Starting phenix.real_space_refine on Mon Sep 30 09:19:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/09_2024/6wvt_21925.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/09_2024/6wvt_21925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/09_2024/6wvt_21925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/09_2024/6wvt_21925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/09_2024/6wvt_21925.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/09_2024/6wvt_21925.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 13.82, per 1000 atoms: 0.55 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: 5.62 Conformation dependent library (CDL) restraints added in 3.1 seconds 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6048 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 30 sheets defined 51.1% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 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: 8.52 Time building geometry restraints manager: 6.63 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: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 53.330 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 25716 Z= 0.454 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.002 TRP F 356 HIS 0.016 0.002 HIS I 161 PHE 0.015 0.002 PHE E 255 TYR 0.034 0.002 TYR B 166 ARG 0.016 0.001 ARG E 62 *********************** 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 fitting. rotamer outliers: 144 poor density : 918 time to evaluate : 2.907 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: 0.8285 (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: 0.8196 (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: 0.3500 time to fit residues: 553.7038 Evaluate side-chains 762 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 689 time to evaluate : 2.780 ------------------------------------------------------------------------------- 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 268 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 249 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 173 HIS B 263 GLN D 41 GLN D 263 GLN E 41 GLN E 92 ASN E 115 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 824 ASN N 718 GLN X 824 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 25716 Z= 0.295 Angle : 0.684 14.065 34788 Z= 0.340 Chirality : 0.045 0.177 3924 Planarity : 0.004 0.036 4422 Dihedral : 11.798 157.198 3717 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.12 % Allowed : 20.04 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.14), residues: 3186 helix: -1.14 (0.12), residues: 1608 sheet: -0.74 (0.26), residues: 366 loop : -1.28 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 356 HIS 0.006 0.001 HIS D 161 PHE 0.022 0.001 PHE O 729 TYR 0.019 0.002 TYR B 166 ARG 0.006 0.000 ARG I 116 *********************** 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 833 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 748 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.8260 (ttm) cc_final: 0.8055 (ttp) REVERT: B 128 ASN cc_start: 0.8841 (m110) cc_final: 0.7719 (m-40) REVERT: B 198 TYR cc_start: 0.9115 (m-80) cc_final: 0.8836 (m-80) REVERT: B 215 LYS cc_start: 0.8760 (mttm) cc_final: 0.8475 (mmtp) REVERT: B 305 MET cc_start: 0.8633 (mtp) cc_final: 0.8423 (mtp) REVERT: B 336 LYS cc_start: 0.9118 (ttpt) cc_final: 0.8886 (tttt) REVERT: D 44 MET cc_start: 0.7864 (mmm) cc_final: 0.7638 (mmm) REVERT: D 49 GLN cc_start: 0.7865 (mm110) cc_final: 0.7537 (mm-40) REVERT: D 83 GLU cc_start: 0.8031 (pt0) cc_final: 0.7711 (pt0) REVERT: D 137 GLN cc_start: 0.8625 (tt0) cc_final: 0.8401 (tt0) REVERT: D 226 GLU cc_start: 0.8167 (tp30) cc_final: 0.7848 (tp30) REVERT: D 263 GLN cc_start: 0.8428 (mt0) cc_final: 0.8186 (mt0) REVERT: E 25 ASP cc_start: 0.8071 (p0) cc_final: 0.7862 (p0) REVERT: E 51 ASP cc_start: 0.8136 (t70) cc_final: 0.7838 (t0) REVERT: E 192 ILE cc_start: 0.9452 (tp) cc_final: 0.8920 (tp) REVERT: E 205 GLU cc_start: 0.8071 (mp0) cc_final: 0.7864 (mp0) REVERT: E 211 ASP cc_start: 0.8237 (t0) cc_final: 0.7584 (t0) REVERT: E 280 ASN cc_start: 0.8659 (t0) cc_final: 0.8234 (t0) REVERT: E 313 MET cc_start: 0.9040 (mmm) cc_final: 0.8827 (mmm) REVERT: E 325 MET cc_start: 0.8493 (ppp) cc_final: 0.7576 (ppp) REVERT: E 336 LYS cc_start: 0.9144 (ttpt) cc_final: 0.8907 (tttt) REVERT: F 78 ASN cc_start: 0.8381 (t0) cc_final: 0.8087 (t0) REVERT: F 81 ASP cc_start: 0.8544 (m-30) cc_final: 0.8248 (m-30) REVERT: F 190 MET cc_start: 0.6717 (mtp) cc_final: 0.6480 (mtp) REVERT: F 192 ILE cc_start: 0.7832 (tp) cc_final: 0.7516 (tp) REVERT: F 252 ASN cc_start: 0.8795 (p0) cc_final: 0.8463 (p0) REVERT: F 280 ASN cc_start: 0.8678 (t0) cc_final: 0.8209 (t0) REVERT: F 336 LYS cc_start: 0.9336 (ttpt) cc_final: 0.9081 (tttt) REVERT: H 192 ILE cc_start: 0.9367 (tp) cc_final: 0.8985 (tt) REVERT: H 205 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: H 325 MET cc_start: 0.8244 (ppp) cc_final: 0.7610 (ppp) REVERT: H 336 LYS cc_start: 0.9170 (ttpt) cc_final: 0.8849 (tttt) REVERT: I 25 ASP cc_start: 0.8184 (p0) cc_final: 0.7954 (p0) REVERT: I 81 ASP cc_start: 0.8469 (m-30) cc_final: 0.8127 (m-30) REVERT: I 82 MET cc_start: 0.9200 (tpt) cc_final: 0.8703 (tpt) REVERT: I 83 GLU cc_start: 0.7864 (pt0) cc_final: 0.7524 (pt0) REVERT: I 192 ILE cc_start: 0.9450 (tp) cc_final: 0.9238 (tp) REVERT: I 214 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7639 (mm-30) REVERT: I 269 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7795 (ttt) REVERT: I 280 ASN cc_start: 0.8600 (t0) cc_final: 0.8089 (t0) REVERT: I 314 GLN cc_start: 0.8848 (tt0) cc_final: 0.8556 (tt0) REVERT: I 325 MET cc_start: 0.8174 (ppp) cc_final: 0.7625 (ppp) REVERT: I 336 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8711 (tttt) REVERT: K 781 GLN cc_start: 0.8238 (mt0) cc_final: 0.7922 (mt0) REVERT: K 791 ASN cc_start: 0.8743 (t0) cc_final: 0.8175 (t0) REVERT: K 827 ASN cc_start: 0.8273 (m-40) cc_final: 0.7908 (t0) REVERT: K 837 TYR cc_start: 0.8682 (t80) cc_final: 0.8414 (t80) REVERT: K 845 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8572 (tptp) REVERT: L 718 GLN cc_start: 0.9292 (mt0) cc_final: 0.9008 (mt0) REVERT: L 791 ASN cc_start: 0.8771 (t0) cc_final: 0.8207 (t0) REVERT: L 797 LYS cc_start: 0.9201 (tppt) cc_final: 0.8916 (tppt) REVERT: N 740 SER cc_start: 0.8538 (m) cc_final: 0.8305 (p) REVERT: N 801 GLN cc_start: 0.8903 (tp40) cc_final: 0.8656 (tp-100) REVERT: N 837 TYR cc_start: 0.8731 (t80) cc_final: 0.8392 (t80) REVERT: N 845 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8474 (tptp) REVERT: O 740 SER cc_start: 0.8733 (m) cc_final: 0.8448 (t) REVERT: O 791 ASN cc_start: 0.8774 (t0) cc_final: 0.8497 (m-40) REVERT: O 797 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8532 (mmtm) REVERT: O 827 ASN cc_start: 0.8127 (m-40) cc_final: 0.7725 (t0) REVERT: O 845 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8475 (tptp) REVERT: Q 724 MET cc_start: 0.8570 (tpp) cc_final: 0.8030 (tpt) REVERT: X 801 GLN cc_start: 0.8958 (tp40) cc_final: 0.8662 (tp40) REVERT: X 803 LEU cc_start: 0.9032 (tp) cc_final: 0.8616 (tp) outliers start: 85 outliers final: 49 residues processed: 786 average time/residue: 0.3255 time to fit residues: 418.1945 Evaluate side-chains 725 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 671 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER 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 180 LEU Chi-restraints excluded: chain D residue 199 SER 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 89 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 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 Chi-restraints excluded: chain X residue 833 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 289 optimal weight: 20.0000 chunk 312 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 286 optimal weight: 30.0000 chunk 98 optimal weight: 0.2980 chunk 232 optimal weight: 20.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 128 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 128 ASN ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Q 831 GLN X 718 GLN X 844 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25716 Z= 0.272 Angle : 0.652 13.634 34788 Z= 0.323 Chirality : 0.044 0.186 3924 Planarity : 0.004 0.031 4422 Dihedral : 9.582 168.330 3579 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.49 % Allowed : 22.39 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3186 helix: -0.44 (0.12), residues: 1566 sheet: -0.99 (0.26), residues: 396 loop : -0.90 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 356 HIS 0.009 0.001 HIS Q 788 PHE 0.027 0.001 PHE K 729 TYR 0.019 0.001 TYR K 779 ARG 0.004 0.000 ARG I 116 *********************** 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 795 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 700 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 GLN cc_start: 0.8183 (mt0) cc_final: 0.7975 (tt0) REVERT: B 132 MET cc_start: 0.5182 (ppp) cc_final: 0.4813 (ppp) REVERT: B 198 TYR cc_start: 0.9184 (m-80) cc_final: 0.8790 (m-80) REVERT: B 205 GLU cc_start: 0.8140 (mp0) cc_final: 0.7916 (mp0) REVERT: B 269 MET cc_start: 0.8480 (ttp) cc_final: 0.8221 (ttt) REVERT: B 305 MET cc_start: 0.8669 (mtp) cc_final: 0.8467 (mtp) REVERT: B 336 LYS cc_start: 0.9143 (ttpt) cc_final: 0.8800 (tttt) REVERT: B 355 MET cc_start: -0.5698 (OUTLIER) cc_final: -0.6578 (ttm) REVERT: D 44 MET cc_start: 0.7923 (mmm) cc_final: 0.7553 (mmm) REVERT: D 49 GLN cc_start: 0.7962 (mm110) cc_final: 0.7656 (mm-40) REVERT: D 83 GLU cc_start: 0.8016 (pt0) cc_final: 0.7714 (pt0) REVERT: D 119 MET cc_start: 0.8505 (ttp) cc_final: 0.8276 (ttp) REVERT: D 226 GLU cc_start: 0.8298 (tp30) cc_final: 0.8038 (tp30) REVERT: D 263 GLN cc_start: 0.8457 (mt0) cc_final: 0.8208 (mt0) REVERT: E 8 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8777 (mp) REVERT: E 25 ASP cc_start: 0.7978 (p0) cc_final: 0.7681 (p0) REVERT: E 51 ASP cc_start: 0.8118 (t70) cc_final: 0.7839 (t0) REVERT: E 192 ILE cc_start: 0.9407 (tp) cc_final: 0.9110 (tt) REVERT: E 211 ASP cc_start: 0.8243 (t0) cc_final: 0.7605 (t0) REVERT: E 280 ASN cc_start: 0.8608 (t0) cc_final: 0.8210 (t0) REVERT: E 325 MET cc_start: 0.8602 (ppp) cc_final: 0.7167 (ppp) REVERT: E 336 LYS cc_start: 0.9139 (ttpt) cc_final: 0.8868 (tttt) REVERT: F 192 ILE cc_start: 0.7819 (tp) cc_final: 0.7544 (tp) REVERT: F 325 MET cc_start: 0.8415 (ppp) cc_final: 0.8192 (ppp) REVERT: F 336 LYS cc_start: 0.9350 (ttpt) cc_final: 0.9080 (tttt) REVERT: H 83 GLU cc_start: 0.7915 (pt0) cc_final: 0.7636 (pt0) REVERT: H 192 ILE cc_start: 0.9293 (tp) cc_final: 0.8992 (tt) REVERT: H 205 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: H 325 MET cc_start: 0.8342 (ppp) cc_final: 0.7728 (ppp) REVERT: H 336 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8904 (tttt) REVERT: I 25 ASP cc_start: 0.8167 (p0) cc_final: 0.7808 (p0) REVERT: I 83 GLU cc_start: 0.7805 (pt0) cc_final: 0.7471 (pt0) REVERT: I 192 ILE cc_start: 0.9509 (tp) cc_final: 0.9204 (tp) REVERT: I 269 MET cc_start: 0.7993 (ttt) cc_final: 0.7676 (ttt) REVERT: I 280 ASN cc_start: 0.8681 (t0) cc_final: 0.8213 (t0) REVERT: I 314 GLN cc_start: 0.8814 (tt0) cc_final: 0.8547 (tt0) REVERT: I 325 MET cc_start: 0.8278 (ppp) cc_final: 0.7903 (ppp) REVERT: I 326 LYS cc_start: 0.8166 (pttp) cc_final: 0.7808 (ptpp) REVERT: I 336 LYS cc_start: 0.9148 (ttpt) cc_final: 0.8787 (tttt) REVERT: I 372 ARG cc_start: 0.8165 (ptt-90) cc_final: 0.7843 (mtm110) REVERT: K 758 LYS cc_start: 0.8605 (mmtm) cc_final: 0.8328 (mmtm) REVERT: K 781 GLN cc_start: 0.8126 (mt0) cc_final: 0.7813 (mt0) REVERT: K 791 ASN cc_start: 0.8700 (t0) cc_final: 0.8169 (t0) REVERT: K 827 ASN cc_start: 0.8246 (m-40) cc_final: 0.7809 (t0) REVERT: K 845 LYS cc_start: 0.8995 (tttp) cc_final: 0.8521 (tptp) REVERT: L 718 GLN cc_start: 0.9223 (mt0) cc_final: 0.8967 (mt0) REVERT: L 751 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7354 (tm-30) REVERT: L 791 ASN cc_start: 0.8687 (t0) cc_final: 0.8212 (t0) REVERT: N 723 MET cc_start: 0.8176 (tpt) cc_final: 0.7879 (tpt) REVERT: N 740 SER cc_start: 0.8461 (m) cc_final: 0.8231 (p) REVERT: N 837 TYR cc_start: 0.8679 (t80) cc_final: 0.8332 (t80) REVERT: N 845 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8500 (tptp) REVERT: O 723 MET cc_start: 0.8067 (tmm) cc_final: 0.7309 (tmm) REVERT: O 740 SER cc_start: 0.8770 (m) cc_final: 0.8468 (t) REVERT: O 791 ASN cc_start: 0.8703 (t0) cc_final: 0.8184 (t0) REVERT: O 845 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8518 (tptp) REVERT: Q 724 MET cc_start: 0.8613 (tpp) cc_final: 0.8052 (tpt) REVERT: Q 779 TYR cc_start: 0.8976 (m-80) cc_final: 0.8743 (m-80) REVERT: X 801 GLN cc_start: 0.8983 (tp40) cc_final: 0.8567 (tp-100) REVERT: X 826 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7206 (ptt) outliers start: 95 outliers final: 61 residues processed: 738 average time/residue: 0.3186 time to fit residues: 381.6854 Evaluate side-chains 743 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 676 time to evaluate : 2.557 ------------------------------------------------------------------------------- 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 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER 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 180 LEU Chi-restraints excluded: chain D residue 199 SER 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 89 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 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 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 H residue 349 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 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 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 740 SER Chi-restraints excluded: chain K residue 789 GLN Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain 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 789 GLN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.2980 chunk 217 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 290 optimal weight: 6.9990 chunk 307 optimal weight: 8.9990 chunk 151 optimal weight: 0.0470 chunk 275 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.4680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 49 GLN E 92 ASN E 128 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN K 718 GLN ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25716 Z= 0.173 Angle : 0.600 11.886 34788 Z= 0.297 Chirality : 0.042 0.162 3924 Planarity : 0.003 0.028 4422 Dihedral : 9.204 176.885 3574 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.52 % Allowed : 23.79 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3186 helix: -0.05 (0.13), residues: 1584 sheet: -0.37 (0.27), residues: 366 loop : -0.86 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 356 HIS 0.004 0.001 HIS D 161 PHE 0.021 0.001 PHE L 729 TYR 0.026 0.001 TYR F 166 ARG 0.004 0.000 ARG B 183 *********************** 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 806 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 710 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.5385 (ppp) cc_final: 0.4961 (ppp) REVERT: B 198 TYR cc_start: 0.9146 (m-80) cc_final: 0.8759 (m-80) REVERT: B 211 ASP cc_start: 0.8316 (t0) cc_final: 0.7964 (t0) REVERT: B 259 GLU cc_start: 0.8639 (tp30) cc_final: 0.8417 (tp30) REVERT: B 269 MET cc_start: 0.8492 (ttp) cc_final: 0.8215 (ttt) REVERT: B 305 MET cc_start: 0.8631 (mtp) cc_final: 0.8427 (mtp) REVERT: B 336 LYS cc_start: 0.9158 (ttpt) cc_final: 0.8834 (tttt) REVERT: D 44 MET cc_start: 0.7755 (mmm) cc_final: 0.7279 (mmm) REVERT: D 83 GLU cc_start: 0.7984 (pt0) cc_final: 0.7667 (pt0) REVERT: D 226 GLU cc_start: 0.8301 (tp30) cc_final: 0.8068 (tp30) REVERT: D 263 GLN cc_start: 0.8417 (mt0) cc_final: 0.8178 (mt0) REVERT: D 316 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7700 (mm-30) REVERT: E 8 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8776 (mp) REVERT: E 25 ASP cc_start: 0.7870 (p0) cc_final: 0.7516 (p0) REVERT: E 51 ASP cc_start: 0.8078 (t70) cc_final: 0.7778 (t0) REVERT: E 192 ILE cc_start: 0.9382 (tp) cc_final: 0.8944 (tt) REVERT: E 211 ASP cc_start: 0.8250 (t0) cc_final: 0.7609 (t0) REVERT: E 280 ASN cc_start: 0.8525 (t0) cc_final: 0.8042 (t0) REVERT: E 325 MET cc_start: 0.8618 (ppp) cc_final: 0.7380 (ppp) REVERT: E 336 LYS cc_start: 0.9112 (ttpt) cc_final: 0.8854 (tttt) REVERT: F 192 ILE cc_start: 0.7745 (tp) cc_final: 0.7500 (tp) REVERT: F 325 MET cc_start: 0.8433 (ppp) cc_final: 0.7988 (ppp) REVERT: F 336 LYS cc_start: 0.9321 (ttpt) cc_final: 0.9025 (tttt) REVERT: H 72 GLU cc_start: 0.7307 (pp20) cc_final: 0.7052 (pp20) REVERT: H 83 GLU cc_start: 0.7893 (pt0) cc_final: 0.7563 (pt0) REVERT: H 192 ILE cc_start: 0.9250 (tp) cc_final: 0.8971 (tt) REVERT: H 205 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: H 325 MET cc_start: 0.8302 (ppp) cc_final: 0.7687 (ppp) REVERT: H 336 LYS cc_start: 0.9162 (ttpt) cc_final: 0.8895 (tttt) REVERT: I 25 ASP cc_start: 0.8180 (p0) cc_final: 0.7693 (p0) REVERT: I 83 GLU cc_start: 0.7818 (pt0) cc_final: 0.7469 (pt0) REVERT: I 192 ILE cc_start: 0.9486 (tp) cc_final: 0.8846 (tp) REVERT: I 280 ASN cc_start: 0.8527 (t0) cc_final: 0.8088 (t0) REVERT: I 314 GLN cc_start: 0.8800 (tt0) cc_final: 0.8560 (tt0) REVERT: I 336 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8791 (tttt) REVERT: I 372 ARG cc_start: 0.8131 (ptt-90) cc_final: 0.7886 (mtm110) REVERT: K 758 LYS cc_start: 0.8574 (mmtm) cc_final: 0.8294 (mmtm) REVERT: K 791 ASN cc_start: 0.8612 (t0) cc_final: 0.8157 (t0) REVERT: K 844 GLN cc_start: 0.9005 (tp40) cc_final: 0.8709 (tp-100) REVERT: K 845 LYS cc_start: 0.8997 (tttp) cc_final: 0.8516 (tptp) REVERT: L 715 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7936 (pt) REVERT: L 718 GLN cc_start: 0.9205 (mt0) cc_final: 0.8939 (mt0) REVERT: L 751 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7436 (tm-30) REVERT: L 791 ASN cc_start: 0.8652 (t0) cc_final: 0.8210 (t0) REVERT: N 740 SER cc_start: 0.8451 (m) cc_final: 0.8231 (p) REVERT: N 845 LYS cc_start: 0.8980 (tttp) cc_final: 0.8523 (tptp) REVERT: O 723 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7327 (tmm) REVERT: O 740 SER cc_start: 0.8759 (m) cc_final: 0.8464 (t) REVERT: O 797 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8479 (mmtm) REVERT: O 845 LYS cc_start: 0.9060 (tttp) cc_final: 0.8530 (tptp) REVERT: Q 724 MET cc_start: 0.8616 (tpp) cc_final: 0.8061 (tpt) REVERT: Q 779 TYR cc_start: 0.8920 (m-80) cc_final: 0.8659 (m-80) REVERT: X 801 GLN cc_start: 0.8944 (tp40) cc_final: 0.8620 (tp40) REVERT: X 826 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7155 (ptt) outliers start: 96 outliers final: 60 residues processed: 747 average time/residue: 0.3198 time to fit residues: 391.0639 Evaluate side-chains 735 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 670 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain 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 145 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER 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 93 GLU Chi-restraints excluded: chain F residue 107 GLU 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 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 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 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 787 CYS Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 715 LEU Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 783 ILE Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 789 GLN Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 754 SER Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 789 GLN Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Chi-restraints excluded: chain X residue 833 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 4.9990 chunk 174 optimal weight: 0.0980 chunk 4 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 262 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 92 ASN E 128 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 ASN K 789 GLN O 844 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25716 Z= 0.313 Angle : 0.649 11.051 34788 Z= 0.320 Chirality : 0.045 0.166 3924 Planarity : 0.003 0.029 4422 Dihedral : 9.010 175.150 3562 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.55 % Allowed : 24.08 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3186 helix: 0.11 (0.13), residues: 1602 sheet: -0.10 (0.29), residues: 330 loop : -0.82 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 79 HIS 0.004 0.001 HIS O 788 PHE 0.021 0.001 PHE O 729 TYR 0.019 0.001 TYR F 166 ARG 0.003 0.000 ARG I 116 *********************** 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 811 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 687 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 LYS cc_start: 0.8886 (mmtm) cc_final: 0.8639 (mttm) REVERT: B 336 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8917 (tttt) REVERT: B 355 MET cc_start: -0.5610 (OUTLIER) cc_final: -0.6434 (ttm) REVERT: D 44 MET cc_start: 0.7830 (mmm) cc_final: 0.7431 (mmm) REVERT: D 263 GLN cc_start: 0.8514 (mt0) cc_final: 0.8273 (mt0) REVERT: D 316 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7674 (mm-30) REVERT: E 51 ASP cc_start: 0.8112 (t70) cc_final: 0.7824 (t0) REVERT: E 192 ILE cc_start: 0.9302 (tp) cc_final: 0.9051 (tp) REVERT: E 227 MET cc_start: 0.8645 (tpp) cc_final: 0.8352 (tpp) REVERT: E 269 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7886 (ttt) REVERT: E 297 ASN cc_start: 0.8799 (m-40) cc_final: 0.8436 (m-40) REVERT: E 325 MET cc_start: 0.8709 (ppp) cc_final: 0.7649 (ppp) REVERT: E 336 LYS cc_start: 0.9118 (ttpt) cc_final: 0.8886 (tttt) REVERT: F 192 ILE cc_start: 0.7992 (tp) cc_final: 0.7744 (tp) REVERT: F 325 MET cc_start: 0.8570 (ppp) cc_final: 0.7917 (ppp) REVERT: F 336 LYS cc_start: 0.9328 (ttpt) cc_final: 0.9033 (tttt) REVERT: H 83 GLU cc_start: 0.7922 (pt0) cc_final: 0.7590 (pt0) REVERT: H 192 ILE cc_start: 0.9241 (tp) cc_final: 0.9015 (tp) REVERT: H 205 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: H 325 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7892 (ppp) REVERT: H 336 LYS cc_start: 0.9228 (ttpt) cc_final: 0.8986 (tttt) REVERT: I 25 ASP cc_start: 0.8198 (p0) cc_final: 0.7806 (p0) REVERT: I 83 GLU cc_start: 0.7853 (pt0) cc_final: 0.7512 (pt0) REVERT: I 192 ILE cc_start: 0.9404 (tp) cc_final: 0.8922 (tp) REVERT: I 253 GLU cc_start: 0.8339 (mp0) cc_final: 0.8129 (mp0) REVERT: I 269 MET cc_start: 0.8147 (ttp) cc_final: 0.7818 (ttt) REVERT: I 280 ASN cc_start: 0.8687 (t0) cc_final: 0.8253 (t0) REVERT: I 336 LYS cc_start: 0.9204 (ttpt) cc_final: 0.8882 (tttt) REVERT: I 372 ARG cc_start: 0.8115 (ptt-90) cc_final: 0.7876 (mtm110) REVERT: K 791 ASN cc_start: 0.8638 (t0) cc_final: 0.8143 (t0) REVERT: K 837 TYR cc_start: 0.8577 (t80) cc_final: 0.8366 (t80) REVERT: K 845 LYS cc_start: 0.8989 (tttp) cc_final: 0.8515 (tptp) REVERT: L 715 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7980 (pt) REVERT: L 718 GLN cc_start: 0.9183 (mt0) cc_final: 0.8916 (mt0) REVERT: L 751 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7526 (tm-30) REVERT: L 791 ASN cc_start: 0.8650 (t0) cc_final: 0.8197 (t0) REVERT: N 845 LYS cc_start: 0.9029 (tttp) cc_final: 0.8534 (tptp) REVERT: O 723 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7368 (tmm) REVERT: O 740 SER cc_start: 0.8772 (m) cc_final: 0.8494 (t) REVERT: O 797 LYS cc_start: 0.8890 (mmtm) cc_final: 0.8514 (mmtm) REVERT: O 803 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8255 (mp) REVERT: O 845 LYS cc_start: 0.9078 (tttp) cc_final: 0.8541 (tptp) REVERT: Q 724 MET cc_start: 0.8612 (tpp) cc_final: 0.8005 (tpt) REVERT: Q 779 TYR cc_start: 0.8921 (m-80) cc_final: 0.8663 (m-80) REVERT: X 801 GLN cc_start: 0.8986 (tp40) cc_final: 0.8642 (tp40) REVERT: X 826 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7366 (ptt) outliers start: 124 outliers final: 85 residues processed: 735 average time/residue: 0.3147 time to fit residues: 378.8065 Evaluate side-chains 757 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 664 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 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 E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 360 GLN 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 179 ASP Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 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 202 THR Chi-restraints excluded: chain I residue 236 LEU 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 740 SER Chi-restraints excluded: chain K residue 787 CYS Chi-restraints excluded: chain K residue 789 GLN Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 715 LEU Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain N residue 714 VAL 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 O residue 787 CYS Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain O residue 803 LEU 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 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 103 optimal weight: 6.9990 chunk 276 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 180 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 142 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 161 optimal weight: 8.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN D 137 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 831 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2988 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= 0.183 Angle : 0.606 10.299 34788 Z= 0.298 Chirality : 0.043 0.151 3924 Planarity : 0.003 0.028 4422 Dihedral : 8.830 177.586 3560 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.63 % Allowed : 25.22 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3186 helix: 0.56 (0.14), residues: 1512 sheet: 0.03 (0.29), residues: 330 loop : -0.52 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 356 HIS 0.005 0.001 HIS O 788 PHE 0.019 0.001 PHE K 729 TYR 0.018 0.001 TYR F 166 ARG 0.002 0.000 ARG B 183 *********************** 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 796 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 697 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 TYR cc_start: 0.9222 (m-80) cc_final: 0.8876 (m-80) REVERT: B 211 ASP cc_start: 0.8276 (t0) cc_final: 0.7959 (t0) REVERT: B 215 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8487 (mttm) REVERT: B 299 MET cc_start: 0.4134 (mtm) cc_final: 0.3591 (mtm) REVERT: B 336 LYS cc_start: 0.9181 (ttpt) cc_final: 0.8901 (tttt) REVERT: B 355 MET cc_start: -0.5713 (OUTLIER) cc_final: -0.6721 (ttm) REVERT: D 44 MET cc_start: 0.7675 (mmm) cc_final: 0.7251 (mmm) REVERT: D 263 GLN cc_start: 0.8446 (mt0) cc_final: 0.8227 (mt0) REVERT: D 316 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7679 (mm-30) REVERT: E 51 ASP cc_start: 0.8042 (t70) cc_final: 0.7749 (t0) REVERT: E 82 MET cc_start: 0.9230 (tpt) cc_final: 0.9014 (tpt) REVERT: E 192 ILE cc_start: 0.9291 (tp) cc_final: 0.8959 (tt) REVERT: E 211 ASP cc_start: 0.8237 (t0) cc_final: 0.7606 (t0) REVERT: E 227 MET cc_start: 0.8620 (tpp) cc_final: 0.8322 (tpp) REVERT: E 269 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8054 (ttt) REVERT: E 325 MET cc_start: 0.8724 (ppp) cc_final: 0.7707 (ppp) REVERT: E 336 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8834 (tttt) REVERT: F 192 ILE cc_start: 0.7879 (tp) cc_final: 0.7655 (tp) REVERT: F 325 MET cc_start: 0.8553 (ppp) cc_final: 0.7711 (ppp) REVERT: F 336 LYS cc_start: 0.9306 (ttpt) cc_final: 0.9013 (tttt) REVERT: H 83 GLU cc_start: 0.7905 (pt0) cc_final: 0.7650 (pt0) REVERT: H 192 ILE cc_start: 0.9208 (tp) cc_final: 0.8962 (tt) REVERT: H 205 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: H 325 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7855 (ppp) REVERT: H 336 LYS cc_start: 0.9209 (ttpt) cc_final: 0.8988 (tttt) REVERT: I 25 ASP cc_start: 0.8190 (p0) cc_final: 0.7510 (p0) REVERT: I 83 GLU cc_start: 0.7840 (pt0) cc_final: 0.7473 (pt0) REVERT: I 192 ILE cc_start: 0.9317 (tp) cc_final: 0.8990 (tp) REVERT: I 280 ASN cc_start: 0.8526 (t0) cc_final: 0.8154 (t0) REVERT: I 316 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7732 (mm-30) REVERT: I 325 MET cc_start: 0.8773 (ppp) cc_final: 0.8135 (ppp) REVERT: I 336 LYS cc_start: 0.9166 (ttpt) cc_final: 0.8817 (tttt) REVERT: I 372 ARG cc_start: 0.8092 (ptt-90) cc_final: 0.7855 (mtm110) REVERT: K 791 ASN cc_start: 0.8561 (t0) cc_final: 0.8193 (t0) REVERT: K 844 GLN cc_start: 0.9019 (tp40) cc_final: 0.8702 (tp40) REVERT: K 845 LYS cc_start: 0.8985 (tttp) cc_final: 0.8507 (tptp) REVERT: L 715 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7934 (pt) REVERT: L 718 GLN cc_start: 0.9192 (mt0) cc_final: 0.8922 (mt0) REVERT: L 751 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7503 (tm-30) REVERT: L 791 ASN cc_start: 0.8619 (t0) cc_final: 0.8135 (t0) REVERT: N 845 LYS cc_start: 0.9031 (tttp) cc_final: 0.8538 (tptp) REVERT: N 861 MET cc_start: 0.7488 (ptp) cc_final: 0.7253 (ptp) REVERT: O 723 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7368 (tmm) REVERT: O 740 SER cc_start: 0.8752 (m) cc_final: 0.8473 (t) REVERT: O 797 LYS cc_start: 0.8802 (mmtm) cc_final: 0.8486 (mmtm) REVERT: O 845 LYS cc_start: 0.9076 (tttp) cc_final: 0.8536 (tptp) REVERT: Q 724 MET cc_start: 0.8574 (tpp) cc_final: 0.8081 (tpt) REVERT: Q 779 TYR cc_start: 0.8866 (m-80) cc_final: 0.8589 (m-80) REVERT: X 791 ASN cc_start: 0.8555 (t0) cc_final: 0.8035 (t0) REVERT: X 826 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7338 (ptt) outliers start: 99 outliers final: 67 residues processed: 727 average time/residue: 0.3160 time to fit residues: 376.5320 Evaluate side-chains 741 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 667 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 61 LYS 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 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 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 E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL 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 149 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 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 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 740 SER Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 715 LEU Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 789 GLN Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 787 CYS 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 789 GLN 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 296 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 174 optimal weight: 0.0060 chunk 259 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 789 GLN K 831 GLN N 718 GLN Q 718 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25716 Z= 0.260 Angle : 0.634 10.044 34788 Z= 0.312 Chirality : 0.044 0.157 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.640 173.282 3558 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.19 % Allowed : 25.66 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3186 helix: 0.66 (0.14), residues: 1512 sheet: 0.08 (0.30), residues: 330 loop : -0.44 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 356 HIS 0.004 0.001 HIS O 788 PHE 0.019 0.001 PHE O 729 TYR 0.017 0.001 TYR F 166 ARG 0.003 0.000 ARG I 116 *********************** 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 fitting. rotamer outliers: 114 poor density : 676 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7917 (mm-30) REVERT: B 215 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8566 (mttp) REVERT: B 336 LYS cc_start: 0.9212 (ttpt) cc_final: 0.8928 (tttt) REVERT: B 355 MET cc_start: -0.5892 (OUTLIER) cc_final: -0.6726 (ttm) REVERT: D 44 MET cc_start: 0.7763 (mmm) cc_final: 0.7377 (mmm) REVERT: D 83 GLU cc_start: 0.8041 (pt0) cc_final: 0.7837 (pt0) REVERT: D 263 GLN cc_start: 0.8474 (mt0) cc_final: 0.8249 (mt0) REVERT: D 316 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7679 (mm-30) REVERT: E 51 ASP cc_start: 0.8090 (t70) cc_final: 0.7782 (t0) REVERT: E 82 MET cc_start: 0.9314 (tpt) cc_final: 0.8958 (tpt) REVERT: E 192 ILE cc_start: 0.9232 (tp) cc_final: 0.9008 (tp) REVERT: E 224 GLU cc_start: 0.7790 (mp0) cc_final: 0.7530 (mp0) REVERT: E 227 MET cc_start: 0.8641 (tpp) cc_final: 0.8301 (tpp) REVERT: E 269 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8072 (ttt) REVERT: E 325 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7762 (ppp) REVERT: E 336 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8882 (tttt) REVERT: F 25 ASP cc_start: 0.7911 (p0) cc_final: 0.7680 (p0) REVERT: F 192 ILE cc_start: 0.7992 (tp) cc_final: 0.7757 (tp) REVERT: F 253 GLU cc_start: 0.8361 (mp0) cc_final: 0.8105 (mp0) REVERT: F 269 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7836 (ttt) REVERT: F 325 MET cc_start: 0.8545 (ppp) cc_final: 0.7377 (ppp) REVERT: F 336 LYS cc_start: 0.9315 (ttpt) cc_final: 0.9027 (tttt) REVERT: H 83 GLU cc_start: 0.7932 (pt0) cc_final: 0.7704 (pt0) REVERT: H 192 ILE cc_start: 0.9203 (tp) cc_final: 0.8991 (tp) REVERT: H 205 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: H 224 GLU cc_start: 0.8022 (mp0) cc_final: 0.7812 (mp0) REVERT: H 325 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7904 (ppp) REVERT: H 336 LYS cc_start: 0.9260 (ttpt) cc_final: 0.9049 (tttt) REVERT: I 25 ASP cc_start: 0.8156 (p0) cc_final: 0.7494 (p0) REVERT: I 83 GLU cc_start: 0.7870 (pt0) cc_final: 0.7547 (pt0) REVERT: I 192 ILE cc_start: 0.9343 (tp) cc_final: 0.8885 (tp) REVERT: I 269 MET cc_start: 0.8314 (ttp) cc_final: 0.7840 (ttt) REVERT: I 316 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7754 (mm-30) REVERT: I 325 MET cc_start: 0.8814 (ppp) cc_final: 0.8181 (ppp) REVERT: I 336 LYS cc_start: 0.9207 (ttpt) cc_final: 0.8875 (tttt) REVERT: I 372 ARG cc_start: 0.8104 (ptt-90) cc_final: 0.7871 (mtm110) REVERT: K 791 ASN cc_start: 0.8562 (t0) cc_final: 0.8161 (t0) REVERT: K 845 LYS cc_start: 0.8993 (tttp) cc_final: 0.8515 (tptp) REVERT: L 715 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7941 (pt) REVERT: L 721 MET cc_start: 0.8987 (ppp) cc_final: 0.8723 (ptm) REVERT: L 751 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7516 (tm-30) REVERT: L 791 ASN cc_start: 0.8566 (t0) cc_final: 0.8200 (t0) REVERT: L 816 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8353 (tpp) REVERT: N 845 LYS cc_start: 0.9029 (tttp) cc_final: 0.8543 (tptp) REVERT: O 723 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7371 (tmm) REVERT: O 724 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8093 (tpt) REVERT: O 740 SER cc_start: 0.8756 (m) cc_final: 0.8487 (t) REVERT: O 845 LYS cc_start: 0.9087 (tttp) cc_final: 0.8542 (tptp) REVERT: Q 724 MET cc_start: 0.8616 (tpp) cc_final: 0.8016 (tpt) REVERT: Q 779 TYR cc_start: 0.8872 (m-80) cc_final: 0.8622 (m-80) REVERT: X 791 ASN cc_start: 0.8554 (t0) cc_final: 0.8056 (t0) REVERT: X 826 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7347 (ptt) outliers start: 114 outliers final: 83 residues processed: 712 average time/residue: 0.3100 time to fit residues: 362.7500 Evaluate side-chains 749 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 655 time to evaluate : 2.989 ------------------------------------------------------------------------------- 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 61 LYS 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 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 201 VAL 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 57 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 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 149 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 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 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 167 GLU 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 740 SER Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 715 LEU Chi-restraints excluded: chain L residue 725 GLU Chi-restraints excluded: chain L residue 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 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 826 MET Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 724 MET Chi-restraints excluded: chain O residue 787 CYS Chi-restraints excluded: chain O residue 792 ILE 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 789 GLN 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 189 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 208 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 28 optimal weight: 50.0000 chunk 240 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 789 GLN K 831 GLN L 718 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25716 Z= 0.274 Angle : 0.636 8.277 34788 Z= 0.315 Chirality : 0.044 0.176 3924 Planarity : 0.003 0.030 4422 Dihedral : 8.526 172.087 3558 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.37 % Allowed : 25.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3186 helix: 0.84 (0.14), residues: 1476 sheet: 0.07 (0.30), residues: 330 loop : -0.33 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 356 HIS 0.004 0.001 HIS O 788 PHE 0.020 0.001 PHE K 729 TYR 0.016 0.001 TYR E 166 ARG 0.002 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 675 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 LYS cc_start: 0.8876 (mmtm) cc_final: 0.8549 (mttm) REVERT: B 336 LYS cc_start: 0.9168 (ttpt) cc_final: 0.8907 (tttt) REVERT: B 355 MET cc_start: -0.5977 (OUTLIER) cc_final: -0.7148 (ttm) REVERT: D 44 MET cc_start: 0.7780 (mmm) cc_final: 0.7384 (mmm) REVERT: D 263 GLN cc_start: 0.8492 (mt0) cc_final: 0.8272 (mt0) REVERT: D 316 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7685 (mm-30) REVERT: D 326 LYS cc_start: 0.8337 (pttp) cc_final: 0.7963 (mtmm) REVERT: E 51 ASP cc_start: 0.8105 (t70) cc_final: 0.7799 (t0) REVERT: E 82 MET cc_start: 0.9325 (tpt) cc_final: 0.9066 (tpt) REVERT: E 192 ILE cc_start: 0.9240 (tp) cc_final: 0.9019 (tp) REVERT: E 227 MET cc_start: 0.8682 (tpp) cc_final: 0.8334 (tpp) REVERT: E 269 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8071 (ttt) REVERT: E 325 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7774 (ppp) REVERT: E 336 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8884 (tttt) REVERT: F 192 ILE cc_start: 0.8041 (tp) cc_final: 0.7813 (tp) REVERT: F 253 GLU cc_start: 0.8382 (mp0) cc_final: 0.8118 (mp0) REVERT: F 269 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7836 (ttt) REVERT: F 325 MET cc_start: 0.8553 (ppp) cc_final: 0.7469 (ppp) REVERT: F 336 LYS cc_start: 0.9328 (ttpt) cc_final: 0.9029 (tttt) REVERT: H 83 GLU cc_start: 0.7918 (pt0) cc_final: 0.7687 (pt0) REVERT: H 192 ILE cc_start: 0.9200 (tp) cc_final: 0.8992 (tp) REVERT: H 205 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: H 269 MET cc_start: 0.8375 (ttp) cc_final: 0.8135 (ttt) REVERT: H 325 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7938 (ppp) REVERT: H 336 LYS cc_start: 0.9283 (ttpt) cc_final: 0.9079 (tttt) REVERT: I 25 ASP cc_start: 0.8136 (p0) cc_final: 0.7602 (p0) REVERT: I 83 GLU cc_start: 0.7892 (pt0) cc_final: 0.7551 (pt0) REVERT: I 192 ILE cc_start: 0.9305 (tp) cc_final: 0.8976 (tp) REVERT: I 269 MET cc_start: 0.8314 (ttp) cc_final: 0.8022 (ttt) REVERT: I 316 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7792 (mm-30) REVERT: I 325 MET cc_start: 0.8819 (ppp) cc_final: 0.8249 (ppp) REVERT: I 336 LYS cc_start: 0.9235 (ttpt) cc_final: 0.8902 (tttt) REVERT: K 791 ASN cc_start: 0.8583 (t0) cc_final: 0.8180 (t0) REVERT: K 845 LYS cc_start: 0.9004 (tttp) cc_final: 0.8505 (tptp) REVERT: L 751 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7527 (tm-30) REVERT: L 791 ASN cc_start: 0.8552 (t0) cc_final: 0.8212 (t0) REVERT: N 723 MET cc_start: 0.8373 (tmm) cc_final: 0.8063 (tmm) REVERT: N 845 LYS cc_start: 0.9043 (tttp) cc_final: 0.8553 (tptp) REVERT: O 723 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7390 (tmm) REVERT: O 724 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8077 (tpt) REVERT: O 740 SER cc_start: 0.8760 (m) cc_final: 0.8477 (t) REVERT: O 845 LYS cc_start: 0.9091 (tttp) cc_final: 0.8547 (tptp) REVERT: Q 724 MET cc_start: 0.8630 (tpp) cc_final: 0.8018 (tpt) REVERT: Q 779 TYR cc_start: 0.8886 (m-80) cc_final: 0.8639 (m-80) REVERT: X 791 ASN cc_start: 0.8514 (t0) cc_final: 0.8028 (t0) REVERT: X 801 GLN cc_start: 0.8956 (tp40) cc_final: 0.8577 (tm-30) REVERT: X 826 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7411 (ptt) outliers start: 119 outliers final: 90 residues processed: 712 average time/residue: 0.3173 time to fit residues: 369.2122 Evaluate side-chains 761 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 662 time to evaluate : 2.753 ------------------------------------------------------------------------------- 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 61 LYS 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 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 201 VAL 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 65 LEU 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 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 149 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 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 246 GLN Chi-restraints excluded: chain H residue 278 THR 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 167 GLU 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 740 SER 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 796 VAL Chi-restraints excluded: chain N residue 829 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 724 MET Chi-restraints excluded: chain O residue 787 CYS Chi-restraints excluded: chain O residue 792 ILE 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 285 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 270 optimal weight: 40.0000 chunk 284 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 831 GLN ** K 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 718 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25716 Z= 0.275 Angle : 0.651 11.672 34788 Z= 0.320 Chirality : 0.044 0.176 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.422 172.815 3558 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.04 % Allowed : 25.99 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3186 helix: 0.86 (0.14), residues: 1476 sheet: 0.10 (0.30), residues: 330 loop : -0.26 (0.18), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 356 HIS 0.004 0.001 HIS O 788 PHE 0.021 0.001 PHE K 729 TYR 0.017 0.001 TYR K 837 ARG 0.010 0.000 ARG I 372 *********************** 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 792 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 682 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8547 (mttm) REVERT: B 336 LYS cc_start: 0.9192 (ttpt) cc_final: 0.8908 (tttt) REVERT: B 355 MET cc_start: -0.5997 (OUTLIER) cc_final: -0.7038 (ttm) REVERT: D 263 GLN cc_start: 0.8487 (mt0) cc_final: 0.8274 (mt0) REVERT: D 326 LYS cc_start: 0.8450 (pttp) cc_final: 0.8177 (pttm) REVERT: E 51 ASP cc_start: 0.8109 (t70) cc_final: 0.7803 (t0) REVERT: E 82 MET cc_start: 0.9337 (tpt) cc_final: 0.8990 (tpt) REVERT: E 192 ILE cc_start: 0.9247 (tp) cc_final: 0.9021 (tp) REVERT: E 227 MET cc_start: 0.8689 (tpp) cc_final: 0.8328 (tpp) REVERT: E 269 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8089 (ttt) REVERT: E 325 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7909 (ppp) REVERT: E 336 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8864 (tttt) REVERT: F 192 ILE cc_start: 0.8041 (tp) cc_final: 0.7819 (tp) REVERT: F 253 GLU cc_start: 0.8392 (mp0) cc_final: 0.8125 (mp0) REVERT: F 325 MET cc_start: 0.8558 (ppp) cc_final: 0.7569 (ppp) REVERT: F 336 LYS cc_start: 0.9325 (ttpt) cc_final: 0.9023 (tttt) REVERT: H 83 GLU cc_start: 0.7948 (pt0) cc_final: 0.7712 (pt0) REVERT: H 192 ILE cc_start: 0.9195 (tp) cc_final: 0.8990 (tp) REVERT: H 205 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: H 269 MET cc_start: 0.8393 (ttp) cc_final: 0.8177 (ttt) REVERT: H 325 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7977 (ppp) REVERT: I 25 ASP cc_start: 0.8174 (p0) cc_final: 0.7519 (p0) REVERT: I 83 GLU cc_start: 0.7876 (pt0) cc_final: 0.7557 (pt0) REVERT: I 192 ILE cc_start: 0.9284 (tp) cc_final: 0.8955 (tp) REVERT: I 269 MET cc_start: 0.8245 (ttp) cc_final: 0.8000 (ttt) REVERT: I 316 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7787 (mm-30) REVERT: I 325 MET cc_start: 0.8831 (ppp) cc_final: 0.8273 (ppp) REVERT: I 336 LYS cc_start: 0.9251 (ttpt) cc_final: 0.8923 (tttt) REVERT: K 791 ASN cc_start: 0.8585 (t0) cc_final: 0.8215 (t0) REVERT: K 845 LYS cc_start: 0.8990 (tttp) cc_final: 0.8511 (tptp) REVERT: L 751 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7550 (tm-30) REVERT: L 791 ASN cc_start: 0.8532 (t0) cc_final: 0.8220 (t0) REVERT: N 723 MET cc_start: 0.8148 (tmm) cc_final: 0.7899 (tpt) REVERT: N 845 LYS cc_start: 0.9047 (tttp) cc_final: 0.8555 (tptp) REVERT: O 723 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7408 (tmm) REVERT: O 724 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8080 (tpt) REVERT: O 740 SER cc_start: 0.8748 (m) cc_final: 0.8470 (t) REVERT: O 845 LYS cc_start: 0.9093 (tttp) cc_final: 0.8549 (tptp) REVERT: Q 724 MET cc_start: 0.8614 (tpp) cc_final: 0.8347 (tpp) REVERT: Q 779 TYR cc_start: 0.8891 (m-80) cc_final: 0.8600 (m-80) REVERT: X 791 ASN cc_start: 0.8517 (t0) cc_final: 0.8035 (t0) REVERT: X 801 GLN cc_start: 0.8936 (tp40) cc_final: 0.8588 (tm-30) REVERT: X 826 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7420 (ptt) outliers start: 110 outliers final: 84 residues processed: 715 average time/residue: 0.3220 time to fit residues: 375.2651 Evaluate side-chains 760 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 668 time to evaluate : 2.745 ------------------------------------------------------------------------------- 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 61 LYS 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 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 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 57 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain 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 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 246 GLN Chi-restraints excluded: chain H residue 278 THR 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 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 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 740 SER Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 718 GLN 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 796 VAL Chi-restraints excluded: chain N residue 829 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 724 MET Chi-restraints excluded: chain O residue 787 CYS Chi-restraints excluded: chain O residue 792 ILE 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 792 ILE 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 187 optimal weight: 10.0000 chunk 302 optimal weight: 40.0000 chunk 184 optimal weight: 6.9990 chunk 143 optimal weight: 0.0870 chunk 209 optimal weight: 4.9990 chunk 316 optimal weight: 9.9990 chunk 291 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 194 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 overall best weight: 2.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 718 GLN K 831 GLN ** K 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 718 GLN O 844 GLN X 718 GLN ** X 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25716 Z= 0.242 Angle : 0.650 10.605 34788 Z= 0.320 Chirality : 0.044 0.211 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.329 175.407 3558 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.74 % Allowed : 26.36 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3186 helix: 0.80 (0.14), residues: 1512 sheet: 0.13 (0.30), residues: 330 loop : -0.28 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 356 HIS 0.004 0.001 HIS O 788 PHE 0.022 0.001 PHE K 729 TYR 0.019 0.001 TYR O 779 ARG 0.010 0.000 ARG I 372 ********************** 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 791 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 689 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 211 ASP cc_start: 0.8299 (t0) cc_final: 0.7991 (t0) REVERT: B 215 LYS cc_start: 0.8895 (mmtm) cc_final: 0.8503 (mttm) REVERT: B 336 LYS cc_start: 0.9170 (ttpt) cc_final: 0.8861 (tttt) REVERT: B 355 MET cc_start: -0.5888 (OUTLIER) cc_final: -0.6954 (ttm) REVERT: D 44 MET cc_start: 0.7600 (mmm) cc_final: 0.7238 (mmm) REVERT: D 192 ILE cc_start: 0.9231 (tp) cc_final: 0.8909 (tp) REVERT: D 263 GLN cc_start: 0.8474 (mt0) cc_final: 0.8254 (mt0) REVERT: D 297 ASN cc_start: 0.8362 (m-40) cc_final: 0.8103 (m-40) REVERT: D 326 LYS cc_start: 0.8402 (pttp) cc_final: 0.8157 (pttm) REVERT: E 51 ASP cc_start: 0.8104 (t70) cc_final: 0.7788 (t0) REVERT: E 82 MET cc_start: 0.9325 (tpt) cc_final: 0.8995 (tpt) REVERT: E 192 ILE cc_start: 0.9244 (tp) cc_final: 0.9020 (tp) REVERT: E 227 MET cc_start: 0.8697 (tpp) cc_final: 0.8339 (tpp) REVERT: E 269 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8098 (ttt) REVERT: E 325 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7911 (ppp) REVERT: E 336 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8859 (tttt) REVERT: F 192 ILE cc_start: 0.8010 (tp) cc_final: 0.7791 (tp) REVERT: F 253 GLU cc_start: 0.8379 (mp0) cc_final: 0.8113 (mp0) REVERT: F 325 MET cc_start: 0.8542 (ppp) cc_final: 0.7639 (ppp) REVERT: F 336 LYS cc_start: 0.9321 (ttpt) cc_final: 0.9018 (tttt) REVERT: H 83 GLU cc_start: 0.7947 (pt0) cc_final: 0.7694 (pt0) REVERT: H 205 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: H 325 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7990 (ppp) REVERT: I 25 ASP cc_start: 0.8126 (p0) cc_final: 0.7578 (p0) REVERT: I 83 GLU cc_start: 0.7866 (pt0) cc_final: 0.7538 (pt0) REVERT: I 192 ILE cc_start: 0.9286 (tp) cc_final: 0.8950 (tp) REVERT: I 316 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7790 (mm-30) REVERT: I 325 MET cc_start: 0.8844 (ppp) cc_final: 0.8302 (ppp) REVERT: I 336 LYS cc_start: 0.9221 (ttpt) cc_final: 0.8909 (tttt) REVERT: K 791 ASN cc_start: 0.8577 (t0) cc_final: 0.8215 (t0) REVERT: K 837 TYR cc_start: 0.8636 (t80) cc_final: 0.8170 (t80) REVERT: K 844 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8682 (tp-100) REVERT: K 845 LYS cc_start: 0.8989 (tttp) cc_final: 0.8502 (tptp) REVERT: L 751 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7570 (tm-30) REVERT: L 791 ASN cc_start: 0.8509 (t0) cc_final: 0.8258 (t0) REVERT: N 845 LYS cc_start: 0.9044 (tttp) cc_final: 0.8542 (tptp) REVERT: O 723 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7383 (tmm) REVERT: O 724 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8093 (tpt) REVERT: O 740 SER cc_start: 0.8747 (m) cc_final: 0.8458 (t) REVERT: O 845 LYS cc_start: 0.9093 (tttp) cc_final: 0.8549 (tptp) REVERT: Q 701 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: Q 724 MET cc_start: 0.8643 (tpp) cc_final: 0.8379 (tpp) REVERT: Q 779 TYR cc_start: 0.8870 (m-80) cc_final: 0.8582 (m-80) REVERT: X 791 ASN cc_start: 0.8537 (t0) cc_final: 0.8058 (t0) REVERT: X 801 GLN cc_start: 0.8921 (tp40) cc_final: 0.8598 (tm-30) REVERT: X 826 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7372 (ptt) outliers start: 102 outliers final: 82 residues processed: 719 average time/residue: 0.3201 time to fit residues: 377.8061 Evaluate side-chains 763 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 672 time to evaluate : 2.537 ------------------------------------------------------------------------------- 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 61 LYS 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 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 E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain 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 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 246 GLN Chi-restraints excluded: chain H residue 278 THR 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 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 167 GLU 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 740 SER Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 718 GLN Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 829 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 724 MET Chi-restraints excluded: chain O residue 787 CYS Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain Q residue 701 GLU Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 754 SER Chi-restraints excluded: chain Q residue 787 CYS Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 787 CYS Chi-restraints excluded: chain X residue 792 ILE Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 9.9990 chunk 268 optimal weight: 0.0570 chunk 77 optimal weight: 9.9990 chunk 232 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 chunk 31 optimal weight: 40.0000 chunk 46 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN D 137 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 831 GLN ** K 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 718 GLN N 718 GLN O 844 GLN X 789 GLN ** X 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.157870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110825 restraints weight = 34548.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116006 restraints weight = 18237.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119392 restraints weight = 12321.968| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25716 Z= 0.222 Angle : 0.645 11.433 34788 Z= 0.318 Chirality : 0.044 0.252 3924 Planarity : 0.003 0.037 4422 Dihedral : 8.252 176.106 3558 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.74 % Allowed : 26.25 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3186 helix: 0.81 (0.14), residues: 1512 sheet: 0.09 (0.30), residues: 342 loop : -0.17 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 356 HIS 0.004 0.001 HIS O 788 PHE 0.025 0.001 PHE X 729 TYR 0.023 0.001 TYR O 779 ARG 0.006 0.000 ARG H 256 =============================================================================== Job complete usr+sys time: 6515.37 seconds wall clock time: 116 minutes 22.04 seconds (6982.04 seconds total)