Starting phenix.real_space_refine on Sun Sep 13 17:59:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wvt_21925/09_2026/6wvt_21925.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wvt_21925/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6wvt_21925/09_2026/6wvt_21925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wvt_21925/09_2026/6wvt_21925.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wvt_21925/09_2026/6wvt_21925.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wvt_21925/09_2026/6wvt_21925.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wvt_21925/09_2026/6wvt_21925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wvt_21925/09_2026/6wvt_21925.map" } 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-2.2.1-6174/lib/python3.11/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: 4.72, per 1000 atoms: 0.19 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: 1.98 Conformation dependent library (CDL) restraints added in 1.0 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: 0.71 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: 4.65 Time building geometry restraints manager: 2.52 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: 0.09 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.270 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.590 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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/Z covalent geometry : bond 0.00700 / 0.31 (25716) covalent geometry : angle 0.96717 / 0.53 (34788) hydrogen bonds : bond 0.15847 / 10.90 ( 1194) hydrogen bonds : angle 6.25496 / 4.30 ( 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 : 0.907 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: 0.8179 (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: 0.7741 (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: 0.7645 (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: 0.8158 (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: 0.7650 (mp0) REVERT: E 226 GLU cc_start: 0.8535 (tp30) cc_final: 0.8191 (tp30) REVERT: E 252 ASN cc_start: 0.8805 (p0) cc_final: 0.8406 (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: 0.8211 (t0) REVERT: I 81 ASP cc_start: 0.8389 (m-30) cc_final: 0.7963 (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: 0.8321 (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: 0.1580 time to fit residues: 253.9971 Evaluate side-chains 762 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 689 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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... 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 = 0.3874 r_free = 0.3874 target = 0.160630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113923 restraints weight = 35018.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119235 restraints weight = 18224.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122650 restraints weight = 12200.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124741 restraints weight = 9542.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126030 restraints weight = 8245.141| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25716 Z= 0.137 Angle : 0.653 14.073 34788 Z= 0.324 Chirality : 0.043 0.181 3924 Planarity : 0.004 0.036 4422 Dihedral : 11.859 156.712 3717 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.64 % Allowed : 19.90 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.14), residues: 3186 helix: -1.08 (0.12), residues: 1584 sheet: -0.73 (0.26), residues: 366 loop : -1.24 (0.17), residues: 1236 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 0.023 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/Z covalent geometry : bond 0.00311 / 0.14 (25716) covalent geometry : angle 0.65337 / 0.32 (34788) hydrogen bonds : bond 0.03970 / 2.66 ( 1194) hydrogen bonds : angle 4.32826 / 3.00 ( 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 819 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 747 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8491 (mttt) cc_final: 0.8129 (mmtm) REVERT: B 119 MET cc_start: 0.8294 (ttm) cc_final: 0.8047 (ttp) REVERT: B 121 GLN cc_start: 0.8547 (tt0) cc_final: 0.8342 (tt0) REVERT: B 128 ASN cc_start: 0.8802 (m110) cc_final: 0.8521 (m-40) REVERT: B 132 MET cc_start: 0.5499 (ppp) cc_final: 0.4743 (ppp) REVERT: B 198 TYR cc_start: 0.9008 (m-80) cc_final: 0.8787 (m-80) REVERT: B 211 ASP cc_start: 0.8107 (t0) cc_final: 0.7715 (t0) REVERT: B 215 LYS cc_start: 0.8598 (mttm) cc_final: 0.8308 (mmtp) REVERT: B 305 MET cc_start: 0.8597 (mtp) cc_final: 0.8393 (mtp) REVERT: B 336 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8782 (tttt) REVERT: D 44 MET cc_start: 0.7805 (mmm) cc_final: 0.7542 (mmm) REVERT: D 49 GLN cc_start: 0.7770 (mm110) cc_final: 0.7442 (mm-40) REVERT: D 83 GLU cc_start: 0.7946 (pt0) cc_final: 0.7652 (pt0) REVERT: D 226 GLU cc_start: 0.7996 (tp30) cc_final: 0.7672 (tp30) REVERT: D 263 GLN cc_start: 0.8354 (mt0) cc_final: 0.8141 (mt0) REVERT: E 25 ASP cc_start: 0.8039 (p0) cc_final: 0.7824 (p0) REVERT: E 51 ASP cc_start: 0.8008 (t70) cc_final: 0.7718 (t0) REVERT: E 101 HIS cc_start: 0.8928 (m-70) cc_final: 0.8542 (m90) REVERT: E 132 MET cc_start: 0.8340 (ppp) cc_final: 0.8061 (ttp) REVERT: E 192 ILE cc_start: 0.9438 (tp) cc_final: 0.8917 (tt) REVERT: E 211 ASP cc_start: 0.8246 (t0) cc_final: 0.7586 (t0) REVERT: E 280 ASN cc_start: 0.8575 (t0) cc_final: 0.8152 (t0) REVERT: E 325 MET cc_start: 0.8225 (ppp) cc_final: 0.7682 (ppp) REVERT: E 336 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8836 (tttt) REVERT: F 78 ASN cc_start: 0.8288 (t0) cc_final: 0.7972 (t0) REVERT: F 81 ASP cc_start: 0.8475 (m-30) cc_final: 0.8172 (m-30) REVERT: F 190 MET cc_start: 0.6450 (mtp) cc_final: 0.6177 (mtp) REVERT: F 192 ILE cc_start: 0.7754 (tp) cc_final: 0.7452 (tp) REVERT: F 280 ASN cc_start: 0.8617 (t0) cc_final: 0.8212 (t0) REVERT: F 336 LYS cc_start: 0.9289 (ttpt) cc_final: 0.9053 (tttt) REVERT: H 192 ILE cc_start: 0.9306 (tp) cc_final: 0.8972 (tt) REVERT: H 205 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: H 211 ASP cc_start: 0.8368 (t0) cc_final: 0.8164 (t0) REVERT: H 325 MET cc_start: 0.8016 (ppp) cc_final: 0.7482 (ppp) REVERT: H 336 LYS cc_start: 0.9084 (ttpt) cc_final: 0.8851 (tttt) REVERT: I 25 ASP cc_start: 0.8162 (p0) cc_final: 0.7910 (p0) REVERT: I 81 ASP cc_start: 0.8435 (m-30) cc_final: 0.8127 (m-30) REVERT: I 82 MET cc_start: 0.9215 (tpt) cc_final: 0.8708 (tpt) REVERT: I 83 GLU cc_start: 0.7831 (pt0) cc_final: 0.7504 (pt0) REVERT: I 192 ILE cc_start: 0.9409 (tp) cc_final: 0.9208 (tp) REVERT: I 214 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7448 (mm-30) REVERT: I 269 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7715 (ttt) REVERT: I 314 GLN cc_start: 0.8812 (tt0) cc_final: 0.8510 (tt0) REVERT: I 325 MET cc_start: 0.7804 (ppp) cc_final: 0.7425 (ppp) REVERT: I 336 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8580 (tttt) REVERT: K 781 GLN cc_start: 0.8215 (mt0) cc_final: 0.7889 (mt0) REVERT: K 791 ASN cc_start: 0.8665 (t0) cc_final: 0.8150 (t0) REVERT: K 827 ASN cc_start: 0.8197 (m-40) cc_final: 0.7820 (t0) REVERT: K 837 TYR cc_start: 0.8695 (t80) cc_final: 0.8405 (t80) REVERT: K 845 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8592 (tptp) REVERT: L 718 GLN cc_start: 0.9270 (mt0) cc_final: 0.9033 (mt0) REVERT: L 723 MET cc_start: 0.7655 (tmm) cc_final: 0.7207 (tmm) REVERT: L 791 ASN cc_start: 0.8703 (t0) cc_final: 0.8382 (m-40) REVERT: L 797 LYS cc_start: 0.9176 (tppt) cc_final: 0.8902 (tppt) REVERT: N 740 SER cc_start: 0.8388 (m) cc_final: 0.8180 (p) REVERT: N 801 GLN cc_start: 0.8779 (tp40) cc_final: 0.8562 (tp-100) REVERT: N 845 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8456 (tptp) REVERT: O 740 SER cc_start: 0.8674 (m) cc_final: 0.8368 (t) REVERT: O 791 ASN cc_start: 0.8725 (t0) cc_final: 0.8223 (t0) REVERT: O 797 LYS cc_start: 0.8882 (mmtm) cc_final: 0.8603 (mmtm) REVERT: O 826 MET cc_start: 0.7166 (ttp) cc_final: 0.6880 (ttp) REVERT: O 827 ASN cc_start: 0.8108 (m-40) cc_final: 0.7683 (t0) REVERT: O 845 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8426 (tptp) REVERT: Q 724 MET cc_start: 0.8471 (tpp) cc_final: 0.7977 (tpt) REVERT: X 756 MET cc_start: 0.8818 (tpp) cc_final: 0.8533 (tpp) REVERT: X 801 GLN cc_start: 0.8829 (tp40) cc_final: 0.8513 (tp40) REVERT: X 803 LEU cc_start: 0.9030 (tp) cc_final: 0.8604 (tp) outliers start: 72 outliers final: 44 residues processed: 775 average time/residue: 0.1406 time to fit residues: 180.5965 Evaluate side-chains 725 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 676 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 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: 0.0270 chunk 175 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 overall best weight: 2.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN B 275 HIS 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 101 HIS 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 718 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.162107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114786 restraints weight = 34946.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120008 restraints weight = 18312.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123353 restraints weight = 12315.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125437 restraints weight = 9674.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126734 restraints weight = 8359.567| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25716 Z= 0.155 Angle : 0.630 13.884 34788 Z= 0.312 Chirality : 0.044 0.185 3924 Planarity : 0.003 0.029 4422 Dihedral : 9.532 167.995 3579 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.41 % Allowed : 22.03 % 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: -0.47 (0.12), residues: 1602 sheet: -0.49 (0.27), residues: 366 loop : -1.01 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 116 TYR 0.020 0.001 TYR D 166 PHE 0.025 0.001 PHE K 729 TRP 0.008 0.001 TRP I 356 HIS 0.010 0.001 HIS Q 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (25716) covalent geometry : angle 0.63034 / 0.31 (34788) hydrogen bonds : bond 0.03873 / 2.59 ( 1194) hydrogen bonds : angle 4.19507 / 2.89 ( 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 798 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 705 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8513 (mttt) cc_final: 0.8252 (mttp) REVERT: B 198 TYR cc_start: 0.9120 (m-80) cc_final: 0.8797 (m-80) REVERT: B 305 MET cc_start: 0.8678 (mtp) cc_final: 0.8452 (mtp) REVERT: B 336 LYS cc_start: 0.9109 (ttpt) cc_final: 0.8776 (tttt) REVERT: D 44 MET cc_start: 0.7817 (mmm) cc_final: 0.7420 (mmm) REVERT: D 83 GLU cc_start: 0.7935 (pt0) cc_final: 0.7654 (pt0) REVERT: D 119 MET cc_start: 0.8517 (ttp) cc_final: 0.8285 (ttp) REVERT: D 226 GLU cc_start: 0.8102 (tp30) cc_final: 0.7845 (tp30) REVERT: D 263 GLN cc_start: 0.8410 (mt0) cc_final: 0.8196 (mt0) REVERT: E 25 ASP cc_start: 0.7912 (p0) cc_final: 0.7600 (p0) REVERT: E 51 ASP cc_start: 0.8016 (t70) cc_final: 0.7719 (t0) REVERT: E 192 ILE cc_start: 0.9412 (tp) cc_final: 0.9103 (tt) REVERT: E 211 ASP cc_start: 0.8207 (t0) cc_final: 0.7535 (t0) REVERT: E 280 ASN cc_start: 0.8587 (t0) cc_final: 0.8150 (t0) REVERT: E 325 MET cc_start: 0.8369 (ppp) cc_final: 0.7273 (ppp) REVERT: E 336 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8848 (tttt) REVERT: F 190 MET cc_start: 0.6569 (mtp) cc_final: 0.6321 (mtp) REVERT: F 192 ILE cc_start: 0.7697 (tp) cc_final: 0.7416 (tp) REVERT: F 325 MET cc_start: 0.8275 (ppp) cc_final: 0.7996 (ppp) REVERT: F 336 LYS cc_start: 0.9330 (ttpt) cc_final: 0.9086 (tttt) REVERT: H 192 ILE cc_start: 0.9308 (tp) cc_final: 0.8947 (tt) REVERT: H 325 MET cc_start: 0.8092 (ppp) cc_final: 0.7624 (ppp) REVERT: H 336 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8837 (tttt) REVERT: I 25 ASP cc_start: 0.8166 (p0) cc_final: 0.7833 (p0) REVERT: I 83 GLU cc_start: 0.7784 (pt0) cc_final: 0.7477 (pt0) REVERT: I 192 ILE cc_start: 0.9487 (tp) cc_final: 0.9016 (tp) REVERT: I 253 GLU cc_start: 0.8331 (mp0) cc_final: 0.8093 (mp0) REVERT: I 269 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7739 (ttt) REVERT: I 280 ASN cc_start: 0.8575 (t0) cc_final: 0.8076 (t0) REVERT: I 314 GLN cc_start: 0.8813 (tt0) cc_final: 0.8559 (tt0) REVERT: I 336 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8666 (tttt) REVERT: K 758 LYS cc_start: 0.8587 (mmtm) cc_final: 0.8303 (mmtm) REVERT: K 791 ASN cc_start: 0.8634 (t0) cc_final: 0.8065 (t0) REVERT: K 827 ASN cc_start: 0.8227 (m-40) cc_final: 0.7825 (t0) REVERT: K 845 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8501 (tptp) REVERT: L 718 GLN cc_start: 0.9240 (mt0) cc_final: 0.8993 (mt0) REVERT: L 791 ASN cc_start: 0.8676 (t0) cc_final: 0.8203 (t0) REVERT: N 723 MET cc_start: 0.8077 (tpt) cc_final: 0.7843 (tpt) REVERT: N 740 SER cc_start: 0.8321 (m) cc_final: 0.8088 (p) REVERT: N 845 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8467 (tptp) REVERT: O 723 MET cc_start: 0.7989 (tmm) cc_final: 0.7236 (tmm) REVERT: O 740 SER cc_start: 0.8698 (m) cc_final: 0.8370 (t) REVERT: O 845 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8466 (tptp) REVERT: Q 724 MET cc_start: 0.8549 (tpp) cc_final: 0.8046 (tpt) REVERT: Q 779 TYR cc_start: 0.9018 (m-80) cc_final: 0.8804 (m-80) REVERT: X 801 GLN cc_start: 0.8907 (tp40) cc_final: 0.8610 (tp40) REVERT: X 803 LEU cc_start: 0.8987 (tp) cc_final: 0.8624 (tp) REVERT: X 816 MET cc_start: 0.8339 (mmm) cc_final: 0.7917 (mpp) REVERT: X 826 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7155 (ptt) outliers start: 93 outliers final: 61 residues processed: 742 average time/residue: 0.1469 time to fit residues: 181.8696 Evaluate side-chains 737 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 671 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 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 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 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 288 ASP 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 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 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 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 736 LEU 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 796 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 38 optimal weight: 6.9990 chunk 243 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 270 optimal weight: 50.0000 chunk 192 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 316 optimal weight: 20.0000 chunk 107 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 34 optimal weight: 0.0270 chunk 86 optimal weight: 0.9990 overall best weight: 2.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN D 41 GLN 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 92 ASN F 101 HIS ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 718 GLN ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 844 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.115058 restraints weight = 34534.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120198 restraints weight = 18134.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123549 restraints weight = 12216.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125607 restraints weight = 9594.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126834 restraints weight = 8295.205| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25716 Z= 0.146 Angle : 0.620 11.723 34788 Z= 0.308 Chirality : 0.043 0.171 3924 Planarity : 0.003 0.030 4422 Dihedral : 9.233 177.426 3578 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.71 % Allowed : 23.05 % Favored : 73.24 % 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: -0.72 (0.15), residues: 3186 helix: -0.09 (0.13), residues: 1602 sheet: -0.31 (0.27), residues: 366 loop : -0.87 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 755 TYR 0.024 0.001 TYR D 166 PHE 0.025 0.001 PHE N 729 TRP 0.008 0.001 TRP I 356 HIS 0.005 0.001 HIS F 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (25716) covalent geometry : angle 0.62005 / 0.31 (34788) hydrogen bonds : bond 0.03710 / 2.48 ( 1194) hydrogen bonds : angle 4.08369 / 2.81 ( 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 795 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 694 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8538 (mttt) cc_final: 0.8199 (mmtm) REVERT: B 132 MET cc_start: 0.4987 (ppp) cc_final: 0.4519 (ppp) REVERT: B 198 TYR cc_start: 0.9157 (m-80) cc_final: 0.8764 (m-80) REVERT: B 202 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8539 (t) REVERT: B 205 GLU cc_start: 0.8025 (mp0) cc_final: 0.7641 (mp0) REVERT: B 211 ASP cc_start: 0.8301 (t0) cc_final: 0.7932 (t0) REVERT: B 303 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.9020 (p) REVERT: B 305 MET cc_start: 0.8696 (mtp) cc_final: 0.8465 (mtp) REVERT: B 336 LYS cc_start: 0.9133 (ttpt) cc_final: 0.8828 (tttt) REVERT: D 44 MET cc_start: 0.7796 (mmm) cc_final: 0.7309 (mmm) REVERT: D 83 GLU cc_start: 0.7943 (pt0) cc_final: 0.7660 (pt0) REVERT: D 119 MET cc_start: 0.8539 (ttp) cc_final: 0.8325 (ttp) REVERT: D 263 GLN cc_start: 0.8432 (mt0) cc_final: 0.8223 (mt0) REVERT: D 316 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7632 (mm-30) REVERT: E 8 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8769 (mp) REVERT: E 25 ASP cc_start: 0.7877 (p0) cc_final: 0.7549 (p0) REVERT: E 51 ASP cc_start: 0.8014 (t70) cc_final: 0.7711 (t0) REVERT: E 100 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7657 (mp0) REVERT: E 192 ILE cc_start: 0.9394 (tp) cc_final: 0.9016 (tp) REVERT: E 211 ASP cc_start: 0.8192 (t0) cc_final: 0.7524 (t0) REVERT: E 280 ASN cc_start: 0.8556 (t0) cc_final: 0.8102 (t0) REVERT: E 325 MET cc_start: 0.8469 (ppp) cc_final: 0.7317 (ppp) REVERT: E 336 LYS cc_start: 0.9083 (ttpt) cc_final: 0.8842 (tttt) REVERT: F 132 MET cc_start: 0.8327 (tmm) cc_final: 0.8003 (tmm) REVERT: F 190 MET cc_start: 0.6614 (mtp) cc_final: 0.6386 (mtp) REVERT: F 192 ILE cc_start: 0.7782 (tp) cc_final: 0.7524 (tp) REVERT: F 325 MET cc_start: 0.8273 (ppp) cc_final: 0.7853 (ppp) REVERT: F 336 LYS cc_start: 0.9319 (ttpt) cc_final: 0.9027 (tttt) REVERT: H 72 GLU cc_start: 0.7230 (pp20) cc_final: 0.6974 (pp20) REVERT: H 83 GLU cc_start: 0.7900 (pt0) cc_final: 0.7638 (pt0) REVERT: H 192 ILE cc_start: 0.9244 (tp) cc_final: 0.8957 (tt) REVERT: H 205 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: H 325 MET cc_start: 0.8189 (ppp) cc_final: 0.7631 (ppp) REVERT: H 336 LYS cc_start: 0.9144 (ttpt) cc_final: 0.8870 (tttt) REVERT: I 25 ASP cc_start: 0.8178 (p0) cc_final: 0.7732 (p0) REVERT: I 83 GLU cc_start: 0.7815 (pt0) cc_final: 0.7486 (pt0) REVERT: I 192 ILE cc_start: 0.9438 (tp) cc_final: 0.8822 (tp) REVERT: I 195 GLU cc_start: 0.7583 (pt0) cc_final: 0.7375 (pt0) REVERT: I 253 GLU cc_start: 0.8347 (mp0) cc_final: 0.8103 (mp0) REVERT: I 269 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7755 (ttt) REVERT: I 280 ASN cc_start: 0.8585 (t0) cc_final: 0.8123 (t0) REVERT: I 314 GLN cc_start: 0.8772 (tt0) cc_final: 0.8567 (tt0) REVERT: I 336 LYS cc_start: 0.9098 (ttpt) cc_final: 0.8796 (tttt) REVERT: K 758 LYS cc_start: 0.8573 (mmtm) cc_final: 0.8303 (mmtm) REVERT: K 791 ASN cc_start: 0.8594 (t0) cc_final: 0.8177 (t0) REVERT: K 844 GLN cc_start: 0.9011 (tp40) cc_final: 0.8740 (tp40) REVERT: K 845 LYS cc_start: 0.8917 (tttp) cc_final: 0.8520 (tptp) REVERT: L 718 GLN cc_start: 0.9205 (mt0) cc_final: 0.8955 (mt0) REVERT: L 751 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7430 (tm-30) REVERT: L 791 ASN cc_start: 0.8632 (t0) cc_final: 0.8188 (t0) REVERT: N 723 MET cc_start: 0.7995 (tpt) cc_final: 0.7527 (tpt) REVERT: N 779 TYR cc_start: 0.8807 (m-80) cc_final: 0.8574 (m-80) REVERT: N 837 TYR cc_start: 0.8636 (t80) cc_final: 0.8336 (t80) REVERT: N 845 LYS cc_start: 0.8886 (tttp) cc_final: 0.8509 (tptp) REVERT: O 723 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7238 (tmm) REVERT: O 740 SER cc_start: 0.8714 (m) cc_final: 0.8400 (t) REVERT: O 797 LYS cc_start: 0.8863 (mmtm) cc_final: 0.8491 (mmtm) REVERT: O 845 LYS cc_start: 0.8937 (tttp) cc_final: 0.8433 (tptp) REVERT: Q 724 MET cc_start: 0.8615 (tpp) cc_final: 0.8080 (tpt) REVERT: Q 779 TYR cc_start: 0.8954 (m-80) cc_final: 0.8705 (m-80) REVERT: X 801 GLN cc_start: 0.8912 (tp40) cc_final: 0.8581 (tp40) REVERT: X 826 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7234 (ptt) outliers start: 101 outliers final: 67 residues processed: 738 average time/residue: 0.1525 time to fit residues: 186.8326 Evaluate side-chains 736 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 662 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 202 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain D residue 8 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 330 ILE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 14 SER 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 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 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 75 ILE Chi-restraints excluded: chain H residue 107 GLU 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 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 787 CYS Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 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 N residue 829 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 246 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 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: 6.9990 chunk 117 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 789 GLN O 789 GLN O 844 GLN Q 718 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.108539 restraints weight = 34515.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.113625 restraints weight = 18038.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116881 restraints weight = 12098.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118890 restraints weight = 9492.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120139 restraints weight = 8201.412| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 25716 Z= 0.236 Angle : 0.678 10.779 34788 Z= 0.336 Chirality : 0.046 0.165 3924 Planarity : 0.004 0.031 4422 Dihedral : 9.031 170.737 3562 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.74 % Allowed : 23.13 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 3186 helix: 0.06 (0.13), residues: 1602 sheet: -0.27 (0.28), residues: 366 loop : -0.80 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 183 TYR 0.019 0.001 TYR I 143 PHE 0.023 0.001 PHE N 729 TRP 0.010 0.001 TRP F 79 HIS 0.004 0.001 HIS O 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (25716) covalent geometry : angle 0.67835 / 0.34 (34788) hydrogen bonds : bond 0.04055 / 2.73 ( 1194) hydrogen bonds : angle 4.15385 / 2.86 ( 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 806 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 677 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8542 (mttt) cc_final: 0.8239 (mttm) REVERT: B 132 MET cc_start: 0.5253 (ppp) cc_final: 0.4905 (ppp) REVERT: B 202 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8708 (t) REVERT: B 205 GLU cc_start: 0.8073 (mp0) cc_final: 0.7754 (mp0) REVERT: B 215 LYS cc_start: 0.8925 (mmtm) cc_final: 0.8642 (mttm) REVERT: B 303 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8934 (p) REVERT: B 305 MET cc_start: 0.8716 (mtp) cc_final: 0.8469 (mtp) REVERT: B 313 MET cc_start: 0.0623 (OUTLIER) cc_final: 0.0403 (tmm) REVERT: B 336 LYS cc_start: 0.9216 (ttpt) cc_final: 0.8899 (tttt) REVERT: D 44 MET cc_start: 0.7838 (mmm) cc_final: 0.7459 (mmm) REVERT: D 143 TYR cc_start: 0.9180 (m-80) cc_final: 0.8959 (m-80) REVERT: D 316 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7637 (mm-30) REVERT: E 51 ASP cc_start: 0.8073 (t70) cc_final: 0.7779 (t0) REVERT: E 157 ASP cc_start: 0.8582 (t70) cc_final: 0.8017 (t0) REVERT: E 192 ILE cc_start: 0.9324 (tp) cc_final: 0.9058 (tp) REVERT: E 211 ASP cc_start: 0.8234 (t0) cc_final: 0.7833 (t0) REVERT: E 224 GLU cc_start: 0.7960 (mp0) cc_final: 0.7739 (mp0) REVERT: E 269 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8016 (ttt) REVERT: E 297 ASN cc_start: 0.8820 (m-40) cc_final: 0.8565 (m110) REVERT: E 325 MET cc_start: 0.8583 (ppp) cc_final: 0.7580 (ppp) REVERT: E 336 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8896 (tttt) REVERT: F 132 MET cc_start: 0.8467 (tmm) cc_final: 0.8218 (tmm) REVERT: F 192 ILE cc_start: 0.8039 (tp) cc_final: 0.7795 (tp) REVERT: F 325 MET cc_start: 0.8491 (ppp) cc_final: 0.7740 (ppp) REVERT: F 336 LYS cc_start: 0.9333 (ttpt) cc_final: 0.9079 (tttt) REVERT: H 78 ASN cc_start: 0.8507 (t0) cc_final: 0.7889 (t0) REVERT: H 83 GLU cc_start: 0.7910 (pt0) cc_final: 0.7621 (pt0) REVERT: H 192 ILE cc_start: 0.9234 (tp) cc_final: 0.9014 (tp) REVERT: H 205 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: H 325 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7763 (ppp) REVERT: H 336 LYS cc_start: 0.9253 (ttpt) cc_final: 0.9014 (tttt) REVERT: I 25 ASP cc_start: 0.8150 (p0) cc_final: 0.7645 (p0) REVERT: I 83 GLU cc_start: 0.7819 (pt0) cc_final: 0.7482 (pt0) REVERT: I 192 ILE cc_start: 0.9442 (tp) cc_final: 0.8846 (tp) REVERT: I 195 GLU cc_start: 0.7632 (pt0) cc_final: 0.7386 (pt0) REVERT: I 253 GLU cc_start: 0.8332 (mp0) cc_final: 0.8114 (mp0) REVERT: I 269 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7732 (ttt) REVERT: I 314 GLN cc_start: 0.8811 (tt0) cc_final: 0.8575 (tt0) REVERT: I 325 MET cc_start: 0.8578 (ppp) cc_final: 0.7876 (ppp) REVERT: I 336 LYS cc_start: 0.9186 (ttpt) cc_final: 0.8867 (tttt) REVERT: K 791 ASN cc_start: 0.8600 (t0) cc_final: 0.8147 (t0) REVERT: K 844 GLN cc_start: 0.9040 (tp40) cc_final: 0.8668 (tp40) REVERT: K 845 LYS cc_start: 0.8923 (tttp) cc_final: 0.8517 (tptp) REVERT: L 718 GLN cc_start: 0.9214 (mt0) cc_final: 0.8893 (mt0) REVERT: L 751 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7436 (tm-30) REVERT: L 791 ASN cc_start: 0.8662 (t0) cc_final: 0.8221 (t0) REVERT: N 845 LYS cc_start: 0.8941 (tttp) cc_final: 0.8511 (tptp) REVERT: O 723 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7390 (tmm) REVERT: O 740 SER cc_start: 0.8755 (m) cc_final: 0.8466 (t) REVERT: O 791 ASN cc_start: 0.8567 (t0) cc_final: 0.7995 (t0) REVERT: O 797 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8542 (mmtm) REVERT: O 803 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8317 (mp) REVERT: O 843 TYR cc_start: 0.8238 (m-80) cc_final: 0.8035 (m-80) REVERT: O 845 LYS cc_start: 0.8959 (tttp) cc_final: 0.8558 (tptp) REVERT: Q 701 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: Q 724 MET cc_start: 0.8584 (tpp) cc_final: 0.8095 (tpt) REVERT: Q 779 TYR cc_start: 0.8956 (m-80) cc_final: 0.8700 (m-80) REVERT: X 801 GLN cc_start: 0.8915 (tp40) cc_final: 0.8580 (tp40) REVERT: X 826 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7202 (ptt) outliers start: 129 outliers final: 87 residues processed: 726 average time/residue: 0.1513 time to fit residues: 182.9781 Evaluate side-chains 736 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 638 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 199 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain D residue 8 LEU 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 217 CYS 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 45 VAL 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 180 LEU 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 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 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 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 313 MET Chi-restraints excluded: chain H residue 325 MET 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 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 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 725 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 787 CYS 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 803 LEU Chi-restraints excluded: chain Q residue 701 GLU 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 787 CYS Chi-restraints excluded: chain X residue 789 GLN Chi-restraints excluded: chain X residue 792 ILE Chi-restraints excluded: chain X residue 796 VAL 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: 0.6980 chunk 1 optimal weight: 4.9990 chunk 257 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 293 optimal weight: 8.9990 chunk 230 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN B 246 GLN 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 789 GLN K 831 GLN O 789 GLN Q 718 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.157890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110904 restraints weight = 34694.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116098 restraints weight = 18256.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119430 restraints weight = 12284.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121469 restraints weight = 9666.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122732 restraints weight = 8373.760| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.003 0.045 25716 Z= 0.130 Angle : 0.616 10.434 34788 Z= 0.304 Chirality : 0.043 0.157 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.850 179.622 3558 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.67 % Allowed : 25.15 % Favored : 71.18 % 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: -0.28 (0.15), residues: 3186 helix: 0.29 (0.13), residues: 1602 sheet: -0.12 (0.28), residues: 366 loop : -0.69 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 372 TYR 0.020 0.001 TYR D 166 PHE 0.019 0.001 PHE N 729 TRP 0.009 0.001 TRP E 356 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (25716) covalent geometry : angle 0.61619 / 0.30 (34788) hydrogen bonds : bond 0.03641 / 2.43 ( 1194) hydrogen bonds : angle 4.03457 / 2.78 ( 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 780 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 680 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.5187 (ppp) cc_final: 0.4829 (ppp) REVERT: B 202 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8715 (t) REVERT: B 211 ASP cc_start: 0.8258 (t0) cc_final: 0.7950 (t0) REVERT: B 215 LYS cc_start: 0.8853 (mmtm) cc_final: 0.8516 (mttm) REVERT: B 305 MET cc_start: 0.8674 (mtp) cc_final: 0.8437 (mtp) REVERT: B 336 LYS cc_start: 0.9198 (ttpt) cc_final: 0.8907 (tttt) REVERT: D 44 MET cc_start: 0.7685 (mmm) cc_final: 0.7220 (mmm) REVERT: D 107 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: D 143 TYR cc_start: 0.9100 (m-80) cc_final: 0.8847 (m-80) REVERT: D 224 GLU cc_start: 0.7708 (mp0) cc_final: 0.7484 (mp0) REVERT: D 316 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7589 (mm-30) REVERT: E 51 ASP cc_start: 0.8017 (t70) cc_final: 0.7725 (t0) REVERT: E 82 MET cc_start: 0.9133 (tpt) cc_final: 0.8827 (tpt) REVERT: E 157 ASP cc_start: 0.8481 (t70) cc_final: 0.7982 (t0) REVERT: E 192 ILE cc_start: 0.9279 (tp) cc_final: 0.9032 (tp) REVERT: E 224 GLU cc_start: 0.7965 (mp0) cc_final: 0.7735 (mp0) REVERT: E 269 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7912 (ttt) REVERT: E 325 MET cc_start: 0.8548 (ppp) cc_final: 0.7632 (ppp) REVERT: E 336 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8828 (tttt) REVERT: F 132 MET cc_start: 0.8398 (tmm) cc_final: 0.8077 (tmm) REVERT: F 192 ILE cc_start: 0.7875 (tp) cc_final: 0.7653 (tp) REVERT: F 325 MET cc_start: 0.8458 (ppp) cc_final: 0.7477 (ppp) REVERT: F 336 LYS cc_start: 0.9281 (ttpt) cc_final: 0.8994 (tttt) REVERT: H 83 GLU cc_start: 0.7871 (pt0) cc_final: 0.7645 (pt0) REVERT: H 192 ILE cc_start: 0.9233 (tp) cc_final: 0.8989 (tt) REVERT: H 205 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: H 325 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7718 (ppp) REVERT: H 336 LYS cc_start: 0.9209 (ttpt) cc_final: 0.8992 (tttt) REVERT: I 25 ASP cc_start: 0.8146 (p0) cc_final: 0.7552 (p0) REVERT: I 83 GLU cc_start: 0.7783 (pt0) cc_final: 0.7441 (pt0) REVERT: I 192 ILE cc_start: 0.9467 (tp) cc_final: 0.8853 (tp) REVERT: I 195 GLU cc_start: 0.7524 (pt0) cc_final: 0.7323 (pt0) REVERT: I 253 GLU cc_start: 0.8291 (mp0) cc_final: 0.8078 (mp0) REVERT: I 269 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7748 (ttt) REVERT: I 280 ASN cc_start: 0.8568 (t0) cc_final: 0.8202 (t0) REVERT: I 316 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7656 (mm-30) REVERT: I 325 MET cc_start: 0.8622 (ppp) cc_final: 0.8025 (ppp) REVERT: I 336 LYS cc_start: 0.9153 (ttpt) cc_final: 0.8849 (tttt) REVERT: K 791 ASN cc_start: 0.8529 (t0) cc_final: 0.8151 (t0) REVERT: K 844 GLN cc_start: 0.9040 (tp40) cc_final: 0.8700 (tp40) REVERT: K 845 LYS cc_start: 0.8909 (tttp) cc_final: 0.8518 (tptp) REVERT: L 718 GLN cc_start: 0.9181 (mt0) cc_final: 0.8914 (mt0) REVERT: L 751 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: L 791 ASN cc_start: 0.8636 (t0) cc_final: 0.8193 (t0) REVERT: N 779 TYR cc_start: 0.8790 (m-80) cc_final: 0.8529 (m-80) REVERT: N 845 LYS cc_start: 0.8918 (tttp) cc_final: 0.8514 (tptp) REVERT: O 723 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7330 (tmm) REVERT: O 740 SER cc_start: 0.8701 (m) cc_final: 0.8397 (t) REVERT: O 791 ASN cc_start: 0.8504 (t0) cc_final: 0.8016 (t0) REVERT: O 845 LYS cc_start: 0.8983 (tttp) cc_final: 0.8518 (tptp) REVERT: Q 724 MET cc_start: 0.8574 (tpp) cc_final: 0.8023 (tpt) REVERT: Q 779 TYR cc_start: 0.8925 (m-80) cc_final: 0.8655 (m-80) REVERT: X 791 ASN cc_start: 0.8564 (t0) cc_final: 0.8046 (t0) REVERT: X 826 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7273 (ptt) outliers start: 100 outliers final: 66 residues processed: 707 average time/residue: 0.1558 time to fit residues: 182.7394 Evaluate side-chains 726 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 651 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL 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 199 SER 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 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 288 ASP Chi-restraints excluded: chain E residue 14 SER 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 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 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 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 132 MET 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 325 MET Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 349 LEU 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 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 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 796 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 10 optimal weight: 0.0370 chunk 284 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 287 optimal weight: 10.0000 chunk 160 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 overall best weight: 1.8864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN B 246 GLN D 41 GLN D 101 HIS ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** 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** I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 GLN K 831 GLN N 718 GLN O 789 GLN ** O 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 718 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 = 0.3853 r_free = 0.3853 target = 0.158435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111390 restraints weight = 34658.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116593 restraints weight = 18282.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119868 restraints weight = 12323.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121945 restraints weight = 9720.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123182 restraints weight = 8407.236| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.003 0.044 25716 Z= 0.128 Angle : 0.610 8.505 34788 Z= 0.302 Chirality : 0.043 0.149 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.610 170.527 3558 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.93 % Allowed : 26.32 % Favored : 69.75 % 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: 0.22 (0.15), residues: 3186 helix: 0.70 (0.14), residues: 1512 sheet: 0.17 (0.30), residues: 330 loop : -0.37 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 372 TYR 0.020 0.001 TYR D 166 PHE 0.020 0.001 PHE K 729 TRP 0.008 0.001 TRP E 356 HIS 0.008 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (25716) covalent geometry : angle 0.61030 / 0.30 (34788) hydrogen bonds : bond 0.03560 / 2.37 ( 1194) hydrogen bonds : angle 3.97344 / 2.73 ( 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 790 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 683 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8507 (mttt) cc_final: 0.8185 (mmtm) REVERT: B 132 MET cc_start: 0.5179 (ppp) cc_final: 0.4742 (ppp) REVERT: B 202 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8667 (t) REVERT: B 211 ASP cc_start: 0.8258 (t0) cc_final: 0.7979 (t0) REVERT: B 215 LYS cc_start: 0.8877 (mmtm) cc_final: 0.8499 (mttm) REVERT: B 305 MET cc_start: 0.8626 (mtp) cc_final: 0.8410 (mtp) REVERT: B 336 LYS cc_start: 0.9162 (ttpt) cc_final: 0.8840 (tttt) REVERT: B 355 MET cc_start: -0.5209 (OUTLIER) cc_final: -0.6980 (ttm) REVERT: D 44 MET cc_start: 0.7657 (mmm) cc_final: 0.7256 (mmm) REVERT: D 143 TYR cc_start: 0.9100 (m-80) cc_final: 0.8882 (m-80) REVERT: E 51 ASP cc_start: 0.8021 (t70) cc_final: 0.7723 (t0) REVERT: E 82 MET cc_start: 0.9223 (tpt) cc_final: 0.8995 (tpt) REVERT: E 157 ASP cc_start: 0.8462 (t70) cc_final: 0.7980 (t0) REVERT: E 192 ILE cc_start: 0.9274 (tp) cc_final: 0.9018 (tp) REVERT: E 224 GLU cc_start: 0.7976 (mp0) cc_final: 0.7768 (mp0) REVERT: E 269 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.8010 (ttt) REVERT: E 325 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7609 (ppp) REVERT: E 336 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8800 (tttt) REVERT: F 25 ASP cc_start: 0.7870 (p0) cc_final: 0.7612 (p0) REVERT: F 132 MET cc_start: 0.8409 (tmm) cc_final: 0.8045 (tmm) REVERT: F 192 ILE cc_start: 0.7858 (tp) cc_final: 0.7637 (tp) REVERT: F 325 MET cc_start: 0.8408 (ppp) cc_final: 0.7402 (ppp) REVERT: F 336 LYS cc_start: 0.9269 (ttpt) cc_final: 0.8996 (tttt) REVERT: H 83 GLU cc_start: 0.7877 (pt0) cc_final: 0.7639 (pt0) REVERT: H 192 ILE cc_start: 0.9195 (tp) cc_final: 0.8962 (tt) REVERT: H 205 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: H 325 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7748 (ppp) REVERT: H 336 LYS cc_start: 0.9236 (ttpt) cc_final: 0.9024 (tttt) REVERT: I 25 ASP cc_start: 0.8119 (p0) cc_final: 0.7473 (p0) REVERT: I 83 GLU cc_start: 0.7835 (pt0) cc_final: 0.7532 (pt0) REVERT: I 192 ILE cc_start: 0.9467 (tp) cc_final: 0.8816 (tp) REVERT: I 195 GLU cc_start: 0.7550 (pt0) cc_final: 0.7314 (pt0) REVERT: I 253 GLU cc_start: 0.8308 (mp0) cc_final: 0.8061 (mp0) REVERT: I 316 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7678 (mm-30) REVERT: I 325 MET cc_start: 0.8616 (ppp) cc_final: 0.8091 (ppp) REVERT: I 336 LYS cc_start: 0.9160 (ttpt) cc_final: 0.8841 (tttt) REVERT: K 791 ASN cc_start: 0.8491 (t0) cc_final: 0.8160 (t0) REVERT: K 844 GLN cc_start: 0.9026 (tp40) cc_final: 0.8684 (tp40) REVERT: K 845 LYS cc_start: 0.8919 (tttp) cc_final: 0.8518 (tptp) REVERT: L 718 GLN cc_start: 0.9183 (mt0) cc_final: 0.8883 (mt0) REVERT: L 751 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: L 791 ASN cc_start: 0.8547 (t0) cc_final: 0.8198 (t0) REVERT: N 845 LYS cc_start: 0.8937 (tttp) cc_final: 0.8542 (tptp) REVERT: O 723 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7321 (tmm) REVERT: O 740 SER cc_start: 0.8689 (m) cc_final: 0.8389 (t) REVERT: O 791 ASN cc_start: 0.8480 (t0) cc_final: 0.8018 (t0) REVERT: O 845 LYS cc_start: 0.8981 (tttp) cc_final: 0.8521 (tptp) REVERT: Q 724 MET cc_start: 0.8605 (tpp) cc_final: 0.8027 (tpt) REVERT: Q 779 TYR cc_start: 0.8894 (m-80) cc_final: 0.8620 (m-80) REVERT: X 791 ASN cc_start: 0.8539 (t0) cc_final: 0.8042 (t0) REVERT: X 826 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7308 (ptt) outliers start: 107 outliers final: 70 residues processed: 720 average time/residue: 0.1561 time to fit residues: 187.1823 Evaluate side-chains 739 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 660 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 124 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 SER 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 30 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 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 145 SER 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 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 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 149 THR 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 349 LEU 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 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 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 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 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 X residue 714 VAL 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: 10.0000 chunk 120 optimal weight: 0.1980 chunk 225 optimal weight: 10.0000 chunk 211 optimal weight: 0.0870 chunk 249 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 276 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 overall best weight: 2.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN 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 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 ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 789 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.157874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111289 restraints weight = 34552.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116414 restraints weight = 18131.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119668 restraints weight = 12198.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121699 restraints weight = 9606.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122806 restraints weight = 8315.838| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3264 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= 0.139 Angle : 0.629 8.385 34788 Z= 0.311 Chirality : 0.043 0.179 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.464 169.620 3558 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.82 % Allowed : 26.73 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3186 helix: 0.77 (0.14), residues: 1512 sheet: 0.19 (0.30), residues: 330 loop : -0.31 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 372 TYR 0.022 0.001 TYR I 166 PHE 0.020 0.001 PHE X 729 TRP 0.008 0.001 TRP E 356 HIS 0.004 0.001 HIS O 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (25716) covalent geometry : angle 0.62942 / 0.31 (34788) hydrogen bonds : bond 0.03585 / 2.39 ( 1194) hydrogen bonds : angle 3.97213 / 2.74 ( 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 782 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 678 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8501 (mttt) cc_final: 0.8188 (mmtm) REVERT: B 198 TYR cc_start: 0.9254 (m-80) cc_final: 0.8870 (m-80) REVERT: B 202 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8666 (t) REVERT: B 211 ASP cc_start: 0.8265 (t0) cc_final: 0.7977 (t0) REVERT: B 215 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8473 (mttm) REVERT: B 299 MET cc_start: 0.2810 (mtm) cc_final: 0.2447 (mtm) REVERT: B 336 LYS cc_start: 0.9167 (ttpt) cc_final: 0.8850 (tttt) REVERT: B 355 MET cc_start: -0.5063 (OUTLIER) cc_final: -0.6176 (ttm) REVERT: D 143 TYR cc_start: 0.9118 (m-80) cc_final: 0.8826 (m-80) REVERT: E 51 ASP cc_start: 0.8009 (t70) cc_final: 0.7693 (t0) REVERT: E 82 MET cc_start: 0.9258 (tpt) cc_final: 0.8974 (tpt) REVERT: E 157 ASP cc_start: 0.8469 (t70) cc_final: 0.7984 (t0) REVERT: E 192 ILE cc_start: 0.9265 (tp) cc_final: 0.9005 (tp) REVERT: E 211 ASP cc_start: 0.8236 (t0) cc_final: 0.7760 (t0) REVERT: E 244 ASP cc_start: 0.9004 (p0) cc_final: 0.8708 (p0) REVERT: E 269 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8021 (ttt) REVERT: E 325 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7680 (ppp) REVERT: E 336 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8801 (tttt) REVERT: F 192 ILE cc_start: 0.7894 (tp) cc_final: 0.7675 (tp) REVERT: F 325 MET cc_start: 0.8335 (ppp) cc_final: 0.7754 (ptp) REVERT: F 336 LYS cc_start: 0.9279 (ttpt) cc_final: 0.9002 (tttt) REVERT: H 83 GLU cc_start: 0.7877 (pt0) cc_final: 0.7675 (pt0) REVERT: H 192 ILE cc_start: 0.9187 (tp) cc_final: 0.8981 (tp) REVERT: H 205 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: H 224 GLU cc_start: 0.7903 (mp0) cc_final: 0.7662 (mp0) REVERT: H 325 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7771 (ppp) REVERT: H 336 LYS cc_start: 0.9251 (ttpt) cc_final: 0.9032 (tttt) REVERT: I 25 ASP cc_start: 0.8107 (p0) cc_final: 0.7439 (p0) REVERT: I 83 GLU cc_start: 0.7805 (pt0) cc_final: 0.7522 (pt0) REVERT: I 192 ILE cc_start: 0.9461 (tp) cc_final: 0.8827 (tp) REVERT: I 195 GLU cc_start: 0.7552 (pt0) cc_final: 0.7290 (pt0) REVERT: I 269 MET cc_start: 0.8158 (ttp) cc_final: 0.7765 (ttt) REVERT: I 316 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7726 (mm-30) REVERT: I 325 MET cc_start: 0.8601 (ppp) cc_final: 0.8122 (ppp) REVERT: I 336 LYS cc_start: 0.9177 (ttpt) cc_final: 0.8853 (tttt) REVERT: K 758 LYS cc_start: 0.8506 (mmtm) cc_final: 0.8250 (mmtm) REVERT: K 791 ASN cc_start: 0.8479 (t0) cc_final: 0.8166 (t0) REVERT: K 844 GLN cc_start: 0.9034 (tp40) cc_final: 0.8668 (tp40) REVERT: K 845 LYS cc_start: 0.8929 (tttp) cc_final: 0.8507 (tptp) REVERT: L 718 GLN cc_start: 0.9158 (mt0) cc_final: 0.8863 (mt0) REVERT: L 751 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: L 791 ASN cc_start: 0.8503 (t0) cc_final: 0.8191 (t0) REVERT: N 845 LYS cc_start: 0.8937 (tttp) cc_final: 0.8551 (tptp) REVERT: O 723 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7335 (tmm) REVERT: O 740 SER cc_start: 0.8664 (m) cc_final: 0.8352 (t) REVERT: O 791 ASN cc_start: 0.8491 (t0) cc_final: 0.8062 (t0) REVERT: O 845 LYS cc_start: 0.8981 (tttp) cc_final: 0.8512 (tptp) REVERT: Q 779 TYR cc_start: 0.8892 (m-80) cc_final: 0.8626 (m-80) REVERT: X 791 ASN cc_start: 0.8520 (t0) cc_final: 0.8061 (t0) REVERT: X 801 GLN cc_start: 0.8870 (tp40) cc_final: 0.8513 (tm-30) REVERT: X 826 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7315 (ptt) outliers start: 104 outliers final: 79 residues processed: 712 average time/residue: 0.1538 time to fit residues: 182.3370 Evaluate side-chains 744 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 656 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 199 SER Chi-restraints excluded: chain B residue 202 THR 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 30 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 D residue 217 CYS Chi-restraints excluded: chain D residue 288 ASP 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 151 ILE 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 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 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 149 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET 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 349 LEU 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 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 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 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 796 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET 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 787 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 195 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 297 optimal weight: 20.0000 chunk 299 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 239 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN 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 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 N 718 GLN O 844 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3859 r_free = 0.3859 target = 0.158945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.111748 restraints weight = 34541.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116942 restraints weight = 18313.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120258 restraints weight = 12390.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122296 restraints weight = 9774.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123546 restraints weight = 8483.229| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25716 Z= 0.133 Angle : 0.631 15.016 34788 Z= 0.310 Chirality : 0.043 0.203 3924 Planarity : 0.003 0.030 4422 Dihedral : 8.365 170.551 3558 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.71 % Allowed : 26.98 % Favored : 69.31 % 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: 0.46 (0.15), residues: 3186 helix: 0.92 (0.14), residues: 1470 sheet: 0.18 (0.30), residues: 330 loop : -0.21 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 372 TYR 0.031 0.001 TYR I 166 PHE 0.021 0.001 PHE X 729 TRP 0.011 0.001 TRP E 340 HIS 0.004 0.001 HIS O 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (25716) covalent geometry : angle 0.63087 / 0.31 (34788) hydrogen bonds : bond 0.03527 / 2.36 ( 1194) hydrogen bonds : angle 3.96470 / 2.73 ( 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 772 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 671 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8511 (mttt) cc_final: 0.8196 (mmtm) REVERT: B 198 TYR cc_start: 0.9249 (m-80) cc_final: 0.8882 (m-80) REVERT: B 202 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8637 (t) REVERT: B 211 ASP cc_start: 0.8263 (t0) cc_final: 0.8010 (t0) REVERT: B 336 LYS cc_start: 0.9167 (ttpt) cc_final: 0.8863 (tttt) REVERT: B 355 MET cc_start: -0.4993 (OUTLIER) cc_final: -0.6636 (ttm) REVERT: D 44 MET cc_start: 0.7484 (mmm) cc_final: 0.7109 (mmm) REVERT: D 143 TYR cc_start: 0.9104 (m-80) cc_final: 0.8828 (m-80) REVERT: D 325 MET cc_start: 0.7957 (pmm) cc_final: 0.7623 (ptp) REVERT: E 51 ASP cc_start: 0.7996 (t70) cc_final: 0.7690 (t0) REVERT: E 82 MET cc_start: 0.9268 (tpt) cc_final: 0.8896 (tpt) REVERT: E 157 ASP cc_start: 0.8442 (t70) cc_final: 0.7996 (t0) REVERT: E 192 ILE cc_start: 0.9273 (tp) cc_final: 0.9017 (tp) REVERT: E 211 ASP cc_start: 0.8260 (t0) cc_final: 0.7766 (t0) REVERT: E 244 ASP cc_start: 0.8953 (p0) cc_final: 0.8741 (p0) REVERT: E 269 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7913 (ttt) REVERT: E 325 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7645 (ppp) REVERT: E 336 LYS cc_start: 0.9067 (ttpt) cc_final: 0.8828 (tttt) REVERT: F 192 ILE cc_start: 0.7909 (tp) cc_final: 0.7683 (tp) REVERT: F 325 MET cc_start: 0.8257 (ppp) cc_final: 0.7772 (ptp) REVERT: F 336 LYS cc_start: 0.9269 (ttpt) cc_final: 0.9001 (tttt) REVERT: H 83 GLU cc_start: 0.7916 (pt0) cc_final: 0.7672 (pt0) REVERT: H 192 ILE cc_start: 0.9174 (tp) cc_final: 0.8970 (tp) REVERT: H 205 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: H 224 GLU cc_start: 0.7890 (mp0) cc_final: 0.7680 (mp0) REVERT: H 325 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7785 (ppp) REVERT: H 336 LYS cc_start: 0.9238 (ttpt) cc_final: 0.9025 (tttt) REVERT: I 25 ASP cc_start: 0.8049 (p0) cc_final: 0.7369 (p0) REVERT: I 83 GLU cc_start: 0.7806 (pt0) cc_final: 0.7503 (pt0) REVERT: I 192 ILE cc_start: 0.9469 (tp) cc_final: 0.8843 (tp) REVERT: I 195 GLU cc_start: 0.7552 (pt0) cc_final: 0.7292 (pt0) REVERT: I 316 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7718 (mm-30) REVERT: I 325 MET cc_start: 0.8590 (ppp) cc_final: 0.8127 (ppp) REVERT: I 336 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8871 (tttt) REVERT: K 791 ASN cc_start: 0.8427 (t0) cc_final: 0.8198 (t0) REVERT: K 844 GLN cc_start: 0.9016 (tp40) cc_final: 0.8660 (tp40) REVERT: K 845 LYS cc_start: 0.8918 (tttp) cc_final: 0.8505 (tptp) REVERT: L 718 GLN cc_start: 0.9156 (mt0) cc_final: 0.8863 (mt0) REVERT: L 751 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: L 791 ASN cc_start: 0.8486 (t0) cc_final: 0.8144 (t0) REVERT: N 723 MET cc_start: 0.7890 (tpt) cc_final: 0.7653 (tpt) REVERT: N 799 GLU cc_start: 0.8029 (tt0) cc_final: 0.7621 (tt0) REVERT: N 831 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8484 (mm110) REVERT: N 845 LYS cc_start: 0.8915 (tttp) cc_final: 0.8530 (tptp) REVERT: O 723 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7321 (tmm) REVERT: O 740 SER cc_start: 0.8637 (m) cc_final: 0.8340 (t) REVERT: Q 779 TYR cc_start: 0.8878 (m-80) cc_final: 0.8642 (m-80) REVERT: X 791 ASN cc_start: 0.8491 (t0) cc_final: 0.8117 (t0) REVERT: X 801 GLN cc_start: 0.8837 (tp40) cc_final: 0.8525 (tm-30) REVERT: X 826 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7355 (ptt) outliers start: 101 outliers final: 78 residues processed: 704 average time/residue: 0.1531 time to fit residues: 179.7325 Evaluate side-chains 739 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 652 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 199 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 355 MET 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 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 D residue 217 CYS Chi-restraints excluded: chain D residue 288 ASP 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 151 ILE 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 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 122 ILE 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 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 149 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET 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 349 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 129 VAL 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 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 796 VAL 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 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 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 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 42 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 143 optimal weight: 0.2980 chunk 44 optimal weight: 4.9990 chunk 253 optimal weight: 50.0000 chunk 231 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN D 41 GLN D 137 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 137 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 137 GLN ** 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 K 831 GLN N 718 GLN N 789 GLN X 718 GLN ** X 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.154656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108191 restraints weight = 34668.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113228 restraints weight = 18254.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116473 restraints weight = 12277.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118532 restraints weight = 9635.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119748 restraints weight = 8309.220| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25716 Z= 0.180 Angle : 0.668 13.676 34788 Z= 0.329 Chirality : 0.045 0.222 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.410 173.195 3558 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.60 % Allowed : 27.06 % Favored : 69.35 % 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: 0.38 (0.15), residues: 3186 helix: 0.80 (0.14), residues: 1512 sheet: 0.14 (0.30), residues: 330 loop : -0.20 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 372 TYR 0.025 0.001 TYR I 166 PHE 0.022 0.001 PHE K 729 TRP 0.007 0.001 TRP E 340 HIS 0.004 0.001 HIS O 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (25716) covalent geometry : angle 0.66770 / 0.33 (34788) hydrogen bonds : bond 0.03740 / 2.49 ( 1194) hydrogen bonds : angle 4.03165 / 2.78 ( 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 760 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 662 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.8518 (mttt) cc_final: 0.8213 (mttm) REVERT: B 132 MET cc_start: 0.5345 (ppp) cc_final: 0.4970 (ppp) REVERT: B 202 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8717 (t) REVERT: B 211 ASP cc_start: 0.8326 (t0) cc_final: 0.8037 (t0) REVERT: B 336 LYS cc_start: 0.9186 (ttpt) cc_final: 0.8867 (tttt) REVERT: B 355 MET cc_start: -0.5019 (OUTLIER) cc_final: -0.7033 (ttm) REVERT: D 44 MET cc_start: 0.7553 (mmm) cc_final: 0.7161 (mmm) REVERT: D 143 TYR cc_start: 0.9142 (m-80) cc_final: 0.8908 (m-80) REVERT: D 325 MET cc_start: 0.7984 (pmm) cc_final: 0.7713 (ptp) REVERT: D 326 LYS cc_start: 0.8353 (pttp) cc_final: 0.8101 (pttm) REVERT: E 51 ASP cc_start: 0.8047 (t70) cc_final: 0.7724 (t0) REVERT: E 82 MET cc_start: 0.9286 (tpt) cc_final: 0.8946 (tpt) REVERT: E 157 ASP cc_start: 0.8489 (t70) cc_final: 0.8019 (t0) REVERT: E 192 ILE cc_start: 0.9267 (tp) cc_final: 0.9005 (tp) REVERT: E 211 ASP cc_start: 0.8263 (t0) cc_final: 0.7800 (t0) REVERT: E 244 ASP cc_start: 0.9008 (p0) cc_final: 0.8728 (p0) REVERT: E 269 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8058 (ttt) REVERT: E 325 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7667 (ppp) REVERT: E 336 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8863 (tttt) REVERT: F 192 ILE cc_start: 0.8065 (tp) cc_final: 0.7849 (tp) REVERT: F 325 MET cc_start: 0.8310 (ppp) cc_final: 0.7895 (ptp) REVERT: F 336 LYS cc_start: 0.9290 (ttpt) cc_final: 0.9011 (tttt) REVERT: H 83 GLU cc_start: 0.7939 (pt0) cc_final: 0.7685 (pt0) REVERT: H 137 GLN cc_start: 0.8698 (mm110) cc_final: 0.8256 (mm-40) REVERT: H 192 ILE cc_start: 0.9174 (tp) cc_final: 0.8960 (tp) REVERT: H 205 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: H 269 MET cc_start: 0.8388 (ttp) cc_final: 0.8184 (ttt) REVERT: H 325 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7763 (ppp) REVERT: H 336 LYS cc_start: 0.9267 (ttpt) cc_final: 0.9061 (tttt) REVERT: I 25 ASP cc_start: 0.8122 (p0) cc_final: 0.7455 (p0) REVERT: I 83 GLU cc_start: 0.7841 (pt0) cc_final: 0.7531 (pt0) REVERT: I 192 ILE cc_start: 0.9453 (tp) cc_final: 0.8846 (tp) REVERT: I 195 GLU cc_start: 0.7588 (pt0) cc_final: 0.7319 (pt0) REVERT: I 269 MET cc_start: 0.8182 (ttp) cc_final: 0.7860 (ttt) REVERT: I 316 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7751 (mm-30) REVERT: I 325 MET cc_start: 0.8661 (ppp) cc_final: 0.8181 (ppp) REVERT: I 336 LYS cc_start: 0.9207 (ttpt) cc_final: 0.8886 (tttt) REVERT: K 791 ASN cc_start: 0.8481 (t0) cc_final: 0.8231 (t0) REVERT: K 844 GLN cc_start: 0.9005 (tp40) cc_final: 0.8612 (tp40) REVERT: K 845 LYS cc_start: 0.8929 (tttp) cc_final: 0.8508 (tptp) REVERT: L 718 GLN cc_start: 0.9186 (mt0) cc_final: 0.8941 (mt0) REVERT: L 751 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: L 791 ASN cc_start: 0.8450 (t0) cc_final: 0.8193 (t0) REVERT: N 723 MET cc_start: 0.7949 (tpt) cc_final: 0.7677 (tpt) REVERT: N 799 GLU cc_start: 0.8009 (tt0) cc_final: 0.7572 (tt0) REVERT: N 845 LYS cc_start: 0.8948 (tttp) cc_final: 0.8556 (tptp) REVERT: O 723 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7349 (tmm) REVERT: O 740 SER cc_start: 0.8642 (m) cc_final: 0.8337 (t) REVERT: Q 779 TYR cc_start: 0.8904 (m-80) cc_final: 0.8625 (m-80) REVERT: X 791 ASN cc_start: 0.8528 (t0) cc_final: 0.8123 (t0) REVERT: X 801 GLN cc_start: 0.8871 (tp40) cc_final: 0.8555 (tm-30) REVERT: X 826 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7392 (ptt) outliers start: 98 outliers final: 77 residues processed: 697 average time/residue: 0.1521 time to fit residues: 175.9733 Evaluate side-chains 738 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 652 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 199 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 355 MET 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 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 D residue 288 ASP 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 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 205 GLU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 309 ILE 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 149 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET 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 349 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 VAL 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 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 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 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 816 MET 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 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 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: 8.9990 chunk 153 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 chunk 262 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN D 41 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 137 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 N 718 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 = 0.3775 r_free = 0.3775 target = 0.152211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104787 restraints weight = 34921.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.109745 restraints weight = 18612.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112985 restraints weight = 12697.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114981 restraints weight = 10024.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116195 restraints weight = 8701.477| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 25716 Z= 0.348 Angle : 0.772 12.438 34788 Z= 0.382 Chirality : 0.049 0.246 3924 Planarity : 0.004 0.046 4422 Dihedral : 8.596 172.866 3558 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.78 % Allowed : 27.09 % Favored : 69.13 % 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: -0.02 (0.15), residues: 3186 helix: 0.43 (0.13), residues: 1566 sheet: 0.00 (0.30), residues: 330 loop : -0.42 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 372 TYR 0.023 0.002 TYR I 166 PHE 0.020 0.001 PHE O 729 TRP 0.011 0.001 TRP H 79 HIS 0.005 0.001 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.35 (25716) covalent geometry : angle 0.77240 / 0.38 (34788) hydrogen bonds : bond 0.04385 / 2.94 ( 1194) hydrogen bonds : angle 4.30429 / 2.98 ( 3276) =============================================================================== Job complete usr+sys time: 5273.05 seconds wall clock time: 91 minutes 51.19 seconds (5511.19 seconds total)