Starting phenix.real_space_refine (version: dev) on Thu Apr 7 05:09:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/04_2022/6wvt_21925_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/04_2022/6wvt_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_21925/04_2022/6wvt_21925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/04_2022/6wvt_21925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/04_2022/6wvt_21925_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/04_2022/6wvt_21925_updated.pdb" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 701": "OE1" <-> "OE2" Residue "L GLU 701": "OE1" <-> "OE2" Residue "N GLU 701": "OE1" <-> "OE2" Residue "O GLU 701": "OE1" <-> "OE2" Residue "Q GLU 701": "OE1" <-> "OE2" Residue "X GLU 701": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: 14.32, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 11.02 Conformation dependent library (CDL) restraints added in 3.7 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... running ksdssp... Secondary structure from input PDB file: 156 helices and 24 sheets defined 47.2% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 90 removed outlier: 3.825A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 139 through 144 removed outlier: 3.755A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.623A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.924A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 318 Processing helix chain 'B' and resid 335 through 348 removed outlier: 4.891A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 359 through 362 No H-bonds generated for 'chain 'B' and resid 359 through 362' Processing helix chain 'B' and resid 366 through 374 removed outlier: 3.636A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 372 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS B 374 " --> pdb=" O HIS B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 374' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.825A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 139 through 144 removed outlier: 3.754A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.624A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.924A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 276 through 282 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 318 Processing helix chain 'D' and resid 335 through 348 removed outlier: 4.891A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 346 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 359 through 362 No H-bonds generated for 'chain 'D' and resid 359 through 362' Processing helix chain 'D' and resid 366 through 374 removed outlier: 3.636A pdb=" N ILE D 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 372 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS D 374 " --> pdb=" O HIS D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 366 through 374' Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 90 removed outlier: 3.825A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 139 through 144 removed outlier: 3.755A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 194 removed outlier: 3.910A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.624A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.925A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 276 through 282 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 318 Processing helix chain 'E' and resid 335 through 348 removed outlier: 4.891A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU E 346 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 359 through 362 No H-bonds generated for 'chain 'E' and resid 359 through 362' Processing helix chain 'E' and resid 366 through 374 removed outlier: 3.635A pdb=" N ILE E 369 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG E 372 " --> pdb=" O ILE E 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS E 374 " --> pdb=" O HIS E 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 366 through 374' Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.825A pdb=" N LYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 139 through 144 removed outlier: 3.755A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 223 through 231 removed outlier: 3.624A pdb=" N ALA F 231 " --> pdb=" O MET F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 removed outlier: 3.924A pdb=" N ARG F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 276 through 282 Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 318 Processing helix chain 'F' and resid 335 through 348 removed outlier: 4.892A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU F 346 " --> pdb=" O GLY F 343 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA F 347 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 359 through 362 No H-bonds generated for 'chain 'F' and resid 359 through 362' Processing helix chain 'F' and resid 366 through 374 removed outlier: 3.636A pdb=" N ILE F 369 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL F 370 " --> pdb=" O PRO F 367 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS F 371 " --> pdb=" O SER F 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG F 372 " --> pdb=" O ILE F 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS F 373 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS F 374 " --> pdb=" O HIS F 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 366 through 374' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 79 through 90 removed outlier: 3.824A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 139 through 144 removed outlier: 3.754A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 216 Processing helix chain 'H' and resid 223 through 231 removed outlier: 3.624A pdb=" N ALA H 231 " --> pdb=" O MET H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 256 removed outlier: 3.924A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 261 Processing helix chain 'H' and resid 276 through 282 Processing helix chain 'H' and resid 290 through 294 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 309 through 318 Processing helix chain 'H' and resid 335 through 348 removed outlier: 4.892A pdb=" N VAL H 339 " --> pdb=" O LYS H 336 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY H 342 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU H 346 " --> pdb=" O GLY H 343 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA H 347 " --> pdb=" O SER H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 352 No H-bonds generated for 'chain 'H' and resid 350 through 352' Processing helix chain 'H' and resid 359 through 362 No H-bonds generated for 'chain 'H' and resid 359 through 362' Processing helix chain 'H' and resid 366 through 374 removed outlier: 3.635A pdb=" N ILE H 369 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL H 370 " --> pdb=" O PRO H 367 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS H 371 " --> pdb=" O SER H 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG H 372 " --> pdb=" O ILE H 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS H 373 " --> pdb=" O VAL H 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS H 374 " --> pdb=" O HIS H 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 366 through 374' Processing helix chain 'I' and resid 55 through 59 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 79 through 90 removed outlier: 3.824A pdb=" N LYS I 84 " --> pdb=" O ASP I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 113 through 125 Processing helix chain 'I' and resid 139 through 144 removed outlier: 3.755A pdb=" N TYR I 143 " --> pdb=" O VAL I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 216 Processing helix chain 'I' and resid 223 through 231 removed outlier: 3.623A pdb=" N ALA I 231 " --> pdb=" O MET I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 256 removed outlier: 3.923A pdb=" N ARG I 256 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 261 Processing helix chain 'I' and resid 276 through 282 Processing helix chain 'I' and resid 290 through 294 Processing helix chain 'I' and resid 302 through 304 No H-bonds generated for 'chain 'I' and resid 302 through 304' Processing helix chain 'I' and resid 309 through 318 Processing helix chain 'I' and resid 335 through 348 removed outlier: 4.891A pdb=" N VAL I 339 " --> pdb=" O LYS I 336 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY I 342 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU I 346 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA I 347 " --> pdb=" O SER I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 352 No H-bonds generated for 'chain 'I' and resid 350 through 352' Processing helix chain 'I' and resid 359 through 362 No H-bonds generated for 'chain 'I' and resid 359 through 362' Processing helix chain 'I' and resid 366 through 374 removed outlier: 3.634A pdb=" N ILE I 369 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL I 370 " --> pdb=" O PRO I 367 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS I 371 " --> pdb=" O SER I 368 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG I 372 " --> pdb=" O ILE I 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS I 373 " --> pdb=" O VAL I 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS I 374 " --> pdb=" O HIS I 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 366 through 374' Processing helix chain 'K' and resid 713 through 726 Processing helix chain 'K' and resid 728 through 731 No H-bonds generated for 'chain 'K' and resid 728 through 731' Processing helix chain 'K' and resid 740 through 765 removed outlier: 3.623A pdb=" N ASP K 765 " --> pdb=" O ARG K 761 " (cutoff:3.500A) Processing helix chain 'K' and resid 770 through 803 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 813 through 842 removed outlier: 4.097A pdb=" N LEU K 818 " --> pdb=" O SER K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 849 through 852 No H-bonds generated for 'chain 'K' and resid 849 through 852' Processing helix chain 'L' and resid 713 through 726 Processing helix chain 'L' and resid 728 through 731 No H-bonds generated for 'chain 'L' and resid 728 through 731' Processing helix chain 'L' and resid 740 through 765 removed outlier: 3.623A pdb=" N ASP L 765 " --> pdb=" O ARG L 761 " (cutoff:3.500A) Processing helix chain 'L' and resid 770 through 803 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 813 through 842 removed outlier: 4.098A pdb=" N LEU L 818 " --> pdb=" O SER L 814 " (cutoff:3.500A) Processing helix chain 'L' and resid 849 through 852 No H-bonds generated for 'chain 'L' and resid 849 through 852' Processing helix chain 'N' and resid 713 through 726 Processing helix chain 'N' and resid 728 through 731 No H-bonds generated for 'chain 'N' and resid 728 through 731' Processing helix chain 'N' and resid 740 through 765 removed outlier: 3.624A pdb=" N ASP N 765 " --> pdb=" O ARG N 761 " (cutoff:3.500A) Processing helix chain 'N' and resid 770 through 803 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 813 through 842 removed outlier: 4.098A pdb=" N LEU N 818 " --> pdb=" O SER N 814 " (cutoff:3.500A) Processing helix chain 'N' and resid 849 through 852 No H-bonds generated for 'chain 'N' and resid 849 through 852' Processing helix chain 'O' and resid 713 through 726 Processing helix chain 'O' and resid 728 through 731 No H-bonds generated for 'chain 'O' and resid 728 through 731' Processing helix chain 'O' and resid 740 through 765 removed outlier: 3.623A pdb=" N ASP O 765 " --> pdb=" O ARG O 761 " (cutoff:3.500A) Processing helix chain 'O' and resid 770 through 803 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 813 through 842 removed outlier: 4.099A pdb=" N LEU O 818 " --> pdb=" O SER O 814 " (cutoff:3.500A) Processing helix chain 'O' and resid 849 through 852 No H-bonds generated for 'chain 'O' and resid 849 through 852' Processing helix chain 'Q' and resid 713 through 726 Processing helix chain 'Q' and resid 728 through 731 No H-bonds generated for 'chain 'Q' and resid 728 through 731' Processing helix chain 'Q' and resid 740 through 765 removed outlier: 3.623A pdb=" N ASP Q 765 " --> pdb=" O ARG Q 761 " (cutoff:3.500A) Processing helix chain 'Q' and resid 770 through 803 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 813 through 842 removed outlier: 4.098A pdb=" N LEU Q 818 " --> pdb=" O SER Q 814 " (cutoff:3.500A) Processing helix chain 'Q' and resid 849 through 852 No H-bonds generated for 'chain 'Q' and resid 849 through 852' Processing helix chain 'X' and resid 713 through 726 Processing helix chain 'X' and resid 728 through 731 No H-bonds generated for 'chain 'X' and resid 728 through 731' Processing helix chain 'X' and resid 740 through 765 removed outlier: 3.623A pdb=" N ASP X 765 " --> pdb=" O ARG X 761 " (cutoff:3.500A) Processing helix chain 'X' and resid 770 through 803 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 813 through 842 removed outlier: 4.099A pdb=" N LEU X 818 " --> pdb=" O SER X 814 " (cutoff:3.500A) Processing helix chain 'X' and resid 849 through 852 No H-bonds generated for 'chain 'X' and resid 849 through 852' Processing sheet with id= A, first strand: chain 'B' and resid 29 through 31 removed outlier: 7.643A pdb=" N CYS B 10 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN B 12 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR B 106 " --> pdb=" O ASN B 12 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 65 through 69 Processing sheet with id= C, first strand: chain 'B' and resid 150 through 155 Processing sheet with id= D, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'D' and resid 29 through 31 removed outlier: 7.644A pdb=" N CYS D 10 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU D 104 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN D 12 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR D 106 " --> pdb=" O ASN D 12 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 65 through 69 Processing sheet with id= G, first strand: chain 'D' and resid 150 through 155 Processing sheet with id= H, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'E' and resid 29 through 31 removed outlier: 7.643A pdb=" N CYS E 10 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU E 104 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN E 12 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR E 106 " --> pdb=" O ASN E 12 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 65 through 69 Processing sheet with id= K, first strand: chain 'E' and resid 150 through 155 Processing sheet with id= L, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'F' and resid 29 through 31 removed outlier: 7.643A pdb=" N CYS F 10 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU F 104 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN F 12 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR F 106 " --> pdb=" O ASN F 12 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 65 through 69 Processing sheet with id= O, first strand: chain 'F' and resid 150 through 155 Processing sheet with id= P, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'H' and resid 29 through 31 removed outlier: 7.643A pdb=" N CYS H 10 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU H 104 " --> pdb=" O CYS H 10 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN H 12 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR H 106 " --> pdb=" O ASN H 12 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 65 through 69 Processing sheet with id= S, first strand: chain 'H' and resid 150 through 155 Processing sheet with id= T, first strand: chain 'H' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'I' and resid 29 through 31 removed outlier: 7.643A pdb=" N CYS I 10 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU I 104 " --> pdb=" O CYS I 10 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN I 12 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR I 106 " --> pdb=" O ASN I 12 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 65 through 69 Processing sheet with id= W, first strand: chain 'I' and resid 150 through 155 Processing sheet with id= X, first strand: chain 'I' and resid 238 through 241 1032 hydrogen bonds defined for protein. 2790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.13 Time building geometry restraints manager: 11.71 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=" CB GLU D 316 " pdb=" CG GLU D 316 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.32e+00 bond pdb=" C LYS N 862 " pdb=" N ALA N 863 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.47e-02 4.63e+03 3.29e+00 bond pdb=" C LYS X 862 " pdb=" N ALA X 863 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.47e-02 4.63e+03 3.27e+00 bond pdb=" CB GLU I 316 " pdb=" CG GLU I 316 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.27e+00 bond pdb=" C LYS L 862 " pdb=" N ALA L 863 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.47e-02 4.63e+03 3.27e+00 ... (remaining 25711 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.38: 633 105.38 - 112.97: 13814 112.97 - 120.56: 11644 120.56 - 128.15: 8504 128.15 - 135.74: 193 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: 14792 29.80 - 59.61: 803 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: 3078 0.063 - 0.126: 769 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: 22800 3.22 - 3.78: 39871 3.78 - 4.34: 52987 4.34 - 4.90: 87342 Nonbonded interactions: 203464 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 203459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 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. 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.510 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.210 Process input model: 64.980 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 25716 Z= 0.446 Angle : 0.963 9.326 34788 Z= 0.529 Chirality : 0.054 0.315 3924 Planarity : 0.007 0.062 4422 Dihedral : 17.664 149.025 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 % 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 *********************** 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 : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 51 residues processed: 1010 average time/residue: 0.3554 time to fit residues: 563.1039 Evaluate side-chains 719 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 668 time to evaluate : 2.709 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2544 time to fit residues: 27.1633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 5.9990 chunk 241 optimal weight: 0.3980 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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 252 ASN B 263 GLN D 41 GLN D 263 GLN E 41 GLN E 92 ASN E 252 ASN H 314 GLN I 41 GLN I 263 GLN K 801 GLN K 824 ASN K 844 GLN L 824 ASN N 718 GLN N 824 ASN O 781 GLN O 824 ASN Q 718 GLN Q 824 ASN X 718 GLN X 801 GLN X 824 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 25716 Z= 0.223 Angle : 0.634 12.106 34788 Z= 0.312 Chirality : 0.043 0.140 3924 Planarity : 0.004 0.038 4422 Dihedral : 9.156 156.824 3552 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 2.72 % 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: -2.02 (0.14), residues: 3186 helix: -1.31 (0.12), residues: 1602 sheet: -0.72 (0.26), residues: 366 loop : -1.32 (0.17), residues: 1218 *********************** 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 782 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 708 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 45 residues processed: 738 average time/residue: 0.3242 time to fit residues: 391.8986 Evaluate side-chains 671 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 626 time to evaluate : 2.882 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2350 time to fit residues: 23.6586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 289 optimal weight: 0.6980 chunk 312 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 286 optimal weight: 40.0000 chunk 98 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 275 HIS D 41 GLN E 41 GLN E 128 ASN F 92 ASN H 246 GLN H 314 GLN I 41 GLN K 718 GLN K 789 GLN L 718 GLN N 789 GLN O 844 GLN ** Q 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 788 HIS ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 844 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 25716 Z= 0.287 Angle : 0.642 9.874 34788 Z= 0.315 Chirality : 0.043 0.136 3924 Planarity : 0.003 0.035 4422 Dihedral : 8.891 168.833 3552 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 2.02 % 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: -1.37 (0.14), residues: 3186 helix: -0.71 (0.12), residues: 1602 sheet: -0.53 (0.27), residues: 366 loop : -1.07 (0.17), residues: 1218 *********************** 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 716 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 661 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 23 residues processed: 687 average time/residue: 0.3201 time to fit residues: 363.7411 Evaluate side-chains 656 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 633 time to evaluate : 2.976 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2282 time to fit residues: 13.7664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 32 optimal weight: 0.0570 chunk 138 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 290 optimal weight: 7.9990 chunk 307 optimal weight: 8.9990 chunk 151 optimal weight: 0.3980 chunk 275 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.6904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 162 ASN B 246 GLN D 41 GLN E 41 GLN F 92 ASN H 246 GLN H 314 GLN I 41 GLN K 831 GLN Q 718 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: 0.8370 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 25716 Z= 0.178 Angle : 0.589 7.759 34788 Z= 0.288 Chirality : 0.042 0.139 3924 Planarity : 0.003 0.028 4422 Dihedral : 8.666 179.311 3552 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.91 % 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: -0.88 (0.15), residues: 3186 helix: -0.24 (0.13), residues: 1560 sheet: -0.89 (0.27), residues: 396 loop : -0.72 (0.18), residues: 1230 *********************** 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 729 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 677 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 35 residues processed: 692 average time/residue: 0.3134 time to fit residues: 359.2306 Evaluate side-chains 684 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 649 time to evaluate : 2.982 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2301 time to fit residues: 19.4545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 126 optimal weight: 0.2980 chunk 262 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 275 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 111 ASN D 41 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN F 92 ASN H 59 GLN H 101 HIS H 314 GLN I 41 GLN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 718 GLN N 789 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: 0.8394 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 25716 Z= 0.238 Angle : 0.610 9.427 34788 Z= 0.297 Chirality : 0.043 0.147 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.463 174.843 3552 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 2.06 % 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: -0.62 (0.15), residues: 3186 helix: 0.01 (0.13), residues: 1560 sheet: -0.79 (0.27), residues: 396 loop : -0.61 (0.18), residues: 1230 *********************** 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 711 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 655 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 36 residues processed: 676 average time/residue: 0.3111 time to fit residues: 348.8199 Evaluate side-chains 680 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 644 time to evaluate : 3.077 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2403 time to fit residues: 20.2654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 180 optimal weight: 0.0270 chunk 75 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 115 ASN D 41 GLN D 246 GLN E 41 GLN E 297 ASN F 92 ASN H 101 HIS H 314 GLN I 41 GLN K 831 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: 0.8419 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 25716 Z= 0.313 Angle : 0.638 9.099 34788 Z= 0.310 Chirality : 0.044 0.142 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.368 177.024 3552 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 1.84 % 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: -0.51 (0.15), residues: 3186 helix: 0.11 (0.13), residues: 1560 sheet: -0.76 (0.28), residues: 396 loop : -0.58 (0.18), residues: 1230 *********************** 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 710 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 660 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 33 residues processed: 675 average time/residue: 0.3220 time to fit residues: 359.0385 Evaluate side-chains 676 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 643 time to evaluate : 2.907 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2328 time to fit residues: 18.7816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 175 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN E 41 GLN F 92 ASN H 59 GLN H 101 HIS H 314 GLN I 41 GLN K 831 GLN L 781 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: 0.8430 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 25716 Z= 0.324 Angle : 0.653 10.709 34788 Z= 0.317 Chirality : 0.044 0.156 3924 Planarity : 0.003 0.030 4422 Dihedral : 8.185 164.422 3552 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 1.43 % 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: -0.33 (0.15), residues: 3186 helix: 0.32 (0.14), residues: 1512 sheet: -0.75 (0.28), residues: 396 loop : -0.54 (0.18), residues: 1278 *********************** 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 704 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 665 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 25 residues processed: 674 average time/residue: 0.3187 time to fit residues: 354.9753 Evaluate side-chains 662 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 637 time to evaluate : 2.909 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2303 time to fit residues: 14.9643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 28 optimal weight: 40.0000 chunk 240 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 115 ASN B 246 GLN D 41 GLN E 41 GLN E 137 GLN F 92 ASN H 59 GLN H 101 HIS H 314 GLN I 41 GLN K 831 GLN ** L 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 718 GLN X 718 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 25716 Z= 0.181 Angle : 0.624 14.075 34788 Z= 0.301 Chirality : 0.043 0.183 3924 Planarity : 0.003 0.029 4422 Dihedral : 7.914 149.065 3552 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.06 % 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: -0.18 (0.15), residues: 3186 helix: 0.42 (0.14), residues: 1512 sheet: -0.68 (0.28), residues: 396 loop : -0.41 (0.18), residues: 1278 *********************** 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 706 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 677 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 684 average time/residue: 0.3171 time to fit residues: 359.6220 Evaluate side-chains 661 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 643 time to evaluate : 2.635 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2207 time to fit residues: 11.3500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.7980 chunk 293 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 285 optimal weight: 30.0000 chunk 171 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 258 optimal weight: 20.0000 chunk 270 optimal weight: 40.0000 chunk 284 optimal weight: 20.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 E 41 GLN E 137 GLN F 92 ASN H 101 HIS H 314 GLN I 41 GLN ** L 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8435 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 25716 Z= 0.348 Angle : 0.688 12.217 34788 Z= 0.333 Chirality : 0.045 0.180 3924 Planarity : 0.003 0.029 4422 Dihedral : 7.886 143.247 3552 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 1.28 % 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: -0.22 (0.15), residues: 3186 helix: 0.37 (0.14), residues: 1512 sheet: -0.69 (0.29), residues: 396 loop : -0.41 (0.18), residues: 1278 *********************** 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 699 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 664 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 668 average time/residue: 0.3212 time to fit residues: 352.9766 Evaluate side-chains 670 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 649 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2320 time to fit residues: 12.8074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 7.9990 chunk 302 optimal weight: 50.0000 chunk 184 optimal weight: 0.8980 chunk 143 optimal weight: 0.1980 chunk 209 optimal weight: 3.9990 chunk 316 optimal weight: 30.0000 chunk 291 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 E 41 GLN F 92 ASN H 101 HIS H 314 GLN I 41 GLN K 831 GLN ** L 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 718 GLN ** X 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 25716 Z= 0.173 Angle : 0.635 10.557 34788 Z= 0.307 Chirality : 0.043 0.190 3924 Planarity : 0.003 0.029 4422 Dihedral : 7.641 128.145 3552 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.40 % 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: -0.10 (0.15), residues: 3186 helix: 0.45 (0.14), residues: 1524 sheet: -0.66 (0.28), residues: 396 loop : -0.31 (0.19), residues: 1266 ********************** 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 694 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 683 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 684 average time/residue: 0.3272 time to fit residues: 369.5905 Evaluate side-chains 662 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 660 time to evaluate : 2.763 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2150 time to fit residues: 4.7801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 8.9990 chunk 268 optimal weight: 0.0060 chunk 77 optimal weight: 10.0000 chunk 232 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 252 optimal weight: 30.0000 chunk 105 optimal weight: 0.0270 chunk 259 optimal weight: 4.9990 chunk 31 optimal weight: 30.0000 chunk 46 optimal weight: 0.7980 overall best weight: 1.3658 ------------------------------------------------------------------------------- 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 ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS H 314 GLN I 41 GLN ** L 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 844 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113868 restraints weight = 34598.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119035 restraints weight = 18228.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122372 restraints weight = 12271.787| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 25716 Z= 0.179 Angle : 0.629 10.792 34788 Z= 0.303 Chirality : 0.043 0.229 3924 Planarity : 0.003 0.029 4422 Dihedral : 7.402 117.997 3552 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.73 % 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: 0.02 (0.16), residues: 3186 helix: 0.52 (0.14), residues: 1524 sheet: -0.61 (0.29), residues: 396 loop : -0.22 (0.19), residues: 1266 =============================================================================== Job complete usr+sys time: 6197.40 seconds wall clock time: 112 minutes 59.32 seconds (6779.32 seconds total)