'O' and resid 812 through 843 removed outlier: 4.099A pdb=" N LEU O 818 " --> pdb=" O SER O 814 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR O 843 " --> pdb=" O ALA O 839 " (cutoff:3.500A) Processing helix chain 'Q' and resid 712 through 727 Processing helix chain 'Q' and resid 739 through 764 Processing helix chain 'Q' and resid 769 through 802 removed outlier: 3.805A pdb=" N LYS Q 773 " --> pdb=" O ASP Q 769 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP Q 775 " --> pdb=" O ALA Q 771 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE Q 792 " --> pdb=" O HIS Q 788 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS Q 795 " --> pdb=" O ASN Q 791 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL Q 796 " --> pdb=" O ILE Q 792 " (cutoff:3.500A) Processing helix chain 'Q' and resid 812 through 843 removed outlier: 4.098A pdb=" N LEU Q 818 " --> pdb=" O SER Q 814 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR Q 843 " --> pdb=" O ALA Q 839 " (cutoff:3.500A) Processing helix chain 'X' and resid 712 through 727 Processing helix chain 'X' and resid 739 through 764 Processing helix chain 'X' and resid 769 through 802 removed outlier: 3.806A pdb=" N LYS X 773 " --> pdb=" O ASP X 769 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP X 775 " --> pdb=" O ALA X 771 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE X 792 " --> pdb=" O HIS X 788 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS X 795 " --> pdb=" O ASN X 791 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL X 796 " --> pdb=" O ILE X 792 " (cutoff:3.500A) Processing helix chain 'X' and resid 812 through 843 removed outlier: 4.099A pdb=" N LEU X 818 " --> pdb=" O SER X 814 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR X 843 " --> pdb=" O ALA X 839 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.907A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.634A pdb=" N ILE B 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AA5, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.907A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'D' and resid 71 through 72 removed outlier: 3.634A pdb=" N ILE D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 176 through 178 Processing sheet with id=AB1, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.907A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'E' and resid 71 through 72 removed outlier: 3.635A pdb=" N ILE E 75 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 176 through 178 Processing sheet with id=AB6, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'F' and resid 29 through 31 removed outlier: 3.907A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'F' and resid 71 through 72 removed outlier: 3.635A pdb=" N ILE F 75 " --> pdb=" O GLU F 72 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 176 through 178 Processing sheet with id=AC2, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.907A pdb=" N THR H 106 " --> pdb=" O CYS H 10 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN H 12 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'H' and resid 71 through 72 removed outlier: 3.634A pdb=" N ILE H 75 " --> pdb=" O GLU H 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 176 through 178 Processing sheet with id=AC7, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'I' and resid 29 through 31 removed outlier: 3.907A pdb=" N THR I 106 " --> pdb=" O CYS I 10 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN I 12 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'I' and resid 71 through 72 removed outlier: 3.635A pdb=" N ILE I 75 " --> pdb=" O GLU I 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 176 through 178 Processing sheet with id=AD3, first strand: chain 'I' and resid 238 through 241 1194 hydrogen bonds defined for protein. 3276 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: 4.33 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8197 1.34 - 1.46: 5023 1.46 - 1.58: 12106 1.58 - 1.70: 18 1.70 - 1.82: 372 Bond restraints: 25716 Sorted by residual: bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" CE1 HIC I 73 " pdb=" NE2 HIC I 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.66e+00 ... (remaining 25711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 32847 1.87 - 3.73: 1604 3.73 - 5.60: 253 5.60 - 7.46: 54 7.46 - 9.33: 30 Bond angle restraints: 34788 Sorted by residual: angle pdb=" N SER N 770 " pdb=" CA SER N 770 " pdb=" C SER N 770 " ideal model delta sigma weight residual 111.28 116.61 -5.33 1.09e+00 8.42e-01 2.39e+01 angle pdb=" N SER K 770 " pdb=" CA SER K 770 " pdb=" C SER K 770 " ideal model delta sigma weight residual 111.28 116.58 -5.30 1.09e+00 8.42e-01 2.36e+01 angle pdb=" N SER X 770 " pdb=" CA SER X 770 " pdb=" C SER X 770 " ideal model delta sigma weight residual 111.28 116.57 -5.29 1.09e+00 8.42e-01 2.36e+01 angle pdb=" N SER O 770 " pdb=" CA SER O 770 " pdb=" C SER O 770 " ideal model delta sigma weight residual 111.28 116.57 -5.29 1.09e+00 8.42e-01 2.36e+01 angle pdb=" N SER L 770 " pdb=" CA SER L 770 " pdb=" C SER L 770 " ideal model delta sigma weight residual 111.28 116.56 -5.28 1.09e+00 8.42e-01 2.35e+01 ... (remaining 34783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.80: 14786 29.80 - 59.61: 809 59.61 - 89.41: 96 89.41 - 119.22: 8 119.22 - 149.02: 3 Dihedral angle restraints: 15702 sinusoidal: 6312 harmonic: 9390 Sorted by residual: dihedral pdb=" O1B ADP I 802 " pdb=" O3A ADP I 802 " pdb=" PB ADP I 802 " pdb=" PA ADP I 802 " ideal model delta sinusoidal sigma weight residual 300.00 150.97 149.02 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP H 802 " pdb=" O5' ADP H 802 " pdb=" PA ADP H 802 " pdb=" O2A ADP H 802 " ideal model delta sinusoidal sigma weight residual -60.00 85.97 -145.97 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP I 802 " pdb=" O5' ADP I 802 " pdb=" PA ADP I 802 " pdb=" O2A ADP I 802 " ideal model delta sinusoidal sigma weight residual -60.00 85.94 -145.94 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 15699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3073 0.063 - 0.126: 774 0.126 - 0.189: 65 0.189 - 0.252: 6 0.252 - 0.315: 6 Chirality restraints: 3924 Sorted by residual: chirality pdb=" CB ILE F 330 " pdb=" CA ILE F 330 " pdb=" CG1 ILE F 330 " pdb=" CG2 ILE F 330 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB ILE H 330 " pdb=" CA ILE H 330 " pdb=" CG1 ILE H 330 " pdb=" CG2 ILE H 330 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB ILE D 330 " pdb=" CA ILE D 330 " pdb=" CG1 ILE D 330 " pdb=" CG2 ILE D 330 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3921 not shown) Planarity restraints: 4422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 66 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C THR D 66 " 0.049 2.00e-02 2.50e+03 pdb=" O THR D 66 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU D 67 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 66 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C THR I 66 " -0.049 2.00e-02 2.50e+03 pdb=" O THR I 66 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU I 67 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 66 " -0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C THR E 66 " 0.049 2.00e-02 2.50e+03 pdb=" O THR E 66 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU E 67 " -0.016 2.00e-02 2.50e+03 ... (remaining 4419 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 464 2.66 - 3.22: 22716 3.22 - 3.78: 39781 3.78 - 4.34: 52612 4.34 - 4.90: 87243 Nonbonded interactions: 202816 Sorted by model distance: nonbonded pdb="MG MG H 801 " pdb=" O1B ADP H 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG F 801 " pdb=" O1B ADP F 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.107 2.170 nonbonded pdb="MG MG E 801 " pdb=" O1B ADP E 802 " model vdw 2.107 2.170 ... (remaining 202811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'X' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.300 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.007 0.056 25716 Z= 0.308 Angle : 0.967 9.326 34788 Z= 0.532 Chirality : 0.054 0.315 3924 Planarity : 0.007 0.062 4422 Dihedral : 17.684 149.025 9654 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.29 % Allowed : 13.44 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.12), residues: 3186 helix: -2.70 (0.09), residues: 1590 sheet: -1.17 (0.25), residues: 378 loop : -1.89 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 62 TYR 0.034 0.002 TYR B 166 PHE 0.015 0.002 PHE E 255 TRP 0.013 0.002 TRP F 356 HIS 0.016 0.002 HIS I 161 Details of bonding type rmsd covalent geometry : bond 0.00700 (25716) covalent geometry : angle 0.96717 (34788) hydrogen bonds : bond 0.15847 ( 1194) hydrogen bonds : angle 6.25496 ( 3276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 918 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.7978 (t70) cc_final: 0.7752 (t0) REVERT: B 68 LYS cc_start: 0.8451 (mttt) cc_final: 0.8180 (mmtm) REVERT: B 119 MET cc_start: 0.8322 (ttm) cc_final: 0.8075 (ttp) REVERT: B 121 GLN cc_start: 0.8618 (tt0) cc_final: 0.8411 (tt0) REVERT: B 125 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 211 ASP cc_start: 0.8130 (t0) cc_final: 0.7742 (t0) REVERT: B 215 LYS cc_start: 0.8689 (mttm) cc_final: 0.8405 (mmtp) REVERT: B 237 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: B 244 ASP cc_start: 0.9020 (p0) cc_final: 0.8814 (p0) REVERT: B 252 ASN cc_start: 0.8665 (p0) cc_final: 0.8284 (p0) REVERT: B 305 MET cc_start: 0.8502 (mtp) cc_final: 0.8159 (mtp) REVERT: B 336 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8632 (tttt) REVERT: B 338 SER cc_start: 0.7948 (OUTLIER) cc_final: 0.7719 (t) REVERT: D 49 GLN cc_start: 0.7877 (mm110) cc_final: 0.7458 (mm-40) REVERT: D 192 ILE cc_start: 0.9433 (tp) cc_final: 0.9218 (tt) REVERT: D 211 ASP cc_start: 0.8197 (t0) cc_final: 0.7893 (t0) REVERT: D 244 ASP cc_start: 0.9049 (p0) cc_final: 0.8686 (p0) REVERT: D 246 GLN cc_start: 0.8328 (mt0) cc_final: 0.8090 (mt0) REVERT: D 326 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7536 (mmtm) REVERT: D 336 LYS cc_start: 0.9198 (ttpt) cc_final: 0.8991 (tttt) REVERT: D 360 GLN cc_start: 0.8877 (pt0) cc_final: 0.8539 (pt0) REVERT: D 361 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8147 (tt0) REVERT: E 51 ASP cc_start: 0.8244 (t70) cc_final: 0.7999 (t0) REVERT: E 101 HIS cc_start: 0.8949 (m-70) cc_final: 0.8670 (m90) REVERT: E 116 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7938 (ttm110) REVERT: E 192 ILE cc_start: 0.9503 (tp) cc_final: 0.9103 (tt) REVERT: E 211 ASP cc_start: 0.8196 (t0) cc_final: 0.7544 (t0) REVERT: E 224 GLU cc_start: 0.7954 (mp0) cc_final: 0.7652 (mp0) REVERT: E 226 GLU cc_start: 0.8535 (tp30) cc_final: 0.8192 (tp30) REVERT: E 252 ASN cc_start: 0.8805 (p0) cc_final: 0.8405 (p0) REVERT: E 271 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8813 (m) REVERT: E 280 ASN cc_start: 0.8930 (t0) cc_final: 0.8571 (t0) REVERT: E 336 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8769 (tttt) REVERT: F 78 ASN cc_start: 0.8538 (t0) cc_final: 0.8080 (t0) REVERT: F 151 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8986 (pt) REVERT: F 190 MET cc_start: 0.6265 (mtp) cc_final: 0.5963 (mtp) REVERT: F 192 ILE cc_start: 0.7643 (tp) cc_final: 0.7341 (tt) REVERT: F 226 GLU cc_start: 0.8194 (tp30) cc_final: 0.7750 (tp30) REVERT: F 271 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8844 (m) REVERT: F 280 ASN cc_start: 0.8825 (t0) cc_final: 0.8440 (t0) REVERT: F 296 ASN cc_start: 0.8790 (m-40) cc_final: 0.8547 (m-40) REVERT: F 336 LYS cc_start: 0.9241 (ttpt) cc_final: 0.8862 (tttt) REVERT: F 338 SER cc_start: 0.9514 (OUTLIER) cc_final: 0.9289 (t) REVERT: F 360 GLN cc_start: 0.8790 (pt0) cc_final: 0.8202 (pt0) REVERT: F 361 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8148 (mt-10) REVERT: F 372 ARG cc_start: 0.8053 (ptt180) cc_final: 0.7851 (ptt-90) REVERT: H 78 ASN cc_start: 0.8469 (t0) cc_final: 0.8210 (t0) REVERT: H 192 ILE cc_start: 0.9482 (tp) cc_final: 0.8821 (tt) REVERT: H 205 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: H 211 ASP cc_start: 0.8356 (t0) cc_final: 0.8104 (t0) REVERT: H 237 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: H 325 MET cc_start: 0.8065 (ppp) cc_final: 0.7288 (ppp) REVERT: H 336 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8682 (tttt) REVERT: I 78 ASN cc_start: 0.8521 (t0) cc_final: 0.8212 (t0) REVERT: I 81 ASP cc_start: 0.8389 (m-30) cc_final: 0.7964 (m-30) REVERT: I 82 MET cc_start: 0.9141 (tpt) cc_final: 0.8557 (tpt) REVERT: I 83 GLU cc_start: 0.7858 (pt0) cc_final: 0.7600 (pt0) REVERT: I 192 ILE cc_start: 0.9485 (tp) cc_final: 0.9057 (tt) REVERT: I 202 THR cc_start: 0.9056 (p) cc_final: 0.8437 (t) REVERT: I 280 ASN cc_start: 0.8644 (t0) cc_final: 0.8143 (t0) REVERT: I 314 GLN cc_start: 0.8717 (tt0) cc_final: 0.8437 (tt0) REVERT: I 325 MET cc_start: 0.7992 (ppp) cc_final: 0.7303 (ppp) REVERT: I 326 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7833 (pttp) REVERT: I 329 ILE cc_start: 0.9603 (mm) cc_final: 0.9395 (mm) REVERT: I 336 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8368 (tttt) REVERT: I 361 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7856 (tt0) REVERT: K 701 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: K 723 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7737 (tmm) REVERT: K 781 GLN cc_start: 0.8276 (mt0) cc_final: 0.7999 (mt0) REVERT: K 791 ASN cc_start: 0.8734 (t0) cc_final: 0.8254 (t0) REVERT: K 801 GLN cc_start: 0.8769 (tp40) cc_final: 0.8505 (tp-100) REVERT: K 827 ASN cc_start: 0.8394 (m-40) cc_final: 0.7894 (t0) REVERT: K 845 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8558 (tptp) REVERT: L 718 GLN cc_start: 0.9266 (mt0) cc_final: 0.9002 (mt0) REVERT: L 723 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6879 (tmm) REVERT: L 751 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7377 (tm-30) REVERT: L 791 ASN cc_start: 0.8740 (t0) cc_final: 0.8393 (m-40) REVERT: N 701 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: N 723 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7166 (tpt) REVERT: N 740 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8132 (p) REVERT: N 791 ASN cc_start: 0.8639 (t0) cc_final: 0.8098 (t0) REVERT: N 845 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8420 (tptp) REVERT: N 853 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8366 (m-40) REVERT: O 701 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: O 740 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8532 (p) REVERT: O 791 ASN cc_start: 0.8834 (t0) cc_final: 0.8262 (t0) REVERT: O 797 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8457 (mmtm) REVERT: O 831 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8501 (mm110) REVERT: O 845 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8384 (tptp) REVERT: Q 701 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: Q 713 ILE cc_start: 0.8960 (mm) cc_final: 0.8751 (mm) REVERT: Q 718 GLN cc_start: 0.8971 (mt0) cc_final: 0.8763 (mt0) REVERT: Q 724 MET cc_start: 0.8389 (tpp) cc_final: 0.7904 (tpt) REVERT: X 701 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: X 718 GLN cc_start: 0.9247 (mt0) cc_final: 0.9033 (mt0) REVERT: X 723 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.6591 (tmm) REVERT: X 792 ILE cc_start: 0.9195 (pt) cc_final: 0.8833 (pt) REVERT: X 801 GLN cc_start: 0.8810 (tp40) cc_final: 0.8505 (tp40) REVERT: X 803 LEU cc_start: 0.8956 (tp) cc_final: 0.8662 (tp) REVERT: X 865 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7729 (mm-30) outliers start: 144 outliers final: 47 residues processed: 1010 average time/residue: 0.1624 time to fit residues: 260.1402 Evaluate side-chains 761 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 688 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 GLU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 237 GLU Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain K residue 701 GLU Chi-restraints excluded: chain K residue 723 MET Chi-restraints excluded: chain K residue 725 GLU Chi-restraints excluded: chain K residue 796 VAL Chi-restraints excluded: chain K residue 800 VAL Chi-restraints excluded: chain K residue 845 LYS Chi-restraints excluded: chain L residue 701 GLU Chi-restraints excluded: chain L residue 723 MET Chi-restraints excluded: chain L residue 725 GLU Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 845 LYS Chi-restraints excluded: chain L residue 865 GLU Chi-restraints excluded: chain N residue 701 GLU Chi-restraints excluded: chain N residue 723 MET Chi-restraints excluded: chain N residue 725 GLU Chi-restraints excluded: chain N residue 740 SER Chi-restraints excluded: chain N residue 845 LYS Chi-restraints excluded: chain N residue 853 ASN Chi-restraints excluded: chain N residue 865 GLU Chi-restraints excluded: chain O residue 701 GLU Chi-restraints excluded: chain O residue 725 GLU Chi-restraints excluded: chain O residue 740 SER Chi-restraints excluded: chain O residue 845 LYS Chi-restraints excluded: chain O residue 865 GLU Chi-restraints excluded: chain Q residue 701 GLU Chi-restraints excluded: chain Q residue 725 GLU Chi-restraints excluded: chain Q residue 740 SER Chi-restraints excluded: chain Q residue 796 VAL Chi-restraints excluded: chain Q residue 800 VAL Chi-restraints excluded: chain X residue 701 GLU Chi-restraints excluded: chain X residue 723 MET Chi-restraints excluded: chain X residue 725 GLU Chi-restraints excluded: chain X residue 865 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 173 HIS B 263 GLN D 41 GLN D 263 GLN E 41 GLN E 92 ASN E 128 ASN F 128 ASN ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 263 GLN K 844 GLN L 824 ASN N 718 GLN X 824 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.114018 restraints weight = 35034.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119327 restraints weight = 18199.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122742 restraints weight = 12175.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124836 restraints weight = 9535.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126084 restraints weight = 8242.441| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25716 Z= 0.141 Angle : 0.658 13.804 34788 Z= 0.326 Chirality : 0.043 0.182 3924 Planarity : 0.004 0.036 4422 Dihedral : 11.822 157.083 3717 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.72 % Allowed : 20.08 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 3186 helix: -1.13 (0.12), residues: 1590 sheet: -0.72 (0.26), residues: 366 loop : -1.23 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 116 TYR 0.019 0.001 TYR B 166 PHE 0.022 0.001 PHE O 729 TRP 0.012 0.001 TRP I 356 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00324 (25716) covalent geometry : angle 0.65801 (34788) hydrogen bonds : bond 0.04129 ( 1194) hydrogen bonds : angle 4.34882 ( 3276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 746 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.7900 (t70) cc_final: 0.7699 (t0) REVERT: B 68 LYS cc_start: 0.8495 (mttt) cc_final: 0.8133 (mmtm) REVERT: B 119 MET cc_start: 0.8309 (ttm) cc_final: 0.8045 (ttp) REVERT: B 121 GLN cc_start: 0.8547 (tt0) cc_final: 0.8340 (tt0) REVERT: B 128 ASN cc_start: 0.8794 (m110) cc_final: 0.7681 (m-40) REVERT: B 132 MET cc_start: 0.5495 (ppp) cc_final: 0.4730 (ppp) REVERT: B 198 TYR cc_start: 0.9020 (m-80) cc_final: 0.8809 (m-80) REVERT: B 211 ASP cc_start: 0.8112 (t0) cc_final: 0.7707 (t0) REVERT: B 214 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7418 (mm-30) REVERT: B 215 LYS cc_start: 0.8591 (mttm) cc_final: 0.8291 (mmtp) REVERT: B 336 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8774 (tttt) REVERT: D 44 MET cc_start: 0.7834 (mmm) cc_final: 0.7570 (mmm) REVERT: D 49 GLN cc_start: 0.7769 (mm110) cc_final: 0.7446 (mm-40) REVERT: D 83 GLU cc_start: 0.7976 (pt0) cc_final: 0.7685 (pt0) REVERT: D 226 GLU cc_start: 0.8009 (tp30) cc_final: 0.7694 (tp30) REVERT: D 263 GLN cc_start: 0.8327 (mt0) cc_final: 0.8116 (mt0) REVERT: E 25 ASP cc_start: 0.8042 (p0) cc_final: 0.7798 (p0) REVERT: E 51 ASP cc_start: 0.8005 (t70) cc_final: 0.7707 (t0) REVERT: E 132 MET cc_start: 0.8345 (ppp) cc_final: 0.8055 (ttp) REVERT: E 192 ILE cc_start: 0.9443 (tp) cc_final: 0.8926 (tt) REVERT: E 211 ASP cc_start: 0.8247 (t0) cc_final: 0.7593 (t0) REVERT: E 280 ASN cc_start: 0.8562 (t0) cc_final: 0.8145 (t0) REVERT: E 325 MET cc_start: 0.8225 (ppp) cc_final: 0.7669 (ppp) REVERT: E 336 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8842 (tttt) REVERT: F 78 ASN cc_start: 0.8279 (t0) cc_final: 0.7851 (t0) REVERT: F 81 ASP cc_start: 0.8478 (m-30) cc_final: 0.8161 (m-30) REVERT: F 190 MET cc_start: 0.6444 (mtp) cc_final: 0.6180 (mtp) REVERT: F 192 ILE cc_start: 0.7756 (tp) cc_final: 0.7397 (tt) REVERT: F 280 ASN cc_start: 0.8617 (t0) cc_final: 0.8266 (t0) REVERT: F 336 LYS cc_start: 0.9297 (ttpt) cc_final: 0.9043 (tttt) REVERT: H 192 ILE cc_start: 0.9307 (tp) cc_final: 0.8976 (tt) REVERT: H 205 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: H 211 ASP cc_start: 0.8371 (t0) cc_final: 0.8170 (t0) REVERT: H 325 MET cc_start: 0.8017 (ppp) cc_final: 0.7491 (ppp) REVERT: H 336 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8855 (tttt) REVERT: I 25 ASP cc_start: 0.8167 (p0) cc_final: 0.7923 (p0) REVERT: I 81 ASP cc_start: 0.8428 (m-30) cc_final: 0.8120 (m-30) REVERT: I 82 MET cc_start: 0.9211 (tpt) cc_final: 0.8703 (tpt) REVERT: I 83 GLU cc_start: 0.7823 (pt0) cc_final: 0.7510 (pt0) REVERT: I 192 ILE cc_start: 0.9409 (tp) cc_final: 0.8964 (tp) REVERT: I 214 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7460 (mm-30) REVERT: I 269 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7715 (ttt) REVERT: I 314 GLN cc_start: 0.8818 (tt0) cc_final: 0.8519 (tt0) REVERT: I 325 MET cc_start: 0.7825 (ppp) cc_final: 0.7465 (ppp) REVERT: I 336 LYS cc_start: 0.8982 (ttpt) cc_final: 0.8587 (tttt) REVERT: K 781 GLN cc_start: 0.8207 (mt0) cc_final: 0.7881 (mt0) REVERT: K 791 ASN cc_start: 0.8663 (t0) cc_final: 0.8148 (t0) REVERT: K 827 ASN cc_start: 0.8267 (m-40) cc_final: 0.7898 (t0) REVERT: K 837 TYR cc_start: 0.8697 (t80) cc_final: 0.8404 (t80) REVERT: K 845 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8590 (tptp) REVERT: L 718 GLN cc_start: 0.9259 (mt0) cc_final: 0.9029 (mt0) REVERT: L 791 ASN cc_start: 0.8704 (t0) cc_final: 0.8383 (m-40) REVERT: L 797 LYS cc_start: 0.9175 (tppt) cc_final: 0.8935 (tppt) REVERT: N 740 SER cc_start: 0.8389 (m) cc_final: 0.8182 (p) REVERT: N 801 GLN cc_start: 0.8777 (tp40) cc_final: 0.8558 (tp-100) REVERT: N 845 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8464 (tptp) REVERT: O 740 SER cc_start: 0.8675 (m) cc_final: 0.8369 (t) REVERT: O 791 ASN cc_start: 0.8733 (t0) cc_final: 0.8222 (t0) REVERT: O 797 LYS cc_start: 0.8876 (mmtm) cc_final: 0.8598 (mmtm) REVERT: O 826 MET cc_start: 0.7192 (ttp) cc_final: 0.6905 (ttp) REVERT: O 827 ASN cc_start: 0.8129 (m-40) cc_final: 0.7702 (t0) REVERT: O 845 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8426 (tptp) REVERT: Q 724 MET cc_start: 0.8468 (tpp) cc_final: 0.7982 (tpt) REVERT: X 756 MET cc_start: 0.8831 (tpp) cc_final: 0.8541 (tpp) REVERT: X 801 GLN cc_start: 0.8835 (tp40) cc_final: 0.8514 (tp40) REVERT: X 803 LEU cc_start: 0.9021 (tp) cc_final: 0.8601 (tp) outliers start: 74 outliers final: 46 residues processed: 775 average time/residue: 0.1403 time to fit residues: 180.6020 Evaluate side-chains 727 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 676 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain K residue 845 LYS Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 845 LYS Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 826 MET Chi-restraints excluded: chain N residue 845 LYS Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 845 LYS Chi-restraints excluded: chain Q residue 754 SER Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 789 GLN Chi-restraints excluded: chain X residue 829 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 273 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 216 optimal weight: 0.0570 chunk 175 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 155 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 304 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 overall best weight: 1.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN D 92 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 92 ASN E 115 ASN E 128 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 128 ASN H 12 ASN H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN K 789 GLN K 844 GLN O 844 GLN Q 718 GLN Q 788 HIS X 718 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.163757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116597 restraints weight = 34866.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121753 restraints weight = 18314.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125194 restraints weight = 12318.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127280 restraints weight = 9635.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128337 restraints weight = 8327.678| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25716 Z= 0.125 Angle : 0.615 13.412 34788 Z= 0.305 Chirality : 0.043 0.184 3924 Planarity : 0.003 0.029 4422 Dihedral : 9.512 167.840 3579 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.38 % Allowed : 22.06 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3186 helix: -0.49 (0.12), residues: 1602 sheet: -0.45 (0.27), residues: 366 loop : -0.99 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 256 TYR 0.022 0.001 TYR D 166 PHE 0.026 0.001 PHE K 729 TRP 0.008 0.001 TRP I 356 HIS 0.009 0.001 HIS Q 788 Details of bonding type rmsd covalent geometry : bond 0.00290 (25716) covalent geometry : angle 0.61479 (34788) hydrogen bonds : bond 0.03782 ( 1194) hydrogen bonds : angle 4.16173 ( 3276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 707 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8491 (mttt) cc_final: 0.8239 (mttp) REVERT: B 119 MET cc_start: 0.8182 (ttm) cc_final: 0.7967 (ttp) REVERT: B 198 TYR cc_start: 0.9062 (m-80) cc_final: 0.8773 (m-80) REVERT: B 205 GLU cc_start: 0.8041 (mp0) cc_final: 0.7812 (mp0) REVERT: B 211 ASP cc_start: 0.8149 (t0) cc_final: 0.7740 (t0) REVERT: B 215 LYS cc_start: 0.8591 (mttm) cc_final: 0.8222 (mmtp) REVERT: B 336 LYS cc_start: 0.9097 (ttpt) cc_final: 0.8755 (tttt) REVERT: D 41 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: D 44 MET cc_start: 0.7758 (mmm) cc_final: 0.7332 (mmm) REVERT: D 83 GLU cc_start: 0.7909 (pt0) cc_final: 0.7622 (pt0) REVERT: D 119 MET cc_start: 0.8543 (ttp) cc_final: 0.8337 (ttp) REVERT: D 226 GLU cc_start: 0.8053 (tp30) cc_final: 0.7790 (tp30) REVERT: D 263 GLN cc_start: 0.8375 (mt0) cc_final: 0.8163 (mt0) REVERT: E 25 ASP cc_start: 0.7891 (p0) cc_final: 0.7594 (p0) REVERT: E 51 ASP cc_start: 0.7921 (t70) cc_final: 0.7631 (t0) REVERT: E 192 ILE cc_start: 0.9377 (tp) cc_final: 0.9089 (tt) REVERT: E 211 ASP cc_start: 0.8161 (t0) cc_final: 0.7483 (t0) REVERT: E 280 ASN cc_start: 0.8541 (t0) cc_final: 0.8088 (t0) REVERT: E 325 MET cc_start: 0.8282 (ppp) cc_final: 0.7327 (ppp) REVERT: E 336 LYS cc_start: 0.9073 (ttpt) cc_final: 0.8844 (tttt) REVERT: F 190 MET cc_start: 0.6586 (mtp) cc_final: 0.6283 (mtp) REVERT: F 192 ILE cc_start: 0.7707 (tp) cc_final: 0.7374 (tt) REVERT: F 336 LYS cc_start: 0.9325 (ttpt) cc_final: 0.9086 (tttt) REVERT: H 192 ILE cc_start: 0.9295 (tp) cc_final: 0.8925 (tt) REVERT: H 211 ASP cc_start: 0.8363 (t0) cc_final: 0.8139 (t0) REVERT: H 325 MET cc_start: 0.8042 (ppp) cc_final: 0.7544 (ppp) REVERT: H 336 LYS cc_start: 0.9077 (ttpt) cc_final: 0.8798 (tttt) REVERT: I 25 ASP cc_start: 0.8167 (p0) cc_final: 0.7790 (p0) REVERT: I 83 GLU cc_start: 0.7787 (pt0) cc_final: 0.7488 (pt0) REVERT: I 176 MET cc_start: 0.7876 (mtp) cc_final: 0.7603 (mtt) REVERT: I 192 ILE cc_start: 0.9418 (tp) cc_final: 0.8753 (tp) REVERT: I 195 GLU cc_start: 0.7453 (pt0) cc_final: 0.7216 (pt0) REVERT: I 269 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7745 (ttt) REVERT: I 314 GLN cc_start: 0.8803 (tt0) cc_final: 0.8554 (tt0) REVERT: I 336 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8633 (tttt) REVERT: K 758 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8301 (mmtm) REVERT: K 791 ASN cc_start: 0.8607 (t0) cc_final: 0.8060 (t0) REVERT: K 827 ASN cc_start: 0.8215 (m-40) cc_final: 0.7815 (t0) REVERT: K 845 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8494 (tptp) REVERT: L 791 ASN cc_start: 0.8641 (t0) cc_final: 0.8189 (t0) REVERT: N 723 MET cc_start: 0.7945 (tpt) cc_final: 0.7664 (tpt) REVERT: N 740 SER cc_start: 0.8321 (m) cc_final: 0.8108 (p) REVERT: N 837 TYR cc_start: 0.8651 (t80) cc_final: 0.8387 (t80) REVERT: N 845 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8465 (tptp) REVERT: O 723 MET cc_start: 0.7968 (tmm) cc_final: 0.7256 (tmm) REVERT: O 740 SER cc_start: 0.8678 (m) cc_final: 0.8360 (t) REVERT: O 797 LYS cc_start: 0.8917 (mmtm) cc_final: 0.8591 (mmtm) REVERT: O 845 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8458 (tptp) REVERT: Q 724 MET cc_start: 0.8538 (tpp) cc_final: 0.8017 (tpt) REVERT: Q 779 TYR cc_start: 0.8985 (m-80) cc_final: 0.8779 (m-80) REVERT: X 801 GLN cc_start: 0.8899 (tp40) cc_final: 0.8601 (tp40) REVERT: X 803 LEU cc_start: 0.8946 (tp) cc_final: 0.8569 (tp) REVERT: X 816 MET cc_start: 0.8336 (mmm) cc_final: 0.7924 (mpp) REVERT: X 826 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7174 (ptt) outliers start: 92 outliers final: 56 residues processed: 742 average time/residue: 0.1443 time to fit residues: 178.1048 Evaluate side-chains 736 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 674 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 789 GLN Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain K residue 845 LYS Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain L residue 845 LYS Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 845 LYS Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 845 LYS Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 754 SER Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 789 GLN Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 38 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 270 optimal weight: 40.0000 chunk 192 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 275 HIS D 92 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 49 GLN E 92 ASN E 128 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN F 92 ASN ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN I 128 ASN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 718 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 844 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.160030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112815 restraints weight = 34590.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117903 restraints weight = 18233.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121202 restraints weight = 12325.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123239 restraints weight = 9694.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124467 restraints weight = 8385.389| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25716 Z= 0.196 Angle : 0.650 12.040 34788 Z= 0.322 Chirality : 0.044 0.174 3924 Planarity : 0.003 0.031 4422 Dihedral : 9.269 178.541 3578 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.04 % Allowed : 23.46 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3186 helix: -0.11 (0.13), residues: 1602 sheet: -0.35 (0.27), residues: 366 loop : -0.91 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 372 TYR 0.026 0.001 TYR D 166 PHE 0.025 0.001 PHE N 729 TRP 0.008 0.001 TRP I 356 HIS 0.006 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00461 (25716) covalent geometry : angle 0.65012 (34788) hydrogen bonds : bond 0.03885 ( 1194) hydrogen bonds : angle 4.13180 ( 3276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 689 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8539 (mttt) cc_final: 0.8239 (mttm) REVERT: B 198 TYR cc_start: 0.9184 (m-80) cc_final: 0.8753 (m-80) REVERT: B 214 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7705 (mm-30) REVERT: B 303 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.9010 (p) REVERT: B 336 LYS cc_start: 0.9150 (ttpt) cc_final: 0.8827 (tttt) REVERT: D 41 GLN cc_start: 0.8191 (tt0) cc_final: 0.7955 (tt0) REVERT: D 44 MET cc_start: 0.7819 (mmm) cc_final: 0.7340 (mmm) REVERT: D 83 GLU cc_start: 0.7954 (pt0) cc_final: 0.7678 (pt0) REVERT: D 119 MET cc_start: 0.8577 (ttp) cc_final: 0.8358 (ttp) REVERT: D 263 GLN cc_start: 0.8450 (mt0) cc_final: 0.8231 (mt0) REVERT: E 25 ASP cc_start: 0.7873 (p0) cc_final: 0.7545 (p0) REVERT: E 51 ASP cc_start: 0.8026 (t70) cc_final: 0.7724 (t0) REVERT: E 192 ILE cc_start: 0.9383 (tp) cc_final: 0.9076 (tt) REVERT: E 280 ASN cc_start: 0.8584 (t0) cc_final: 0.8124 (t0) REVERT: E 325 MET cc_start: 0.8506 (ppp) cc_final: 0.7340 (ppp) REVERT: E 336 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8859 (tttt) REVERT: F 132 MET cc_start: 0.8384 (tmm) cc_final: 0.8064 (tmm) REVERT: F 190 MET cc_start: 0.6587 (mtp) cc_final: 0.6367 (mtp) REVERT: F 192 ILE cc_start: 0.7833 (tp) cc_final: 0.7569 (tp) REVERT: F 269 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7841 (ttt) REVERT: F 325 MET cc_start: 0.8162 (ppp) cc_final: 0.7870 (ppp) REVERT: F 336 LYS cc_start: 0.9317 (ttpt) cc_final: 0.9082 (tttt) REVERT: H 83 GLU cc_start: 0.7907 (pt0) cc_final: 0.7635 (pt0) REVERT: H 192 ILE cc_start: 0.9266 (tp) cc_final: 0.8982 (tt) REVERT: H 205 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: H 325 MET cc_start: 0.8218 (ppp) cc_final: 0.7655 (ppp) REVERT: H 336 LYS cc_start: 0.9167 (ttpt) cc_final: 0.8906 (tttt) REVERT: I 25 ASP cc_start: 0.8150 (p0) cc_final: 0.7716 (p0) REVERT: I 83 GLU cc_start: 0.7831 (pt0) cc_final: 0.7506 (pt0) REVERT: I 192 ILE cc_start: 0.9419 (tp) cc_final: 0.8779 (tp) REVERT: I 195 GLU cc_start: 0.7571 (pt0) cc_final: 0.7350 (pt0) REVERT: I 253 GLU cc_start: 0.8297 (mp0) cc_final: 0.8079 (mp0) REVERT: I 269 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7752 (ttt) REVERT: I 280 ASN cc_start: 0.8644 (t0) cc_final: 0.8185 (t0) REVERT: I 314 GLN cc_start: 0.8796 (tt0) cc_final: 0.8580 (tt0) REVERT: I 336 LYS cc_start: 0.9104 (ttpt) cc_final: 0.8802 (tttt) REVERT: I 372 ARG cc_start: 0.8048 (ptt-90) cc_final: 0.7828 (mtm110) REVERT: K 791 ASN cc_start: 0.8612 (t0) cc_final: 0.8185 (t0) REVERT: K 844 GLN cc_start: 0.9023 (tp40) cc_final: 0.8691 (tp40) REVERT: K 845 LYS cc_start: 0.8918 (tttp) cc_final: 0.8520 (tptp) REVERT: L 718 GLN cc_start: 0.9289 (mt0) cc_final: 0.9059 (mt0) REVERT: L 751 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7401 (tm-30) REVERT: L 791 ASN cc_start: 0.8655 (t0) cc_final: 0.8213 (t0) REVERT: L 797 LYS cc_start: 0.9146 (tppt) cc_final: 0.8854 (mmmt) REVERT: N 837 TYR cc_start: 0.8700 (t80) cc_final: 0.8380 (t80) REVERT: N 845 LYS cc_start: 0.8902 (tttp) cc_final: 0.8516 (tptp) REVERT: O 723 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7234 (tmm) REVERT: O 740 SER cc_start: 0.8696 (m) cc_final: 0.8399 (t) REVERT: O 791 ASN cc_start: 0.8646 (t0) cc_final: 0.8095 (t0) REVERT: O 797 LYS cc_start: 0.8876 (mmtm) cc_final: 0.8512 (mmtm) REVERT: O 845 LYS cc_start: 0.8928 (tttp) cc_final: 0.8470 (tptp) REVERT: Q 724 MET cc_start: 0.8588 (tpp) cc_final: 0.8100 (tpt) REVERT: Q 779 TYR cc_start: 0.8977 (m-80) cc_final: 0.8739 (m-80) REVERT: X 801 GLN cc_start: 0.8936 (tp40) cc_final: 0.8596 (tp40) REVERT: X 803 LEU cc_start: 0.8950 (tp) cc_final: 0.8583 (tp) REVERT: X 826 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7185 (ptt) outliers start: 110 outliers final: 73 residues processed: 734 average time/residue: 0.1424 time to fit residues: 174.0999 Evaluate side-chains 746 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 667 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 217 CYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 313 MET Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 789 GLN Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 789 GLN Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 754 SER Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 789 GLN Chi-restraints excluded: chain X residue 792 ILE Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Chi-restraints excluded: chain X residue 833 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 246 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 61 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 254 optimal weight: 30.0000 chunk 117 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 179 optimal weight: 0.0070 overall best weight: 2.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 92 ASN E 128 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 789 GLN ** O 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 718 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.161501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114367 restraints weight = 34398.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.119479 restraints weight = 18091.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122663 restraints weight = 12199.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124759 restraints weight = 9647.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126002 restraints weight = 8346.711| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25716 Z= 0.144 Angle : 0.616 10.762 34788 Z= 0.306 Chirality : 0.043 0.160 3924 Planarity : 0.003 0.030 4422 Dihedral : 9.043 176.706 3562 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.04 % Allowed : 23.72 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3186 helix: 0.12 (0.13), residues: 1602 sheet: -0.25 (0.28), residues: 366 loop : -0.80 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 372 TYR 0.024 0.001 TYR F 166 PHE 0.021 0.001 PHE N 729 TRP 0.008 0.001 TRP I 356 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00339 (25716) covalent geometry : angle 0.61643 (34788) hydrogen bonds : bond 0.03653 ( 1194) hydrogen bonds : angle 4.04844 ( 3276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 692 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8529 (mttt) cc_final: 0.8181 (mmtm) REVERT: B 132 MET cc_start: 0.4834 (ppp) cc_final: 0.4068 (ppp) REVERT: B 211 ASP cc_start: 0.8351 (t0) cc_final: 0.7995 (t0) REVERT: B 336 LYS cc_start: 0.9154 (ttpt) cc_final: 0.8859 (tttt) REVERT: D 44 MET cc_start: 0.7753 (mmm) cc_final: 0.7247 (mmm) REVERT: D 83 GLU cc_start: 0.7950 (pt0) cc_final: 0.7655 (pt0) REVERT: D 263 GLN cc_start: 0.8426 (mt0) cc_final: 0.8202 (mt0) REVERT: E 51 ASP cc_start: 0.8003 (t70) cc_final: 0.7707 (t0) REVERT: E 192 ILE cc_start: 0.9361 (tp) cc_final: 0.8958 (tt) REVERT: E 269 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7912 (ttt) REVERT: E 280 ASN cc_start: 0.8487 (t0) cc_final: 0.8034 (t0) REVERT: E 325 MET cc_start: 0.8555 (ppp) cc_final: 0.7518 (ppp) REVERT: E 336 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8855 (tttt) REVERT: F 132 MET cc_start: 0.8429 (tmm) cc_final: 0.8217 (tmm) REVERT: F 190 MET cc_start: 0.6581 (mtp) cc_final: 0.6377 (mtp) REVERT: F 192 ILE cc_start: 0.7801 (tp) cc_final: 0.7544 (tp) REVERT: F 325 MET cc_start: 0.8249 (ppp) cc_final: 0.7780 (ppp) REVERT: F 336 LYS cc_start: 0.9304 (ttpt) cc_final: 0.9022 (tttt) REVERT: H 78 ASN cc_start: 0.8459 (t0) cc_final: 0.7871 (t0) REVERT: H 83 GLU cc_start: 0.7919 (pt0) cc_final: 0.7623 (pt0) REVERT: H 192 ILE cc_start: 0.9227 (tp) cc_final: 0.8963 (tt) REVERT: H 205 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: H 325 MET cc_start: 0.8278 (ppp) cc_final: 0.7743 (ppp) REVERT: H 336 LYS cc_start: 0.9172 (ttpt) cc_final: 0.8935 (tttt) REVERT: I 25 ASP cc_start: 0.8164 (p0) cc_final: 0.7655 (p0) REVERT: I 83 GLU cc_start: 0.7803 (pt0) cc_final: 0.7463 (pt0) REVERT: I 192 ILE cc_start: 0.9408 (tp) cc_final: 0.8773 (tp) REVERT: I 195 GLU cc_start: 0.7554 (pt0) cc_final: 0.7301 (pt0) REVERT: I 269 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7780 (ttt) REVERT: I 280 ASN cc_start: 0.8591 (t0) cc_final: 0.8152 (t0) REVERT: I 314 GLN cc_start: 0.8794 (tt0) cc_final: 0.8554 (tt0) REVERT: I 325 MET cc_start: 0.8576 (ppp) cc_final: 0.7971 (ppp) REVERT: I 336 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8817 (tttt) REVERT: I 372 ARG cc_start: 0.8024 (ptt-90) cc_final: 0.7793 (mtm110) REVERT: K 791 ASN cc_start: 0.8534 (t0) cc_final: 0.8081 (t0) REVERT: K 844 GLN cc_start: 0.9037 (tp40) cc_final: 0.8728 (tp-100) REVERT: K 845 LYS cc_start: 0.8933 (tttp) cc_final: 0.8518 (tptp) REVERT: L 751 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7443 (tm-30) REVERT: L 791 ASN cc_start: 0.8618 (t0) cc_final: 0.8217 (t0) REVERT: N 779 TYR cc_start: 0.8856 (m-80) cc_final: 0.8483 (m-80) REVERT: N 845 LYS cc_start: 0.8924 (tttp) cc_final: 0.8532 (tptp) REVERT: O 723 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7343 (tmm) REVERT: O 740 SER cc_start: 0.8704 (m) cc_final: 0.8404 (t) REVERT: O 791 ASN cc_start: 0.8540 (t0) cc_final: 0.7987 (t0) REVERT: O 797 LYS cc_start: 0.8870 (mmtm) cc_final: 0.8550 (mmtm) REVERT: O 803 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8340 (mp) REVERT: O 845 LYS cc_start: 0.8937 (tttp) cc_final: 0.8519 (tptp) REVERT: Q 724 MET cc_start: 0.8567 (tpp) cc_final: 0.8069 (tpt) REVERT: Q 779 TYR cc_start: 0.8926 (m-80) cc_final: 0.8706 (m-80) REVERT: X 801 GLN cc_start: 0.8906 (tp40) cc_final: 0.8564 (tp40) REVERT: X 826 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7247 (ptt) outliers start: 110 outliers final: 72 residues processed: 731 average time/residue: 0.1445 time to fit residues: 176.2641 Evaluate side-chains 744 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 666 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 787 CYS Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 725 GLU Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 829 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 789 GLN Chi-restraints excluded: chain O residue 803 LEU Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 749 ILE Chi-restraints excluded: chain Q residue 754 SER Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 789 GLN Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Chi-restraints excluded: chain X residue 833 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 99 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 292 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 92 ASN E 128 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 789 GLN L 718 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.156576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.109457 restraints weight = 34742.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114625 restraints weight = 18155.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117950 restraints weight = 12199.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120037 restraints weight = 9564.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121267 restraints weight = 8255.906| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25716 Z= 0.198 Angle : 0.653 10.238 34788 Z= 0.323 Chirality : 0.045 0.167 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.869 179.430 3560 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.22 % Allowed : 24.63 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3186 helix: 0.25 (0.13), residues: 1602 sheet: 0.01 (0.29), residues: 330 loop : -0.75 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 372 TYR 0.019 0.001 TYR Q 837 PHE 0.021 0.001 PHE N 729 TRP 0.009 0.001 TRP E 356 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00468 (25716) covalent geometry : angle 0.65315 (34788) hydrogen bonds : bond 0.03843 ( 1194) hydrogen bonds : angle 4.06389 ( 3276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 669 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8529 (mttt) cc_final: 0.8182 (mmtm) REVERT: B 132 MET cc_start: 0.5267 (ppp) cc_final: 0.4524 (ppp) REVERT: B 211 ASP cc_start: 0.8416 (t0) cc_final: 0.8177 (t0) REVERT: B 336 LYS cc_start: 0.9226 (ttpt) cc_final: 0.8925 (tttt) REVERT: D 44 MET cc_start: 0.7751 (mmm) cc_final: 0.7353 (mmm) REVERT: D 83 GLU cc_start: 0.7984 (pt0) cc_final: 0.7686 (pt0) REVERT: D 263 GLN cc_start: 0.8511 (mt0) cc_final: 0.8300 (mt0) REVERT: D 297 ASN cc_start: 0.8353 (m-40) cc_final: 0.8065 (m-40) REVERT: E 51 ASP cc_start: 0.8046 (t70) cc_final: 0.7760 (t0) REVERT: E 192 ILE cc_start: 0.9294 (tp) cc_final: 0.9061 (tp) REVERT: E 211 ASP cc_start: 0.8202 (t0) cc_final: 0.7787 (t0) REVERT: E 269 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7969 (ttt) REVERT: E 325 MET cc_start: 0.8580 (ppp) cc_final: 0.7643 (ppp) REVERT: E 336 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8873 (tttt) REVERT: F 132 MET cc_start: 0.8436 (tmm) cc_final: 0.8135 (tmm) REVERT: F 192 ILE cc_start: 0.7999 (tp) cc_final: 0.7750 (tp) REVERT: F 325 MET cc_start: 0.8438 (ppp) cc_final: 0.7702 (ppp) REVERT: F 336 LYS cc_start: 0.9303 (ttpt) cc_final: 0.9036 (tttt) REVERT: H 83 GLU cc_start: 0.7905 (pt0) cc_final: 0.7640 (pt0) REVERT: H 192 ILE cc_start: 0.9214 (tp) cc_final: 0.9003 (tp) REVERT: H 205 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: H 325 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7775 (ppp) REVERT: H 336 LYS cc_start: 0.9246 (ttpt) cc_final: 0.9026 (tttt) REVERT: I 25 ASP cc_start: 0.8152 (p0) cc_final: 0.7584 (p0) REVERT: I 83 GLU cc_start: 0.7826 (pt0) cc_final: 0.7487 (pt0) REVERT: I 192 ILE cc_start: 0.9429 (tp) cc_final: 0.8808 (tp) REVERT: I 195 GLU cc_start: 0.7654 (pt0) cc_final: 0.7405 (pt0) REVERT: I 253 GLU cc_start: 0.8321 (mp0) cc_final: 0.8054 (mp0) REVERT: I 269 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7740 (ttt) REVERT: I 325 MET cc_start: 0.8637 (ppp) cc_final: 0.8088 (ppp) REVERT: I 336 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8880 (tttt) REVERT: K 791 ASN cc_start: 0.8563 (t0) cc_final: 0.8168 (t0) REVERT: K 844 GLN cc_start: 0.9061 (tp40) cc_final: 0.8736 (tp40) REVERT: K 845 LYS cc_start: 0.8931 (tttp) cc_final: 0.8523 (tptp) REVERT: L 751 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: L 791 ASN cc_start: 0.8647 (t0) cc_final: 0.8199 (t0) REVERT: N 845 LYS cc_start: 0.8976 (tttp) cc_final: 0.8548 (tptp) REVERT: O 723 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7314 (tmm) REVERT: O 740 SER cc_start: 0.8721 (m) cc_final: 0.8434 (t) REVERT: O 791 ASN cc_start: 0.8567 (t0) cc_final: 0.8026 (t0) REVERT: O 845 LYS cc_start: 0.8978 (tttp) cc_final: 0.8549 (tptp) REVERT: Q 724 MET cc_start: 0.8575 (tpp) cc_final: 0.8001 (tpt) REVERT: Q 779 TYR cc_start: 0.8920 (m-80) cc_final: 0.8700 (m-80) REVERT: X 766 HIS cc_start: 0.8304 (m90) cc_final: 0.8099 (m90) REVERT: X 826 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7270 (ptt) outliers start: 115 outliers final: 89 residues processed: 718 average time/residue: 0.1391 time to fit residues: 166.6511 Evaluate side-chains 745 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 649 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 217 CYS Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 372 ARG Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 330 ILE Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 787 CYS Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 715 LEU Chi-restraints excluded: chain L residue 751 GLU Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 792 ILE Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 833 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 789 GLN Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain O residue 829 VAL Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 754 SER Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 789 GLN Chi-restraints excluded: chain X residue 792 ILE Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Chi-restraints excluded: chain X residue 833 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 10 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 223 optimal weight: 0.0770 chunk 287 optimal weight: 7.9990 chunk 160 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 overall best weight: 2.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 GLN K 831 GLN N 718 GLN ** O 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109696 restraints weight = 34577.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.114841 restraints weight = 18302.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118117 restraints weight = 12384.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120199 restraints weight = 9767.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121433 restraints weight = 8459.591| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25716 Z= 0.161 Angle : 0.633 8.668 34788 Z= 0.313 Chirality : 0.044 0.162 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.670 172.960 3558 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.11 % Allowed : 25.55 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 3186 helix: 0.44 (0.13), residues: 1584 sheet: 0.08 (0.30), residues: 330 loop : -0.57 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 372 TYR 0.033 0.001 TYR I 166 PHE 0.019 0.001 PHE O 729 TRP 0.009 0.001 TRP E 356 HIS 0.004 0.001 HIS I 161 Details of bonding type rmsd covalent geometry : bond 0.00382 (25716) covalent geometry : angle 0.63256 (34788) hydrogen bonds : bond 0.03693 ( 1194) hydrogen bonds : angle 4.01537 ( 3276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 681 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8500 (mttt) cc_final: 0.8180 (mmtm) REVERT: B 202 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8725 (t) REVERT: B 211 ASP cc_start: 0.8361 (t0) cc_final: 0.8080 (t0) REVERT: B 336 LYS cc_start: 0.9213 (ttpt) cc_final: 0.8923 (tttt) REVERT: D 44 MET cc_start: 0.7660 (mmm) cc_final: 0.7217 (mmm) REVERT: D 83 GLU cc_start: 0.7947 (pt0) cc_final: 0.7654 (pt0) REVERT: D 224 GLU cc_start: 0.7768 (mp0) cc_final: 0.7527 (mp0) REVERT: D 263 GLN cc_start: 0.8494 (mt0) cc_final: 0.8269 (mt0) REVERT: E 51 ASP cc_start: 0.8035 (t70) cc_final: 0.7740 (t0) REVERT: E 82 MET cc_start: 0.9206 (tpt) cc_final: 0.9000 (tpt) REVERT: E 192 ILE cc_start: 0.9239 (tp) cc_final: 0.8978 (tt) REVERT: E 211 ASP cc_start: 0.8187 (t0) cc_final: 0.7751 (t0) REVERT: E 269 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8009 (ttt) REVERT: E 325 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7726 (ppp) REVERT: E 336 LYS cc_start: 0.9069 (ttpt) cc_final: 0.8830 (tttt) REVERT: F 132 MET cc_start: 0.8385 (tmm) cc_final: 0.8044 (tmm) REVERT: F 192 ILE cc_start: 0.8021 (tp) cc_final: 0.7796 (tp) REVERT: F 325 MET cc_start: 0.8410 (ppp) cc_final: 0.7323 (ppp) REVERT: F 336 LYS cc_start: 0.9284 (ttpt) cc_final: 0.9008 (tttt) REVERT: H 83 GLU cc_start: 0.7875 (pt0) cc_final: 0.7643 (pt0) REVERT: H 205 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: H 325 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7760 (ppp) REVERT: H 336 LYS cc_start: 0.9243 (ttpt) cc_final: 0.9042 (tttt) REVERT: I 25 ASP cc_start: 0.8133 (p0) cc_final: 0.7502 (p0) REVERT: I 83 GLU cc_start: 0.7844 (pt0) cc_final: 0.7537 (pt0) REVERT: I 192 ILE cc_start: 0.9448 (tp) cc_final: 0.8875 (tp) REVERT: I 195 GLU cc_start: 0.7622 (pt0) cc_final: 0.7361 (pt0) REVERT: I 269 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7751 (ttt) REVERT: I 316 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7645 (mm-30) REVERT: I 325 MET cc_start: 0.8653 (ppp) cc_final: 0.8153 (ppp) REVERT: I 336 LYS cc_start: 0.9173 (ttpt) cc_final: 0.8859 (tttt) REVERT: K 791 ASN cc_start: 0.8527 (t0) cc_final: 0.8165 (t0) REVERT: K 837 TYR cc_start: 0.8663 (t80) cc_final: 0.8443 (t80) REVERT: K 844 GLN cc_start: 0.9028 (tp40) cc_final: 0.8721 (tp40) REVERT: K 845 LYS cc_start: 0.8936 (tttp) cc_final: 0.8508 (tptp) REVERT: L 721 MET cc_start: 0.8898 (ppp) cc_final: 0.8616 (ptm) REVERT: L 751 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: L 791 ASN cc_start: 0.8557 (t0) cc_final: 0.8200 (t0) REVERT: N 845 LYS cc_start: 0.8953 (tttp) cc_final: 0.8541 (tptp) REVERT: O 723 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7318 (tmm) REVERT: O 724 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8056 (tpt) REVERT: O 740 SER cc_start: 0.8700 (m) cc_final: 0.8414 (t) REVERT: O 845 LYS cc_start: 0.8969 (tttp) cc_final: 0.8514 (tptp) REVERT: Q 701 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: Q 724 MET cc_start: 0.8559 (tpp) cc_final: 0.8054 (tpt) REVERT: Q 779 TYR cc_start: 0.8915 (m-80) cc_final: 0.8654 (m-80) REVERT: X 766 HIS cc_start: 0.8262 (m90) cc_final: 0.8018 (m90) REVERT: X 791 ASN cc_start: 0.8562 (t0) cc_final: 0.8057 (t0) REVERT: X 826 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7253 (ptt) outliers start: 112 outliers final: 86 residues processed: 715 average time/residue: 0.1427 time to fit residues: 170.3681 Evaluate side-chains 756 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 659 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 372 ARG Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 330 ILE Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 715 LEU Chi-restraints excluded: chain L residue 725 GLU Chi-restraints excluded: chain L residue 751 GLU Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 718 GLN Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 829 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 724 MET Chi-restraints excluded: chain O residue 789 GLN Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain Q residue 701 GLU Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 754 SER Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 789 GLN Chi-restraints excluded: chain X residue 796 VAL Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 258 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 225 optimal weight: 8.9990 chunk 211 optimal weight: 0.0060 chunk 249 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 276 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 chunk 284 optimal weight: 30.0000 overall best weight: 5.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 831 GLN L 718 GLN ** X 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.154553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108019 restraints weight = 34643.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113068 restraints weight = 18119.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116282 restraints weight = 12167.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118261 restraints weight = 9570.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119434 restraints weight = 8291.696| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25716 Z= 0.269 Angle : 0.703 8.528 34788 Z= 0.348 Chirality : 0.047 0.182 3924 Planarity : 0.003 0.034 4422 Dihedral : 8.603 167.129 3558 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.26 % Allowed : 26.10 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3186 helix: 0.33 (0.13), residues: 1602 sheet: -0.02 (0.30), residues: 330 loop : -0.59 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 256 TYR 0.020 0.001 TYR I 166 PHE 0.020 0.001 PHE K 729 TRP 0.010 0.001 TRP F 79 HIS 0.005 0.001 HIS Q 788 Details of bonding type rmsd covalent geometry : bond 0.00631 (25716) covalent geometry : angle 0.70325 (34788) hydrogen bonds : bond 0.04124 ( 1194) hydrogen bonds : angle 4.16270 ( 3276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 678 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8519 (mttt) cc_final: 0.8252 (mttm) REVERT: B 192 ILE cc_start: 0.9437 (tt) cc_final: 0.9207 (tt) REVERT: B 202 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8790 (t) REVERT: B 211 ASP cc_start: 0.8416 (t0) cc_final: 0.8115 (t0) REVERT: B 336 LYS cc_start: 0.9201 (ttpt) cc_final: 0.8997 (tttt) REVERT: D 83 GLU cc_start: 0.8013 (pt0) cc_final: 0.7707 (pt0) REVERT: D 263 GLN cc_start: 0.8515 (mt0) cc_final: 0.8287 (mt0) REVERT: D 326 LYS cc_start: 0.8447 (pttp) cc_final: 0.8199 (pttm) REVERT: E 51 ASP cc_start: 0.8097 (t70) cc_final: 0.7796 (t0) REVERT: E 157 ASP cc_start: 0.8638 (t70) cc_final: 0.7932 (t0) REVERT: E 192 ILE cc_start: 0.9237 (tp) cc_final: 0.8957 (tp) REVERT: E 269 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7940 (ttt) REVERT: E 325 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7805 (ppp) REVERT: E 336 LYS cc_start: 0.9130 (ttpt) cc_final: 0.8879 (tttt) REVERT: F 78 ASN cc_start: 0.8277 (t0) cc_final: 0.8050 (t0) REVERT: F 192 ILE cc_start: 0.8103 (tp) cc_final: 0.7878 (tp) REVERT: F 253 GLU cc_start: 0.8369 (mp0) cc_final: 0.8118 (mp0) REVERT: F 325 MET cc_start: 0.8477 (ppp) cc_final: 0.7304 (ppp) REVERT: F 336 LYS cc_start: 0.9310 (ttpt) cc_final: 0.9046 (tttt) REVERT: H 83 GLU cc_start: 0.7927 (pt0) cc_final: 0.7687 (pt0) REVERT: H 205 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: H 325 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7851 (ppp) REVERT: H 336 LYS cc_start: 0.9322 (ttpt) cc_final: 0.9107 (tttt) REVERT: I 25 ASP cc_start: 0.8207 (p0) cc_final: 0.7699 (p0) REVERT: I 83 GLU cc_start: 0.7881 (pt0) cc_final: 0.7560 (pt0) REVERT: I 192 ILE cc_start: 0.9433 (tp) cc_final: 0.8892 (tp) REVERT: I 195 GLU cc_start: 0.7726 (pt0) cc_final: 0.7463 (pt0) REVERT: I 253 GLU cc_start: 0.8331 (mp0) cc_final: 0.8076 (mp0) REVERT: I 269 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7693 (ttt) REVERT: I 325 MET cc_start: 0.8733 (ppp) cc_final: 0.8260 (ppp) REVERT: K 791 ASN cc_start: 0.8626 (t0) cc_final: 0.8212 (t0) REVERT: K 801 GLN cc_start: 0.8934 (tp40) cc_final: 0.8554 (tp40) REVERT: K 845 LYS cc_start: 0.9028 (tttp) cc_final: 0.8529 (tptp) REVERT: L 751 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7403 (tm-30) REVERT: L 791 ASN cc_start: 0.8666 (t0) cc_final: 0.8256 (t0) REVERT: L 826 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7357 (ptt) REVERT: N 845 LYS cc_start: 0.9003 (tttp) cc_final: 0.8546 (tptp) REVERT: O 723 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7435 (tmm) REVERT: O 724 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8132 (tpt) REVERT: O 740 SER cc_start: 0.8751 (m) cc_final: 0.8475 (t) REVERT: O 791 ASN cc_start: 0.8598 (t0) cc_final: 0.8017 (t0) REVERT: O 845 LYS cc_start: 0.8999 (tttp) cc_final: 0.8542 (tptp) REVERT: Q 701 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: Q 779 TYR cc_start: 0.8958 (m-80) cc_final: 0.8639 (m-80) REVERT: X 766 HIS cc_start: 0.8297 (m90) cc_final: 0.7982 (m90) REVERT: X 791 ASN cc_start: 0.8605 (t0) cc_final: 0.8014 (t0) REVERT: X 826 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7396 (ptt) outliers start: 116 outliers final: 93 residues processed: 718 average time/residue: 0.1449 time to fit residues: 173.0353 Evaluate side-chains 774 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 669 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 372 ARG Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 330 ILE Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 787 CYS Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 715 LEU Chi-restraints excluded: chain L residue 718 GLN Chi-restraints excluded: chain L residue 725 GLU Chi-restraints excluded: chain L residue 751 GLU Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 789 GLN Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 829 VAL Chi-restraints excluded: chain N residue 833 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 724 MET Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain Q residue 701 GLU Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 754 SER Chi-restraints excluded: chain Q residue 787 CYS Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain Q residue 849 MET Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 787 CYS Chi-restraints excluded: chain X residue 789 GLN Chi-restraints excluded: chain X residue 792 ILE Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 195 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 297 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 130 optimal weight: 40.0000 chunk 107 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN D 137 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 831 GLN L 718 GLN N 718 GLN O 789 GLN ** O 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.156242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.109977 restraints weight = 34280.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115039 restraints weight = 17878.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118297 restraints weight = 12007.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120300 restraints weight = 9443.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121521 restraints weight = 8159.096| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25716 Z= 0.145 Angle : 0.649 9.509 34788 Z= 0.322 Chirality : 0.044 0.161 3924 Planarity : 0.003 0.030 4422 Dihedral : 8.398 161.027 3558 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.56 % Allowed : 26.76 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3186 helix: 0.61 (0.13), residues: 1548 sheet: 0.07 (0.30), residues: 330 loop : -0.40 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 372 TYR 0.020 0.001 TYR I 166 PHE 0.021 0.001 PHE K 729 TRP 0.010 0.001 TRP E 356 HIS 0.005 0.001 HIS X 788 Details of bonding type rmsd covalent geometry : bond 0.00345 (25716) covalent geometry : angle 0.64919 (34788) hydrogen bonds : bond 0.03710 ( 1194) hydrogen bonds : angle 4.06506 ( 3276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 687 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8483 (mttt) cc_final: 0.8143 (mmtm) REVERT: B 192 ILE cc_start: 0.9445 (tt) cc_final: 0.9210 (tt) REVERT: B 202 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8689 (t) REVERT: B 211 ASP cc_start: 0.8372 (t0) cc_final: 0.8098 (t0) REVERT: B 240 TYR cc_start: 0.9201 (t80) cc_final: 0.8959 (t80) REVERT: B 336 LYS cc_start: 0.9194 (ttpt) cc_final: 0.8921 (tttt) REVERT: D 44 MET cc_start: 0.7601 (mmm) cc_final: 0.7266 (mmm) REVERT: D 83 GLU cc_start: 0.7952 (pt0) cc_final: 0.7645 (pt0) REVERT: D 263 GLN cc_start: 0.8463 (mt0) cc_final: 0.8262 (mt0) REVERT: D 326 LYS cc_start: 0.8401 (pttp) cc_final: 0.8157 (pttm) REVERT: E 51 ASP cc_start: 0.8037 (t70) cc_final: 0.7745 (t0) REVERT: E 82 MET cc_start: 0.9201 (tpt) cc_final: 0.8914 (tpt) REVERT: E 192 ILE cc_start: 0.9239 (tp) cc_final: 0.9034 (tp) REVERT: E 211 ASP cc_start: 0.8209 (t0) cc_final: 0.7783 (t0) REVERT: E 269 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8026 (ttt) REVERT: E 325 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7748 (ppp) REVERT: E 336 LYS cc_start: 0.9067 (ttpt) cc_final: 0.8816 (tttt) REVERT: F 192 ILE cc_start: 0.8059 (tp) cc_final: 0.7845 (tp) REVERT: F 325 MET cc_start: 0.8409 (ppp) cc_final: 0.7281 (ppp) REVERT: F 336 LYS cc_start: 0.9288 (ttpt) cc_final: 0.9012 (tttt) REVERT: H 137 GLN cc_start: 0.8749 (tt0) cc_final: 0.8502 (tt0) REVERT: H 205 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: H 325 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7883 (ppp) REVERT: H 336 LYS cc_start: 0.9288 (ttpt) cc_final: 0.9081 (tttt) REVERT: I 25 ASP cc_start: 0.8181 (p0) cc_final: 0.7517 (p0) REVERT: I 83 GLU cc_start: 0.7828 (pt0) cc_final: 0.7508 (pt0) REVERT: I 192 ILE cc_start: 0.9431 (tp) cc_final: 0.8855 (tp) REVERT: I 195 GLU cc_start: 0.7635 (pt0) cc_final: 0.7404 (pt0) REVERT: I 253 GLU cc_start: 0.8291 (mp0) cc_final: 0.8033 (mp0) REVERT: I 269 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7748 (ttt) REVERT: I 325 MET cc_start: 0.8679 (ppp) cc_final: 0.8212 (ppp) REVERT: K 791 ASN cc_start: 0.8541 (t0) cc_final: 0.8209 (t0) REVERT: K 845 LYS cc_start: 0.8929 (tttp) cc_final: 0.8506 (tptp) REVERT: L 721 MET cc_start: 0.8906 (ppp) cc_final: 0.8629 (ptm) REVERT: L 751 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: L 791 ASN cc_start: 0.8551 (t0) cc_final: 0.8234 (t0) REVERT: N 845 LYS cc_start: 0.8969 (tttp) cc_final: 0.8547 (tptp) REVERT: O 723 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7359 (tpt) REVERT: O 724 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8120 (tpt) REVERT: O 740 SER cc_start: 0.8676 (m) cc_final: 0.8400 (t) REVERT: Q 701 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: Q 779 TYR cc_start: 0.8904 (m-80) cc_final: 0.8657 (m-80) REVERT: X 766 HIS cc_start: 0.8282 (m90) cc_final: 0.7964 (m90) REVERT: X 791 ASN cc_start: 0.8553 (t0) cc_final: 0.8062 (t0) REVERT: X 801 GLN cc_start: 0.8873 (tp40) cc_final: 0.8524 (tm-30) REVERT: X 826 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7355 (ptt) outliers start: 97 outliers final: 74 residues processed: 712 average time/residue: 0.1435 time to fit residues: 170.0778 Evaluate side-chains 754 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 669 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 372 ARG Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 330 ILE Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 702 VAL Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 715 LEU Chi-restraints excluded: chain L residue 718 GLN Chi-restraints excluded: chain L residue 751 GLU Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 718 GLN Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 829 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 724 MET Chi-restraints excluded: chain O residue 789 GLN Chi-restraints excluded: chain Q residue 701 GLU Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 754 SER Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 789 GLN Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 42 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 77 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 285 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 174 optimal weight: 0.0040 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN D 137 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 831 GLN K 844 GLN L 718 GLN N 718 GLN N 789 GLN O 789 GLN X 718 GLN ** X 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.158344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111300 restraints weight = 34506.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116470 restraints weight = 18142.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119820 restraints weight = 12245.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121894 restraints weight = 9620.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123117 restraints weight = 8308.562| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25716 Z= 0.133 Angle : 0.647 10.540 34788 Z= 0.320 Chirality : 0.044 0.204 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.192 157.095 3558 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.27 % Allowed : 27.50 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3186 helix: 0.69 (0.13), residues: 1548 sheet: 0.10 (0.30), residues: 330 loop : -0.33 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 372 TYR 0.019 0.001 TYR I 166 PHE 0.024 0.001 PHE X 729 TRP 0.015 0.001 TRP D 340 HIS 0.007 0.001 HIS O 788 Details of bonding type rmsd covalent geometry : bond 0.00315 (25716) covalent geometry : angle 0.64733 (34788) hydrogen bonds : bond 0.03609 ( 1194) hydrogen bonds : angle 4.01718 ( 3276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 684 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 SER cc_start: 0.9358 (p) cc_final: 0.9121 (p) REVERT: B 68 LYS cc_start: 0.8485 (mttt) cc_final: 0.8137 (mmtm) REVERT: B 211 ASP cc_start: 0.8359 (t0) cc_final: 0.8061 (t0) REVERT: B 269 MET cc_start: 0.8413 (ttt) cc_final: 0.8188 (ttt) REVERT: B 299 MET cc_start: 0.2245 (mtm) cc_final: 0.1537 (mtm) REVERT: B 336 LYS cc_start: 0.9165 (ttpt) cc_final: 0.8862 (tttt) REVERT: D 44 MET cc_start: 0.7499 (mmm) cc_final: 0.7132 (mmm) REVERT: D 83 GLU cc_start: 0.7956 (pt0) cc_final: 0.7637 (pt0) REVERT: D 263 GLN cc_start: 0.8448 (mt0) cc_final: 0.8237 (mt0) REVERT: D 326 LYS cc_start: 0.8421 (pttp) cc_final: 0.8155 (pttm) REVERT: E 51 ASP cc_start: 0.8034 (t70) cc_final: 0.7744 (t0) REVERT: E 82 MET cc_start: 0.9244 (tpt) cc_final: 0.8986 (tpt) REVERT: E 192 ILE cc_start: 0.9242 (tp) cc_final: 0.9036 (tp) REVERT: E 211 ASP cc_start: 0.8207 (t0) cc_final: 0.7737 (t0) REVERT: E 269 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.8027 (ttt) REVERT: E 325 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7749 (ppp) REVERT: E 336 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8856 (tttt) REVERT: F 192 ILE cc_start: 0.8052 (tp) cc_final: 0.7835 (tp) REVERT: F 325 MET cc_start: 0.8363 (ppp) cc_final: 0.7236 (ppp) REVERT: F 336 LYS cc_start: 0.9284 (ttpt) cc_final: 0.8982 (tttt) REVERT: H 137 GLN cc_start: 0.8770 (tt0) cc_final: 0.8565 (tt0) REVERT: H 205 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: H 325 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7872 (ppp) REVERT: H 336 LYS cc_start: 0.9277 (ttpt) cc_final: 0.9070 (tttt) REVERT: I 25 ASP cc_start: 0.8121 (p0) cc_final: 0.7444 (p0) REVERT: I 83 GLU cc_start: 0.7831 (pt0) cc_final: 0.7516 (pt0) REVERT: I 192 ILE cc_start: 0.9432 (tp) cc_final: 0.8865 (tp) REVERT: I 195 GLU cc_start: 0.7587 (pt0) cc_final: 0.7330 (pt0) REVERT: I 269 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7777 (ttt) REVERT: I 316 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7723 (mm-30) REVERT: I 325 MET cc_start: 0.8704 (ppp) cc_final: 0.8302 (ppp) REVERT: I 336 LYS cc_start: 0.9206 (ttpt) cc_final: 0.8863 (tttt) REVERT: K 791 ASN cc_start: 0.8467 (t0) cc_final: 0.8180 (t0) REVERT: K 845 LYS cc_start: 0.8928 (tttp) cc_final: 0.8505 (tptp) REVERT: L 751 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: L 791 ASN cc_start: 0.8497 (t0) cc_final: 0.8223 (t0) REVERT: N 845 LYS cc_start: 0.8984 (tttp) cc_final: 0.8520 (tptp) REVERT: O 723 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7362 (tpt) REVERT: O 724 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8119 (tpt) REVERT: O 740 SER cc_start: 0.8679 (m) cc_final: 0.8406 (t) REVERT: O 791 ASN cc_start: 0.8521 (t0) cc_final: 0.8066 (t0) REVERT: Q 701 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: Q 724 MET cc_start: 0.8602 (tpp) cc_final: 0.8339 (tpp) REVERT: Q 779 TYR cc_start: 0.8864 (m-80) cc_final: 0.8611 (m-80) REVERT: X 766 HIS cc_start: 0.8217 (m90) cc_final: 0.7961 (m90) REVERT: X 791 ASN cc_start: 0.8513 (t0) cc_final: 0.8070 (t0) REVERT: X 801 GLN cc_start: 0.8856 (tp40) cc_final: 0.8542 (tm-30) REVERT: X 826 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7431 (ptt) outliers start: 89 outliers final: 70 residues processed: 708 average time/residue: 0.1381 time to fit residues: 162.1699 Evaluate side-chains 745 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 665 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 372 ARG Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 330 ILE Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 702 VAL Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 751 GLU Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 718 GLN Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 829 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 724 MET Chi-restraints excluded: chain O residue 787 CYS Chi-restraints excluded: chain O residue 789 GLN Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain Q residue 701 GLU Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 754 SER Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 787 CYS Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 227 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 276 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 chunk 262 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 198 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN D 137 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 718 GLN N 718 GLN O 789 GLN ** X 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108658 restraints weight = 34486.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113735 restraints weight = 18344.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117043 restraints weight = 12440.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119027 restraints weight = 9804.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120072 restraints weight = 8534.202| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25716 Z= 0.198 Angle : 0.671 10.929 34788 Z= 0.331 Chirality : 0.045 0.240 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.197 159.264 3558 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.45 % Allowed : 27.46 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3186 helix: 0.68 (0.13), residues: 1548 sheet: 0.02 (0.30), residues: 330 loop : -0.30 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 372 TYR 0.020 0.001 TYR O 779 PHE 0.022 0.001 PHE X 729 TRP 0.009 0.001 TRP D 340 HIS 0.010 0.001 HIS O 788 Details of bonding type rmsd covalent geometry : bond 0.00471 (25716) covalent geometry : angle 0.67134 (34788) hydrogen bonds : bond 0.03822 ( 1194) hydrogen bonds : angle 4.06270 ( 3276) =============================================================================== Job complete usr+sys time: 4926.87 seconds wall clock time: 85 minutes 45.59 seconds (5145.59 seconds total)