Starting phenix.real_space_refine on Mon Feb 19 14:22:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/02_2024/7uuw_26805_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/02_2024/7uuw_26805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/02_2024/7uuw_26805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/02_2024/7uuw_26805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/02_2024/7uuw_26805_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/02_2024/7uuw_26805_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 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 192 5.16 5 C 15654 2.51 5 N 4242 2.21 5 O 4746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C ASP 363": "OD1" <-> "OD2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D ASP 363": "OD1" <-> "OD2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E ARG 206": "NH1" <-> "NH2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E ASP 363": "OD1" <-> "OD2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F ASP 184": "OD1" <-> "OD2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F ARG 206": "NH1" <-> "NH2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "G ARG 750": "NH1" <-> "NH2" Residue "G ARG 873": "NH1" <-> "NH2" Residue "H ARG 750": "NH1" <-> "NH2" Residue "H ARG 873": "NH1" <-> "NH2" Residue "I ARG 750": "NH1" <-> "NH2" Residue "I ARG 873": "NH1" <-> "NH2" Residue "K ARG 750": "NH1" <-> "NH2" Residue "K ARG 873": "NH1" <-> "NH2" Residue "L ARG 750": "NH1" <-> "NH2" Residue "L ARG 873": "NH1" <-> "NH2" Residue "Z ARG 750": "NH1" <-> "NH2" Residue "Z ARG 873": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24852 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "H" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "I" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "K" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "L" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "Z" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.83, per 1000 atoms: 0.52 Number of scatterers: 24852 At special positions: 0 Unit cell: (102.384, 120.528, 222.912, 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 192 16.00 P 12 15.00 Mg 6 11.99 O 4746 8.00 N 4242 7.00 C 15654 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: 10.07 Conformation dependent library (CDL) restraints added in 4.3 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 24 sheets defined 52.8% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 4.238A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.076A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.604A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Proline residue: A 258 - end of helix No H-bonds generated for 'chain 'A' and resid 253 through 260' Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.622A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 335 through 347 removed outlier: 5.048A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.892A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 373 Proline residue: A 367 - end of helix removed outlier: 5.234A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N HIS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 removed outlier: 4.239A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) 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 91 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 137 through 144 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 196 removed outlier: 4.076A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.603A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix No H-bonds generated for 'chain 'B' and resid 253 through 260' Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.622A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 318 Processing helix chain 'B' and resid 335 through 347 removed outlier: 5.048A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.892A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 373 Proline residue: B 367 - end of helix removed outlier: 5.233A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 4.238A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 195 removed outlier: 4.076A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.603A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix No H-bonds generated for 'chain 'C' and resid 253 through 260' Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 287 through 294 removed outlier: 3.623A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 335 through 347 removed outlier: 5.048A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.892A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 373 Proline residue: C 367 - end of helix removed outlier: 5.234A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 4.238A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) 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 91 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 137 through 144 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 195 removed outlier: 4.076A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 253 through 260 removed outlier: 3.603A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Proline residue: D 258 - end of helix No H-bonds generated for 'chain 'D' and resid 253 through 260' Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.622A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR D 294 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 318 Processing helix chain 'D' and resid 335 through 347 removed outlier: 5.048A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.892A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 359 through 373 Proline residue: D 367 - end of helix removed outlier: 5.233A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 4.238A pdb=" N SER E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) 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 91 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 137 through 144 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 195 removed outlier: 4.076A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 253 through 260 removed outlier: 3.603A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix No H-bonds generated for 'chain 'E' and resid 253 through 260' Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 287 through 294 removed outlier: 3.623A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR E 294 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 318 Processing helix chain 'E' and resid 335 through 347 removed outlier: 5.049A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 removed outlier: 3.893A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 359 through 373 Proline residue: E 367 - end of helix removed outlier: 5.234A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 removed outlier: 4.238A pdb=" N SER F 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) 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 91 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 137 through 144 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 196 removed outlier: 4.076A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 253 through 260 removed outlier: 3.603A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix No H-bonds generated for 'chain 'F' and resid 253 through 260' Processing helix chain 'F' and resid 274 through 284 Processing helix chain 'F' and resid 287 through 294 removed outlier: 3.622A pdb=" N ARG F 290 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS F 291 " --> pdb=" O ASP F 288 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR F 294 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 309 through 318 Processing helix chain 'F' and resid 335 through 347 removed outlier: 5.048A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA F 347 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 354 removed outlier: 3.892A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 359 through 373 Proline residue: F 367 - end of helix removed outlier: 5.234A pdb=" N VAL F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N HIS F 371 " --> pdb=" O PRO F 367 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 691 through 695 Processing helix chain 'G' and resid 715 through 737 Processing helix chain 'G' and resid 745 through 772 Processing helix chain 'G' and resid 777 through 809 Processing helix chain 'G' and resid 818 through 847 removed outlier: 4.250A pdb=" N SER G 823 " --> pdb=" O ASP G 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU G 824 " --> pdb=" O SER G 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN G 837 " --> pdb=" O THR G 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR G 838 " --> pdb=" O ALA G 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS G 840 " --> pdb=" O VAL G 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 841 " --> pdb=" O GLN G 837 " (cutoff:3.500A) Processing helix chain 'H' and resid 691 through 695 Processing helix chain 'H' and resid 715 through 737 Processing helix chain 'H' and resid 745 through 772 Processing helix chain 'H' and resid 777 through 809 Processing helix chain 'H' and resid 818 through 847 removed outlier: 4.252A pdb=" N SER H 823 " --> pdb=" O ASP H 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU H 824 " --> pdb=" O SER H 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN H 837 " --> pdb=" O THR H 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR H 838 " --> pdb=" O ALA H 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS H 840 " --> pdb=" O VAL H 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA H 841 " --> pdb=" O GLN H 837 " (cutoff:3.500A) Processing helix chain 'I' and resid 691 through 695 Processing helix chain 'I' and resid 715 through 737 Processing helix chain 'I' and resid 745 through 772 Processing helix chain 'I' and resid 777 through 809 Processing helix chain 'I' and resid 818 through 847 removed outlier: 4.251A pdb=" N SER I 823 " --> pdb=" O ASP I 819 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU I 824 " --> pdb=" O SER I 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN I 837 " --> pdb=" O THR I 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR I 838 " --> pdb=" O ALA I 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS I 840 " --> pdb=" O VAL I 836 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA I 841 " --> pdb=" O GLN I 837 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 695 Processing helix chain 'K' and resid 715 through 737 Processing helix chain 'K' and resid 745 through 772 Processing helix chain 'K' and resid 777 through 809 Processing helix chain 'K' and resid 818 through 847 removed outlier: 4.251A pdb=" N SER K 823 " --> pdb=" O ASP K 819 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU K 824 " --> pdb=" O SER K 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN K 837 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR K 838 " --> pdb=" O ALA K 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS K 840 " --> pdb=" O VAL K 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 841 " --> pdb=" O GLN K 837 " (cutoff:3.500A) Processing helix chain 'L' and resid 691 through 695 Processing helix chain 'L' and resid 715 through 737 Processing helix chain 'L' and resid 745 through 772 Processing helix chain 'L' and resid 777 through 809 Processing helix chain 'L' and resid 818 through 847 removed outlier: 4.250A pdb=" N SER L 823 " --> pdb=" O ASP L 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU L 824 " --> pdb=" O SER L 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN L 837 " --> pdb=" O THR L 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR L 838 " --> pdb=" O ALA L 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS L 840 " --> pdb=" O VAL L 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA L 841 " --> pdb=" O GLN L 837 " (cutoff:3.500A) Processing helix chain 'Z' and resid 691 through 695 Processing helix chain 'Z' and resid 715 through 737 Processing helix chain 'Z' and resid 745 through 772 Processing helix chain 'Z' and resid 777 through 809 Processing helix chain 'Z' and resid 818 through 847 removed outlier: 4.251A pdb=" N SER Z 823 " --> pdb=" O ASP Z 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU Z 824 " --> pdb=" O SER Z 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN Z 837 " --> pdb=" O THR Z 833 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR Z 838 " --> pdb=" O ALA Z 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS Z 840 " --> pdb=" O VAL Z 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Z 841 " --> pdb=" O GLN Z 837 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 10 removed outlier: 3.828A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 16 through 19 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 7.129A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 176 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 8 through 10 removed outlier: 3.828A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 16 through 19 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 7.130A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 8 through 10 removed outlier: 3.828A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 16 through 19 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 7.129A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 176 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 8 through 10 removed outlier: 3.827A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 16 through 19 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 7.129A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 8 through 10 removed outlier: 3.827A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 16 through 19 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 7.129A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET E 176 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'F' and resid 8 through 10 removed outlier: 3.827A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= W, first strand: chain 'F' and resid 297 through 300 removed outlier: 7.129A pdb=" N VAL F 298 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET F 176 " --> pdb=" O ASN F 162 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 238 through 241 1164 hydrogen bonds defined for protein. 3204 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: 7.87 Time building geometry restraints manager: 10.87 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: 8112 1.34 - 1.46: 5463 1.46 - 1.58: 11373 1.58 - 1.70: 18 1.70 - 1.82: 330 Bond restraints: 25296 Sorted by residual: bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.20e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.19e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.15e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.11e+00 ... (remaining 25291 not shown) Histogram of bond angle deviations from ideal: 98.78 - 106.14: 726 106.14 - 113.50: 14411 113.50 - 120.86: 11993 120.86 - 128.22: 6932 128.22 - 135.58: 180 Bond angle restraints: 34242 Sorted by residual: angle pdb=" CB MET F 325 " pdb=" CG MET F 325 " pdb=" SD MET F 325 " ideal model delta sigma weight residual 112.70 98.78 13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET B 325 " pdb=" CG MET B 325 " pdb=" SD MET B 325 " ideal model delta sigma weight residual 112.70 98.80 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET D 325 " pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 112.70 98.80 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET C 325 " pdb=" CG MET C 325 " pdb=" SD MET C 325 " ideal model delta sigma weight residual 112.70 98.81 13.89 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET A 325 " pdb=" CG MET A 325 " pdb=" SD MET A 325 " ideal model delta sigma weight residual 112.70 98.81 13.89 3.00e+00 1.11e-01 2.14e+01 ... (remaining 34237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 14910 34.41 - 68.82: 444 68.82 - 103.24: 48 103.24 - 137.65: 6 137.65 - 172.06: 12 Dihedral angle restraints: 15420 sinusoidal: 6222 harmonic: 9198 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.06 -172.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.06 -172.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.04 -172.04 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 15417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2192 0.034 - 0.068: 1232 0.068 - 0.103: 352 0.103 - 0.137: 113 0.137 - 0.171: 23 Chirality restraints: 3912 Sorted by residual: chirality pdb=" CA MET E 325 " pdb=" N MET E 325 " pdb=" C MET E 325 " pdb=" CB MET E 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA MET C 325 " pdb=" N MET C 325 " pdb=" C MET C 325 " pdb=" CB MET C 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA MET B 325 " pdb=" N MET B 325 " pdb=" C MET B 325 " pdb=" CB MET B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 3909 not shown) Planarity restraints: 4338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO E 243 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO D 243 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 243 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.022 5.00e-02 4.00e+02 ... (remaining 4335 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2993 2.74 - 3.28: 24197 3.28 - 3.82: 39606 3.82 - 4.36: 49930 4.36 - 4.90: 88246 Nonbonded interactions: 204972 Sorted by model distance: nonbonded pdb=" O GLY A 156 " pdb=" OG1 THR A 303 " model vdw 2.202 2.440 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.203 2.440 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.203 2.440 nonbonded pdb=" O GLY C 156 " pdb=" OG1 THR C 303 " model vdw 2.203 2.440 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.204 2.440 ... (remaining 204967 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 7.200 Check model and map are aligned: 0.420 Set scattering table: 0.230 Process input model: 64.140 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.200 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 0.054 25296 Z= 0.454 Angle : 0.750 13.916 34242 Z= 0.392 Chirality : 0.046 0.171 3912 Planarity : 0.004 0.040 4338 Dihedral : 17.000 172.062 9480 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.34 % Allowed : 3.53 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.15), residues: 3096 helix: 0.48 (0.13), residues: 1656 sheet: -1.68 (0.27), residues: 366 loop : -0.22 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 340 HIS 0.003 0.001 HIS C 87 PHE 0.013 0.001 PHE Z 697 TYR 0.014 0.002 TYR D 279 ARG 0.004 0.001 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 329 time to evaluate : 2.709 Fit side-chains REVERT: A 118 LYS cc_start: 0.8375 (mttm) cc_final: 0.7909 (mmmt) REVERT: A 119 MET cc_start: 0.8288 (mtm) cc_final: 0.7662 (mtp) REVERT: A 157 ASP cc_start: 0.8839 (t0) cc_final: 0.8633 (t0) REVERT: A 176 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8123 (mtt) REVERT: A 211 ASP cc_start: 0.8633 (t0) cc_final: 0.8254 (t0) REVERT: A 227 MET cc_start: 0.8660 (mmm) cc_final: 0.8231 (mmt) REVERT: B 123 MET cc_start: 0.8667 (mmt) cc_final: 0.8386 (mmm) REVERT: B 191 LYS cc_start: 0.7348 (tttp) cc_final: 0.6910 (tttt) REVERT: B 313 MET cc_start: 0.8219 (ttt) cc_final: 0.7841 (ttt) REVERT: B 349 LEU cc_start: 0.8477 (mt) cc_final: 0.8178 (mt) REVERT: C 82 MET cc_start: 0.8551 (tpt) cc_final: 0.8341 (tpt) REVERT: C 211 ASP cc_start: 0.8594 (t0) cc_final: 0.8265 (t0) REVERT: C 313 MET cc_start: 0.8000 (ttt) cc_final: 0.7738 (ttm) REVERT: D 119 MET cc_start: 0.8108 (mtm) cc_final: 0.7901 (mtm) REVERT: D 313 MET cc_start: 0.8358 (ttt) cc_final: 0.7942 (ttt) REVERT: D 325 MET cc_start: 0.8023 (mmt) cc_final: 0.7807 (mmt) REVERT: E 100 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7636 (mt-10) REVERT: E 118 LYS cc_start: 0.8579 (mttm) cc_final: 0.8072 (mmmt) REVERT: E 123 MET cc_start: 0.8764 (mmt) cc_final: 0.8548 (mmt) REVERT: E 292 ASP cc_start: 0.7333 (m-30) cc_final: 0.7126 (m-30) REVERT: F 57 GLU cc_start: 0.8328 (pt0) cc_final: 0.8036 (pt0) REVERT: F 299 MET cc_start: 0.8766 (mtm) cc_final: 0.8554 (mtp) REVERT: G 746 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7198 (mmm) REVERT: G 863 MET cc_start: 0.7720 (mtm) cc_final: 0.6798 (ptp) REVERT: H 725 MET cc_start: 0.7749 (mtt) cc_final: 0.7359 (mtt) REVERT: H 822 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8180 (mmp) REVERT: H 863 MET cc_start: 0.8121 (mtm) cc_final: 0.7618 (mtm) REVERT: I 732 MET cc_start: 0.8281 (mtp) cc_final: 0.8017 (mtp) REVERT: K 869 GLN cc_start: 0.8795 (mm110) cc_final: 0.8505 (mm-40) REVERT: L 732 MET cc_start: 0.8189 (mtp) cc_final: 0.7969 (mtm) REVERT: L 746 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7456 (tpt) REVERT: L 794 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8341 (tp40) REVERT: Z 732 MET cc_start: 0.8243 (mtp) cc_final: 0.7921 (mtp) REVERT: Z 746 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7560 (mmm) REVERT: Z 794 GLN cc_start: 0.9079 (tp40) cc_final: 0.8828 (tp40) REVERT: Z 822 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7687 (mmm) REVERT: Z 863 MET cc_start: 0.7501 (mtm) cc_final: 0.7142 (mtm) outliers start: 36 outliers final: 7 residues processed: 335 average time/residue: 0.3505 time to fit residues: 187.9592 Evaluate side-chains 270 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 257 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain G residue 746 MET Chi-restraints excluded: chain H residue 822 MET Chi-restraints excluded: chain L residue 746 MET Chi-restraints excluded: chain Z residue 746 MET Chi-restraints excluded: chain Z residue 822 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 283 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 353 GLN K 794 GLN L 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25296 Z= 0.204 Angle : 0.540 8.572 34242 Z= 0.267 Chirality : 0.041 0.139 3912 Planarity : 0.004 0.038 4338 Dihedral : 12.294 174.882 3511 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.82 % Allowed : 5.99 % Favored : 93.19 % 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: 0.45 (0.16), residues: 3096 helix: 1.09 (0.13), residues: 1644 sheet: -1.47 (0.26), residues: 408 loop : -0.01 (0.21), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 340 HIS 0.006 0.001 HIS C 40 PHE 0.008 0.001 PHE B 127 TYR 0.012 0.001 TYR K 792 ARG 0.008 0.000 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 266 time to evaluate : 2.650 Fit side-chains REVERT: A 118 LYS cc_start: 0.8171 (mttm) cc_final: 0.7795 (mmmt) REVERT: A 119 MET cc_start: 0.8023 (mtm) cc_final: 0.7686 (mtp) REVERT: A 364 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7263 (mt-10) REVERT: B 123 MET cc_start: 0.8687 (mmt) cc_final: 0.8400 (mmm) REVERT: B 191 LYS cc_start: 0.7220 (tttp) cc_final: 0.6834 (tttt) REVERT: B 313 MET cc_start: 0.8125 (ttt) cc_final: 0.7708 (ttt) REVERT: C 82 MET cc_start: 0.8434 (tpt) cc_final: 0.8206 (tpt) REVERT: C 211 ASP cc_start: 0.8546 (t0) cc_final: 0.8221 (t0) REVERT: E 72 GLU cc_start: 0.7402 (tt0) cc_final: 0.7067 (tt0) REVERT: E 100 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7627 (mt-10) REVERT: E 355 MET cc_start: 0.9064 (mtt) cc_final: 0.8831 (mtm) REVERT: F 44 MET cc_start: 0.8447 (mtt) cc_final: 0.8203 (mtp) REVERT: F 57 GLU cc_start: 0.8350 (pt0) cc_final: 0.8125 (pt0) REVERT: F 283 MET cc_start: 0.8062 (mmm) cc_final: 0.7848 (mmt) REVERT: H 725 MET cc_start: 0.7764 (mtt) cc_final: 0.7475 (mtt) REVERT: H 729 MET cc_start: 0.8410 (tpt) cc_final: 0.7582 (tpt) REVERT: H 822 MET cc_start: 0.8344 (mmm) cc_final: 0.8133 (mmm) REVERT: I 732 MET cc_start: 0.8363 (mtp) cc_final: 0.8100 (mtp) REVERT: I 822 MET cc_start: 0.8538 (mmm) cc_final: 0.7902 (mmt) REVERT: K 746 MET cc_start: 0.7762 (mmm) cc_final: 0.7303 (tpp) REVERT: L 729 MET cc_start: 0.7546 (tpt) cc_final: 0.7309 (tpt) REVERT: L 732 MET cc_start: 0.8279 (mtm) cc_final: 0.8063 (mtm) REVERT: L 746 MET cc_start: 0.7262 (tpp) cc_final: 0.6854 (tpt) REVERT: L 822 MET cc_start: 0.8430 (mmp) cc_final: 0.8164 (mmt) REVERT: Z 732 MET cc_start: 0.8337 (mtm) cc_final: 0.7839 (mtp) REVERT: Z 794 GLN cc_start: 0.9045 (tp40) cc_final: 0.8842 (tp40) REVERT: Z 863 MET cc_start: 0.7608 (mtm) cc_final: 0.7137 (mtm) outliers start: 22 outliers final: 19 residues processed: 281 average time/residue: 0.3324 time to fit residues: 155.9554 Evaluate side-chains 271 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 252 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.0370 chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 283 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 281 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 837 GLN L 794 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 25296 Z= 0.312 Angle : 0.560 6.587 34242 Z= 0.275 Chirality : 0.042 0.182 3912 Planarity : 0.004 0.035 4338 Dihedral : 10.847 157.895 3489 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.04 % Allowed : 8.18 % Favored : 90.77 % 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: 0.40 (0.16), residues: 3096 helix: 0.99 (0.13), residues: 1656 sheet: -1.34 (0.26), residues: 372 loop : -0.08 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 340 HIS 0.004 0.001 HIS D 87 PHE 0.010 0.001 PHE C 255 TYR 0.013 0.001 TYR K 792 ARG 0.003 0.000 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 254 time to evaluate : 2.995 Fit side-chains REVERT: A 118 LYS cc_start: 0.8208 (mttm) cc_final: 0.7785 (mmmt) REVERT: A 119 MET cc_start: 0.7857 (mtm) cc_final: 0.7590 (mtp) REVERT: B 123 MET cc_start: 0.8581 (mmt) cc_final: 0.8266 (mmm) REVERT: B 191 LYS cc_start: 0.7438 (tttp) cc_final: 0.7005 (tttt) REVERT: B 305 MET cc_start: 0.8831 (mtp) cc_final: 0.8605 (mmm) REVERT: C 211 ASP cc_start: 0.8625 (t0) cc_final: 0.8279 (t0) REVERT: E 72 GLU cc_start: 0.7443 (tt0) cc_final: 0.7110 (tt0) REVERT: E 355 MET cc_start: 0.9064 (mtt) cc_final: 0.8853 (mtm) REVERT: F 57 GLU cc_start: 0.8243 (pt0) cc_final: 0.7932 (pt0) REVERT: F 325 MET cc_start: 0.8865 (mmp) cc_final: 0.8540 (mmp) REVERT: H 729 MET cc_start: 0.8358 (tpt) cc_final: 0.7414 (tpt) REVERT: H 822 MET cc_start: 0.8369 (mmm) cc_final: 0.8160 (mmp) REVERT: H 863 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7323 (mtm) REVERT: I 822 MET cc_start: 0.8572 (mmm) cc_final: 0.8095 (mmt) REVERT: L 732 MET cc_start: 0.8282 (mtm) cc_final: 0.8081 (mtm) REVERT: L 746 MET cc_start: 0.7221 (tpp) cc_final: 0.6907 (tpt) REVERT: L 822 MET cc_start: 0.8424 (mmp) cc_final: 0.8202 (mmt) REVERT: Z 732 MET cc_start: 0.8329 (mtm) cc_final: 0.8007 (mtm) outliers start: 28 outliers final: 26 residues processed: 273 average time/residue: 0.3615 time to fit residues: 164.5982 Evaluate side-chains 274 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 247 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain H residue 863 MET Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain I residue 863 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 190 optimal weight: 0.0570 chunk 284 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 HIS I 837 GLN L 794 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 25296 Z= 0.293 Angle : 0.547 7.030 34242 Z= 0.267 Chirality : 0.042 0.151 3912 Planarity : 0.004 0.036 4338 Dihedral : 9.664 137.534 3480 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.15 % Allowed : 10.01 % Favored : 88.84 % 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: 0.42 (0.16), residues: 3096 helix: 0.98 (0.13), residues: 1668 sheet: -1.18 (0.26), residues: 360 loop : -0.12 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 340 HIS 0.004 0.001 HIS D 87 PHE 0.010 0.001 PHE C 255 TYR 0.012 0.001 TYR B 143 ARG 0.003 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 2.590 Fit side-chains REVERT: A 72 GLU cc_start: 0.7378 (tt0) cc_final: 0.6963 (mt-10) REVERT: A 118 LYS cc_start: 0.8240 (mttm) cc_final: 0.7814 (mmmt) REVERT: A 119 MET cc_start: 0.7746 (mtm) cc_final: 0.7448 (mtp) REVERT: A 176 MET cc_start: 0.8387 (mmm) cc_final: 0.8139 (mmm) REVERT: B 123 MET cc_start: 0.8628 (mmt) cc_final: 0.8224 (mmm) REVERT: B 191 LYS cc_start: 0.7456 (tttp) cc_final: 0.7017 (tttt) REVERT: B 305 MET cc_start: 0.8843 (mtp) cc_final: 0.8611 (mmm) REVERT: C 211 ASP cc_start: 0.8631 (t0) cc_final: 0.8262 (t0) REVERT: D 353 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8855 (mm110) REVERT: E 72 GLU cc_start: 0.7425 (tt0) cc_final: 0.6941 (tt0) REVERT: F 57 GLU cc_start: 0.8272 (pt0) cc_final: 0.7981 (pt0) REVERT: G 863 MET cc_start: 0.8399 (ttm) cc_final: 0.8133 (mtp) REVERT: H 729 MET cc_start: 0.8340 (tpt) cc_final: 0.7491 (tpt) REVERT: H 863 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8178 (mtp) REVERT: I 732 MET cc_start: 0.8323 (mtm) cc_final: 0.8066 (mtm) REVERT: I 822 MET cc_start: 0.8603 (mmm) cc_final: 0.8279 (mmt) REVERT: K 746 MET cc_start: 0.7550 (mmm) cc_final: 0.7339 (tpp) REVERT: L 732 MET cc_start: 0.8280 (mtm) cc_final: 0.8063 (mtm) REVERT: L 746 MET cc_start: 0.7129 (tpp) cc_final: 0.6872 (tpt) REVERT: Z 732 MET cc_start: 0.8355 (mtm) cc_final: 0.8021 (mtm) outliers start: 31 outliers final: 29 residues processed: 274 average time/residue: 0.3234 time to fit residues: 147.3358 Evaluate side-chains 273 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 243 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain H residue 863 MET Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 9.9990 chunk 171 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 270 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS I 837 GLN L 763 ASN L 794 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25296 Z= 0.219 Angle : 0.512 6.724 34242 Z= 0.248 Chirality : 0.040 0.147 3912 Planarity : 0.003 0.035 4338 Dihedral : 9.442 140.484 3480 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.23 % Allowed : 10.34 % Favored : 88.43 % 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: 0.64 (0.16), residues: 3096 helix: 1.17 (0.13), residues: 1662 sheet: -1.01 (0.26), residues: 354 loop : -0.07 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 340 HIS 0.003 0.001 HIS D 87 PHE 0.008 0.001 PHE F 31 TYR 0.010 0.001 TYR B 143 ARG 0.002 0.000 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 2.676 Fit side-chains REVERT: A 118 LYS cc_start: 0.8257 (mttm) cc_final: 0.7801 (mmmt) REVERT: A 176 MET cc_start: 0.8423 (mmm) cc_final: 0.8199 (mmm) REVERT: B 123 MET cc_start: 0.8624 (mmt) cc_final: 0.8157 (mmm) REVERT: B 191 LYS cc_start: 0.7274 (tttp) cc_final: 0.6834 (tttt) REVERT: B 305 MET cc_start: 0.8826 (mtp) cc_final: 0.8591 (mmm) REVERT: C 211 ASP cc_start: 0.8602 (t0) cc_final: 0.8240 (t0) REVERT: D 353 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8841 (mm110) REVERT: E 72 GLU cc_start: 0.7320 (tt0) cc_final: 0.6842 (tt0) REVERT: F 57 GLU cc_start: 0.8213 (pt0) cc_final: 0.7946 (pt0) REVERT: G 863 MET cc_start: 0.8426 (ttm) cc_final: 0.8067 (mtp) REVERT: H 729 MET cc_start: 0.8334 (tpt) cc_final: 0.7568 (tpt) REVERT: I 732 MET cc_start: 0.8261 (mtm) cc_final: 0.7949 (mtp) REVERT: I 746 MET cc_start: 0.7701 (mmm) cc_final: 0.7426 (tpp) REVERT: I 822 MET cc_start: 0.8559 (mmm) cc_final: 0.7957 (mmt) REVERT: L 732 MET cc_start: 0.8351 (mtm) cc_final: 0.8140 (mtm) REVERT: L 746 MET cc_start: 0.7043 (tpp) cc_final: 0.6738 (tpt) REVERT: L 794 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8358 (tp40) REVERT: Z 732 MET cc_start: 0.8309 (mtm) cc_final: 0.8039 (mtm) REVERT: Z 863 MET cc_start: 0.8174 (ttm) cc_final: 0.7877 (mtp) outliers start: 33 outliers final: 28 residues processed: 278 average time/residue: 0.3315 time to fit residues: 152.8361 Evaluate side-chains 275 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 247 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 301 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25296 Z= 0.213 Angle : 0.505 6.782 34242 Z= 0.243 Chirality : 0.040 0.147 3912 Planarity : 0.003 0.049 4338 Dihedral : 9.163 144.221 3480 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.26 % Allowed : 10.71 % Favored : 88.02 % 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: 0.69 (0.16), residues: 3096 helix: 1.29 (0.13), residues: 1650 sheet: -1.26 (0.25), residues: 390 loop : 0.00 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 340 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE F 31 TYR 0.010 0.001 TYR B 143 ARG 0.002 0.000 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 255 time to evaluate : 2.880 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8370 (tpt) cc_final: 0.8107 (tpt) REVERT: A 118 LYS cc_start: 0.8274 (mttm) cc_final: 0.7812 (mmmt) REVERT: A 176 MET cc_start: 0.8496 (mmm) cc_final: 0.8279 (mmm) REVERT: A 313 MET cc_start: 0.8756 (tpp) cc_final: 0.8109 (ttm) REVERT: B 66 THR cc_start: 0.9214 (p) cc_final: 0.8975 (p) REVERT: B 191 LYS cc_start: 0.7275 (tttp) cc_final: 0.6823 (tttt) REVERT: B 305 MET cc_start: 0.8820 (mtp) cc_final: 0.8595 (mmm) REVERT: C 211 ASP cc_start: 0.8598 (t0) cc_final: 0.8238 (t0) REVERT: D 353 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8826 (mm110) REVERT: E 72 GLU cc_start: 0.7280 (tt0) cc_final: 0.6902 (tt0) REVERT: F 57 GLU cc_start: 0.8200 (pt0) cc_final: 0.7923 (pt0) REVERT: G 795 GLN cc_start: 0.8956 (mt0) cc_final: 0.8692 (mt0) REVERT: G 863 MET cc_start: 0.8399 (ttm) cc_final: 0.8049 (mtp) REVERT: H 729 MET cc_start: 0.8362 (tpt) cc_final: 0.7626 (tpt) REVERT: I 732 MET cc_start: 0.8229 (mtm) cc_final: 0.7928 (mtp) REVERT: I 746 MET cc_start: 0.7656 (mmm) cc_final: 0.7406 (tpp) REVERT: I 805 ASP cc_start: 0.7214 (m-30) cc_final: 0.6770 (m-30) REVERT: I 822 MET cc_start: 0.8541 (mmm) cc_final: 0.7983 (mmt) REVERT: K 746 MET cc_start: 0.7270 (mmm) cc_final: 0.6921 (tpp) REVERT: L 732 MET cc_start: 0.8337 (mtm) cc_final: 0.8101 (mtm) REVERT: L 746 MET cc_start: 0.6966 (tpp) cc_final: 0.6664 (tpt) REVERT: Z 732 MET cc_start: 0.8334 (mtm) cc_final: 0.7978 (mtp) outliers start: 34 outliers final: 29 residues processed: 278 average time/residue: 0.3354 time to fit residues: 152.4214 Evaluate side-chains 282 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 253 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 300 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 763 ASN G 826 GLN H 763 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25296 Z= 0.189 Angle : 0.491 6.917 34242 Z= 0.236 Chirality : 0.040 0.146 3912 Planarity : 0.003 0.042 4338 Dihedral : 8.839 148.834 3480 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.38 % Allowed : 11.09 % Favored : 87.54 % 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: 0.83 (0.16), residues: 3096 helix: 1.40 (0.13), residues: 1650 sheet: -1.19 (0.26), residues: 390 loop : 0.08 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 340 HIS 0.002 0.001 HIS D 161 PHE 0.008 0.001 PHE F 31 TYR 0.009 0.001 TYR B 143 ARG 0.002 0.000 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 254 time to evaluate : 2.655 Fit side-chains revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8312 (mttm) cc_final: 0.7884 (mmmt) REVERT: A 176 MET cc_start: 0.8560 (mmm) cc_final: 0.8353 (mmm) REVERT: B 66 THR cc_start: 0.9222 (p) cc_final: 0.8995 (p) REVERT: B 191 LYS cc_start: 0.7293 (tttp) cc_final: 0.6772 (tttt) REVERT: B 205 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 305 MET cc_start: 0.8807 (mtp) cc_final: 0.8578 (mmm) REVERT: C 211 ASP cc_start: 0.8566 (t0) cc_final: 0.8188 (t0) REVERT: D 353 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8786 (mm110) REVERT: E 72 GLU cc_start: 0.7308 (tt0) cc_final: 0.6929 (tt0) REVERT: F 57 GLU cc_start: 0.8184 (pt0) cc_final: 0.7923 (pt0) REVERT: G 795 GLN cc_start: 0.8938 (mt0) cc_final: 0.8655 (mt0) REVERT: H 729 MET cc_start: 0.8366 (tpt) cc_final: 0.7683 (tpt) REVERT: I 732 MET cc_start: 0.8182 (mtm) cc_final: 0.7875 (mtp) REVERT: I 746 MET cc_start: 0.7628 (mmm) cc_final: 0.7380 (tpp) REVERT: I 805 ASP cc_start: 0.7190 (m-30) cc_final: 0.6758 (m-30) REVERT: I 822 MET cc_start: 0.8520 (mmm) cc_final: 0.7985 (mmt) REVERT: K 746 MET cc_start: 0.7211 (mmm) cc_final: 0.6874 (tpp) REVERT: L 746 MET cc_start: 0.6890 (tpp) cc_final: 0.6587 (tpt) REVERT: Z 732 MET cc_start: 0.8315 (mtm) cc_final: 0.7960 (mtp) REVERT: Z 863 MET cc_start: 0.8005 (ttm) cc_final: 0.7615 (mtp) outliers start: 37 outliers final: 33 residues processed: 280 average time/residue: 0.3341 time to fit residues: 154.5190 Evaluate side-chains 285 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 252 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25296 Z= 0.249 Angle : 0.519 7.161 34242 Z= 0.250 Chirality : 0.041 0.149 3912 Planarity : 0.003 0.040 4338 Dihedral : 8.704 156.036 3480 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.30 % Allowed : 11.31 % Favored : 87.39 % 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: 0.75 (0.16), residues: 3096 helix: 1.31 (0.13), residues: 1650 sheet: -1.19 (0.26), residues: 390 loop : 0.06 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 340 HIS 0.003 0.001 HIS D 161 PHE 0.009 0.001 PHE F 31 TYR 0.011 0.001 TYR B 143 ARG 0.003 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 255 time to evaluate : 2.615 Fit side-chains REVERT: A 72 GLU cc_start: 0.7519 (tt0) cc_final: 0.7143 (mt-10) REVERT: A 118 LYS cc_start: 0.8311 (mttm) cc_final: 0.7887 (mmmt) REVERT: A 326 LYS cc_start: 0.8490 (tttp) cc_final: 0.8136 (tttm) REVERT: B 66 THR cc_start: 0.9216 (p) cc_final: 0.8975 (p) REVERT: B 191 LYS cc_start: 0.7422 (tttp) cc_final: 0.6876 (tttt) REVERT: B 305 MET cc_start: 0.8842 (mtp) cc_final: 0.8611 (mmm) REVERT: C 211 ASP cc_start: 0.8609 (t0) cc_final: 0.8207 (t0) REVERT: D 353 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8793 (mm110) REVERT: E 72 GLU cc_start: 0.7356 (tt0) cc_final: 0.6991 (tt0) REVERT: F 57 GLU cc_start: 0.8219 (pt0) cc_final: 0.7970 (pt0) REVERT: F 299 MET cc_start: 0.8908 (mmm) cc_final: 0.8549 (mtt) REVERT: F 313 MET cc_start: 0.8112 (ttm) cc_final: 0.7828 (ttm) REVERT: G 805 ASP cc_start: 0.7844 (t0) cc_final: 0.7099 (m-30) REVERT: G 863 MET cc_start: 0.8443 (mtm) cc_final: 0.8191 (mtp) REVERT: H 729 MET cc_start: 0.8370 (tpt) cc_final: 0.7695 (tpt) REVERT: I 732 MET cc_start: 0.8210 (mtm) cc_final: 0.7908 (mtp) REVERT: I 746 MET cc_start: 0.7650 (mmm) cc_final: 0.7403 (tpp) REVERT: I 805 ASP cc_start: 0.7125 (m-30) cc_final: 0.6705 (m-30) REVERT: I 822 MET cc_start: 0.8528 (mmm) cc_final: 0.8017 (mmt) REVERT: K 746 MET cc_start: 0.7289 (mmm) cc_final: 0.6963 (tpp) REVERT: L 746 MET cc_start: 0.6895 (tpp) cc_final: 0.6605 (tpt) REVERT: Z 732 MET cc_start: 0.8312 (mtm) cc_final: 0.7958 (mtp) outliers start: 35 outliers final: 30 residues processed: 279 average time/residue: 0.3437 time to fit residues: 157.9823 Evaluate side-chains 283 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 253 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 253 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25296 Z= 0.264 Angle : 0.525 7.072 34242 Z= 0.253 Chirality : 0.041 0.147 3912 Planarity : 0.003 0.040 4338 Dihedral : 8.691 173.169 3480 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.30 % Allowed : 11.35 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.16), residues: 3096 helix: 1.28 (0.13), residues: 1650 sheet: -1.20 (0.26), residues: 390 loop : 0.05 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 340 HIS 0.007 0.001 HIS C 40 PHE 0.009 0.001 PHE F 31 TYR 0.010 0.001 TYR B 143 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 252 time to evaluate : 2.513 Fit side-chains REVERT: A 72 GLU cc_start: 0.7506 (tt0) cc_final: 0.7132 (mt-10) REVERT: A 118 LYS cc_start: 0.8352 (mttm) cc_final: 0.7892 (mmmt) REVERT: A 326 LYS cc_start: 0.8500 (tttp) cc_final: 0.8141 (tttm) REVERT: B 191 LYS cc_start: 0.7415 (tttp) cc_final: 0.6865 (tttt) REVERT: B 305 MET cc_start: 0.8842 (mtp) cc_final: 0.8613 (mmm) REVERT: C 211 ASP cc_start: 0.8609 (t0) cc_final: 0.8207 (t0) REVERT: D 353 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8871 (mm-40) REVERT: E 72 GLU cc_start: 0.7313 (tt0) cc_final: 0.6952 (tt0) REVERT: F 57 GLU cc_start: 0.8250 (pt0) cc_final: 0.7953 (pt0) REVERT: F 227 MET cc_start: 0.8146 (mmt) cc_final: 0.7486 (mmm) REVERT: F 299 MET cc_start: 0.8952 (mmm) cc_final: 0.8655 (mtt) REVERT: G 863 MET cc_start: 0.8481 (mtm) cc_final: 0.8226 (mtp) REVERT: H 729 MET cc_start: 0.8368 (tpt) cc_final: 0.7690 (tpt) REVERT: I 732 MET cc_start: 0.8236 (mtm) cc_final: 0.7929 (mtp) REVERT: I 746 MET cc_start: 0.7666 (mmm) cc_final: 0.7408 (tpp) REVERT: I 822 MET cc_start: 0.8490 (mmm) cc_final: 0.8006 (mmt) REVERT: K 746 MET cc_start: 0.7300 (mmm) cc_final: 0.6971 (tpp) REVERT: K 822 MET cc_start: 0.8131 (tpp) cc_final: 0.7879 (mmt) REVERT: L 746 MET cc_start: 0.6912 (tpp) cc_final: 0.6589 (tpt) REVERT: Z 732 MET cc_start: 0.8332 (mtm) cc_final: 0.7999 (mtp) outliers start: 35 outliers final: 35 residues processed: 277 average time/residue: 0.3357 time to fit residues: 152.2706 Evaluate side-chains 287 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 252 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 8.9990 chunk 180 optimal weight: 0.2980 chunk 140 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 chunk 286 optimal weight: 0.1980 chunk 247 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 151 optimal weight: 0.0670 overall best weight: 0.4320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS I 763 ASN K 763 ASN K 794 GLN Z 763 ASN Z 794 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25296 Z= 0.135 Angle : 0.471 6.146 34242 Z= 0.226 Chirality : 0.039 0.143 3912 Planarity : 0.003 0.039 4338 Dihedral : 8.572 179.752 3480 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.71 % Allowed : 12.17 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.16), residues: 3096 helix: 1.70 (0.14), residues: 1620 sheet: -1.11 (0.26), residues: 390 loop : 0.30 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 340 HIS 0.004 0.001 HIS C 40 PHE 0.007 0.001 PHE Z 697 TYR 0.008 0.001 TYR H 843 ARG 0.002 0.000 ARG Z 862 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 257 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8338 (mttm) cc_final: 0.7866 (mmmt) REVERT: A 227 MET cc_start: 0.8670 (mmm) cc_final: 0.7913 (mmt) REVERT: A 326 LYS cc_start: 0.8478 (tttp) cc_final: 0.8184 (tttm) REVERT: B 66 THR cc_start: 0.9208 (p) cc_final: 0.8978 (p) REVERT: B 123 MET cc_start: 0.8619 (mmt) cc_final: 0.8019 (mmm) REVERT: B 191 LYS cc_start: 0.7214 (tttp) cc_final: 0.6745 (tttt) REVERT: B 205 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 305 MET cc_start: 0.8763 (mtp) cc_final: 0.8518 (mmm) REVERT: C 211 ASP cc_start: 0.8518 (t0) cc_final: 0.8127 (t0) REVERT: D 132 MET cc_start: 0.8349 (ptm) cc_final: 0.8080 (ttp) REVERT: D 353 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8742 (mm110) REVERT: E 72 GLU cc_start: 0.7348 (tt0) cc_final: 0.6979 (tt0) REVERT: F 57 GLU cc_start: 0.8133 (pt0) cc_final: 0.7869 (pt0) REVERT: F 299 MET cc_start: 0.8963 (mmm) cc_final: 0.8605 (mtt) REVERT: G 730 MET cc_start: 0.7530 (tpt) cc_final: 0.7168 (tpt) REVERT: G 805 ASP cc_start: 0.7918 (t0) cc_final: 0.7305 (m-30) REVERT: H 729 MET cc_start: 0.8327 (tpt) cc_final: 0.7706 (tpt) REVERT: I 732 MET cc_start: 0.8084 (mtm) cc_final: 0.7773 (mtp) REVERT: I 746 MET cc_start: 0.7564 (mmm) cc_final: 0.7329 (tpp) REVERT: I 805 ASP cc_start: 0.6992 (m-30) cc_final: 0.6624 (m-30) REVERT: I 822 MET cc_start: 0.8500 (mmm) cc_final: 0.8006 (mmt) REVERT: I 869 GLN cc_start: 0.8900 (mm110) cc_final: 0.8506 (mm110) REVERT: K 746 MET cc_start: 0.7174 (mmm) cc_final: 0.6843 (tpp) REVERT: K 822 MET cc_start: 0.8126 (tpp) cc_final: 0.7836 (mmt) REVERT: L 746 MET cc_start: 0.6791 (tpp) cc_final: 0.6489 (tpt) REVERT: L 795 GLN cc_start: 0.8518 (mt0) cc_final: 0.8281 (mt0) REVERT: L 869 GLN cc_start: 0.8787 (mm110) cc_final: 0.8474 (mm110) REVERT: Z 732 MET cc_start: 0.8279 (mtm) cc_final: 0.7938 (mtp) REVERT: Z 822 MET cc_start: 0.8049 (mmm) cc_final: 0.7849 (mmt) outliers start: 19 outliers final: 17 residues processed: 270 average time/residue: 0.3233 time to fit residues: 144.6423 Evaluate side-chains 265 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 248 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 228 optimal weight: 5.9990 chunk 36 optimal weight: 0.0770 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN K 869 GLN Z 794 GLN Z 795 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.106172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.086073 restraints weight = 28052.129| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 0.96 r_work: 0.2671 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 25296 Z= 0.357 Angle : 0.567 7.146 34242 Z= 0.276 Chirality : 0.043 0.151 3912 Planarity : 0.004 0.041 4338 Dihedral : 8.619 176.944 3480 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.82 % Allowed : 12.13 % Favored : 87.05 % 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: 0.66 (0.16), residues: 3096 helix: 1.19 (0.13), residues: 1656 sheet: -1.21 (0.26), residues: 390 loop : 0.08 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 340 HIS 0.005 0.001 HIS D 161 PHE 0.011 0.001 PHE C 31 TYR 0.013 0.001 TYR D 143 ARG 0.004 0.000 ARG C 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4464.66 seconds wall clock time: 83 minutes 12.77 seconds (4992.77 seconds total)