Starting phenix.real_space_refine on Sun Mar 17 12:10:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/03_2024/7uxf_26860_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/03_2024/7uxf_26860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/03_2024/7uxf_26860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/03_2024/7uxf_26860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/03_2024/7uxf_26860_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/03_2024/7uxf_26860_updated.pdb" } resolution = 2.7 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= 0.000 sd= 0.049 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 126 5.16 5 C 11028 2.51 5 N 2958 2.21 5 O 3426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F ASP 154": "OD1" <-> "OD2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F GLU 214": "OE1" <-> "OE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 256": "NH1" <-> "NH2" Residue "F ARG 372": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17556 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: "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} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 9.50, per 1000 atoms: 0.54 Number of scatterers: 17556 At special positions: 0 Unit cell: (89.134, 97.83, 219.574, 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 126 16.00 P 12 15.00 Mg 6 11.99 O 3426 8.00 N 2958 7.00 C 11028 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: 6.81 Conformation dependent library (CDL) restraints added in 3.1 seconds 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 24 sheets defined 44.9% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.562A 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 196 removed outlier: 4.202A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.787A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 253 through 261 Proline residue: A 258 - end of helix removed outlier: 4.777A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.617A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 292 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.731A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.741A 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 365 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.578A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.561A 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: 4.202A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.787A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 253 through 261 Proline residue: B 258 - end of helix removed outlier: 4.778A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.618A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 292 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.731A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.740A 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 365 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.579A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.561A 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 196 removed outlier: 4.201A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.786A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 253 through 261 Proline residue: C 258 - end of helix removed outlier: 4.778A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 3.617A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 292 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.730A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.740A 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 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.579A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.561A 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 145 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 196 removed outlier: 4.201A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.787A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 253 through 261 Proline residue: D 258 - end of helix removed outlier: 4.778A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.617A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP D 292 " --> pdb=" O ILE D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.730A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.741A 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 365 Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.578A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.561A 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 196 removed outlier: 4.202A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.787A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 253 through 261 Proline residue: E 258 - end of helix removed outlier: 4.778A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 3.617A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP E 292 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.730A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 removed outlier: 3.740A 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 365 Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.579A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 removed outlier: 3.561A 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: 4.202A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 removed outlier: 3.787A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 253 through 261 Proline residue: F 258 - end of helix removed outlier: 4.778A pdb=" N LEU F 261 " --> pdb=" O CYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 287 through 294 removed outlier: 3.617A pdb=" N ARG F 290 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS F 291 " --> pdb=" O ASP F 288 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP F 292 " --> pdb=" O ILE F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 335 through 348 removed outlier: 5.730A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 354 removed outlier: 3.740A 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 365 Processing helix chain 'F' and resid 367 through 373 removed outlier: 3.578A pdb=" N HIS F 371 " --> pdb=" O SER F 368 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS F 373 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.663A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.214A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (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 132 through 136 removed outlier: 6.663A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.215A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (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 132 through 136 removed outlier: 6.664A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.215A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (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 132 through 136 removed outlier: 6.663A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.090A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (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 132 through 136 removed outlier: 6.663A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.214A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (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 132 through 136 removed outlier: 6.663A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= W, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.214A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 238 through 241 637 hydrogen bonds defined for protein. 1497 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: 5.65 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5483 1.33 - 1.46: 3158 1.46 - 1.58: 8993 1.58 - 1.70: 18 1.70 - 1.82: 222 Bond restraints: 17874 Sorted by residual: bond pdb=" N VAL F 159 " pdb=" CA VAL F 159 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.14e-02 7.69e+03 1.44e+01 bond pdb=" N VAL D 159 " pdb=" CA VAL D 159 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.41e+01 bond pdb=" N VAL E 159 " pdb=" CA VAL E 159 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.14e-02 7.69e+03 1.30e+01 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.18e-02 7.18e+03 1.15e+01 ... (remaining 17869 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.54: 463 105.54 - 113.21: 9783 113.21 - 120.88: 8667 120.88 - 128.55: 5231 128.55 - 136.22: 114 Bond angle restraints: 24258 Sorted by residual: angle pdb=" C THR A 303 " pdb=" CA THR A 303 " pdb=" CB THR A 303 " ideal model delta sigma weight residual 109.99 119.47 -9.48 2.09e+00 2.29e-01 2.06e+01 angle pdb=" N ILE D 151 " pdb=" CA ILE D 151 " pdb=" C ILE D 151 " ideal model delta sigma weight residual 107.80 101.81 5.99 1.45e+00 4.76e-01 1.70e+01 angle pdb=" C ILE D 151 " pdb=" N VAL D 152 " pdb=" CA VAL D 152 " ideal model delta sigma weight residual 123.19 118.35 4.84 1.24e+00 6.50e-01 1.52e+01 angle pdb=" N THR A 303 " pdb=" CA THR A 303 " pdb=" C THR A 303 " ideal model delta sigma weight residual 112.89 108.06 4.83 1.24e+00 6.50e-01 1.52e+01 angle pdb=" CA GLY D 150 " pdb=" C GLY D 150 " pdb=" O GLY D 150 " ideal model delta sigma weight residual 121.37 117.70 3.67 1.09e+00 8.42e-01 1.14e+01 ... (remaining 24253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.59: 9920 20.59 - 41.18: 683 41.18 - 61.77: 125 61.77 - 82.36: 24 82.36 - 102.95: 6 Dihedral angle restraints: 10758 sinusoidal: 4344 harmonic: 6414 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 42.95 -102.95 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 42.91 -102.91 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 42.90 -102.90 1 2.00e+01 2.50e-03 2.94e+01 ... (remaining 10755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1939 0.054 - 0.108: 643 0.108 - 0.161: 97 0.161 - 0.215: 13 0.215 - 0.269: 8 Chirality restraints: 2700 Sorted by residual: chirality pdb=" CB VAL F 159 " pdb=" CA VAL F 159 " pdb=" CG1 VAL F 159 " pdb=" CG2 VAL F 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB VAL D 159 " pdb=" CA VAL D 159 " pdb=" CG1 VAL D 159 " pdb=" CG2 VAL D 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL B 159 " pdb=" CA VAL B 159 " pdb=" CG1 VAL B 159 " pdb=" CG2 VAL B 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2697 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 156 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C GLY A 156 " -0.070 2.00e-02 2.50e+03 pdb=" O GLY A 156 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP A 157 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 156 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C GLY F 156 " 0.070 2.00e-02 2.50e+03 pdb=" O GLY F 156 " -0.026 2.00e-02 2.50e+03 pdb=" N ASP F 157 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 156 " 0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C GLY E 156 " -0.068 2.00e-02 2.50e+03 pdb=" O GLY E 156 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP E 157 " 0.024 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 86 2.57 - 3.15: 13896 3.15 - 3.73: 28222 3.73 - 4.32: 43057 4.32 - 4.90: 69841 Nonbonded interactions: 155102 Sorted by model distance: nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.983 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.990 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.997 2.170 nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.015 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.019 2.170 ... (remaining 155097 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' } 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.920 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 48.640 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.110 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.008 0.051 17874 Z= 0.506 Angle : 0.805 9.477 24258 Z= 0.442 Chirality : 0.054 0.269 2700 Planarity : 0.006 0.060 3096 Dihedral : 14.773 102.947 6654 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.71 % Allowed : 3.15 % Favored : 95.14 % Cbeta Deviations : 0.05 % 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: 0.24 (0.18), residues: 2190 helix: -0.00 (0.18), residues: 870 sheet: 0.38 (0.24), residues: 414 loop : 0.49 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.009 0.001 HIS D 161 PHE 0.006 0.001 PHE E 262 TYR 0.014 0.001 TYR D 143 ARG 0.009 0.001 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 275 time to evaluate : 2.167 Fit side-chains REVERT: A 299 MET cc_start: 0.8577 (mtm) cc_final: 0.8280 (mtm) REVERT: A 305 MET cc_start: 0.8891 (mmm) cc_final: 0.8659 (mmp) REVERT: B 25 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6920 (p0) REVERT: B 51 ASP cc_start: 0.7822 (p0) cc_final: 0.7584 (p0) REVERT: B 92 ASN cc_start: 0.9011 (m-40) cc_final: 0.8793 (m110) REVERT: B 119 MET cc_start: 0.8154 (mtm) cc_final: 0.7914 (mtp) REVERT: B 123 MET cc_start: 0.8806 (mmt) cc_final: 0.8329 (mmp) REVERT: B 283 MET cc_start: 0.9134 (mmm) cc_final: 0.8865 (mmm) REVERT: C 25 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7391 (p0) REVERT: C 116 ARG cc_start: 0.8393 (ttm170) cc_final: 0.8190 (ttm170) REVERT: C 123 MET cc_start: 0.9002 (mmt) cc_final: 0.8558 (mmt) REVERT: C 359 LYS cc_start: 0.7762 (tptp) cc_final: 0.7490 (tptt) REVERT: D 153 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8468 (tp) REVERT: E 83 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7223 (mt-10) REVERT: E 132 MET cc_start: 0.8395 (ppp) cc_final: 0.8178 (ppp) REVERT: E 325 MET cc_start: 0.8642 (mmp) cc_final: 0.8222 (mmp) REVERT: E 355 MET cc_start: 0.8294 (mtt) cc_final: 0.7980 (mtp) REVERT: F 153 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8794 (tt) outliers start: 32 outliers final: 6 residues processed: 305 average time/residue: 1.6279 time to fit residues: 542.1006 Evaluate side-chains 195 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 201 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 246 GLN B 41 GLN B 353 GLN C 41 GLN C 225 ASN C 246 GLN C 353 GLN C 354 GLN D 161 HIS D 225 ASN D 353 GLN E 225 ASN E 314 GLN E 353 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17874 Z= 0.199 Angle : 0.575 6.291 24258 Z= 0.282 Chirality : 0.045 0.134 2700 Planarity : 0.005 0.043 3096 Dihedral : 7.464 99.220 2505 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.55 % Allowed : 8.81 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.18), residues: 2190 helix: 0.33 (0.18), residues: 864 sheet: 0.53 (0.23), residues: 408 loop : 0.71 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 340 HIS 0.004 0.001 HIS D 161 PHE 0.007 0.001 PHE F 127 TYR 0.014 0.001 TYR D 143 ARG 0.004 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 1.960 Fit side-chains REVERT: B 25 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6949 (p0) REVERT: B 51 ASP cc_start: 0.7817 (p0) cc_final: 0.7582 (p0) REVERT: B 72 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: B 123 MET cc_start: 0.8784 (mmt) cc_final: 0.7996 (mmp) REVERT: B 283 MET cc_start: 0.9096 (mmm) cc_final: 0.8851 (mmm) REVERT: C 72 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6663 (tm-30) REVERT: C 123 MET cc_start: 0.8936 (mmt) cc_final: 0.8614 (mmt) REVERT: C 314 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: C 372 ARG cc_start: 0.8140 (ptp90) cc_final: 0.7692 (ptp-170) REVERT: D 72 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6818 (tm-30) REVERT: D 153 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8499 (tp) REVERT: D 314 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: E 83 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7129 (mt-10) REVERT: E 132 MET cc_start: 0.8368 (ppp) cc_final: 0.8135 (ppp) REVERT: E 355 MET cc_start: 0.8141 (mtt) cc_final: 0.7836 (mtp) REVERT: F 122 ILE cc_start: 0.8558 (mt) cc_final: 0.8246 (mp) REVERT: F 326 LYS cc_start: 0.8159 (tppt) cc_final: 0.7893 (mptt) REVERT: F 372 ARG cc_start: 0.7792 (ptp90) cc_final: 0.7549 (ptt-90) outliers start: 29 outliers final: 8 residues processed: 226 average time/residue: 1.5591 time to fit residues: 386.9636 Evaluate side-chains 199 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 41 GLN B 115 ASN B 353 GLN C 41 GLN C 115 ASN C 225 ASN C 296 ASN D 115 ASN D 225 ASN D 296 ASN E 246 GLN F 115 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17874 Z= 0.356 Angle : 0.622 7.515 24258 Z= 0.303 Chirality : 0.048 0.147 2700 Planarity : 0.005 0.039 3096 Dihedral : 7.433 104.165 2499 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.76 % Allowed : 10.26 % Favored : 87.98 % 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: 0.30 (0.18), residues: 2190 helix: -0.06 (0.18), residues: 888 sheet: 0.46 (0.25), residues: 390 loop : 0.64 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.004 0.001 HIS F 101 PHE 0.009 0.002 PHE F 127 TYR 0.015 0.001 TYR C 188 ARG 0.006 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 2.174 Fit side-chains REVERT: B 25 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7022 (p0) REVERT: B 51 ASP cc_start: 0.7808 (p0) cc_final: 0.7580 (p0) REVERT: B 72 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: B 123 MET cc_start: 0.8809 (mmt) cc_final: 0.8358 (mmm) REVERT: C 72 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: C 123 MET cc_start: 0.8930 (mmt) cc_final: 0.8509 (mmt) REVERT: C 276 GLU cc_start: 0.7664 (tt0) cc_final: 0.7455 (tt0) REVERT: C 314 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: C 372 ARG cc_start: 0.8210 (ptp90) cc_final: 0.7796 (ptp-170) REVERT: D 72 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: D 227 MET cc_start: 0.8652 (mmm) cc_final: 0.8001 (mmm) REVERT: D 314 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: E 132 MET cc_start: 0.8329 (ppp) cc_final: 0.8056 (ppp) REVERT: E 355 MET cc_start: 0.8094 (mtt) cc_final: 0.7808 (mtp) REVERT: F 47 MET cc_start: 0.6758 (mtm) cc_final: 0.5940 (mtp) REVERT: F 50 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7190 (mttm) REVERT: F 354 GLN cc_start: 0.7897 (mm110) cc_final: 0.7627 (mm110) REVERT: F 364 GLU cc_start: 0.7287 (pp20) cc_final: 0.7080 (pt0) outliers start: 33 outliers final: 18 residues processed: 215 average time/residue: 1.6470 time to fit residues: 387.4526 Evaluate side-chains 211 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 96 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 192 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 225 ASN E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17874 Z= 0.233 Angle : 0.559 7.958 24258 Z= 0.270 Chirality : 0.045 0.142 2700 Planarity : 0.005 0.036 3096 Dihedral : 7.052 103.460 2497 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.82 % Allowed : 11.49 % Favored : 86.70 % 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: 0.35 (0.18), residues: 2190 helix: -0.02 (0.17), residues: 888 sheet: 0.50 (0.25), residues: 390 loop : 0.66 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 340 HIS 0.002 0.001 HIS D 161 PHE 0.008 0.001 PHE F 127 TYR 0.010 0.001 TYR D 69 ARG 0.005 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 2.266 Fit side-chains REVERT: A 364 GLU cc_start: 0.8009 (pp20) cc_final: 0.7616 (tm-30) REVERT: B 25 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7038 (p0) REVERT: B 51 ASP cc_start: 0.7788 (p0) cc_final: 0.7563 (p0) REVERT: B 72 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: B 132 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8014 (ptm) REVERT: C 72 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: C 123 MET cc_start: 0.8895 (mmt) cc_final: 0.8538 (mmt) REVERT: D 72 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: E 132 MET cc_start: 0.8277 (ppp) cc_final: 0.7983 (ppp) REVERT: E 355 MET cc_start: 0.8098 (mtt) cc_final: 0.7798 (mtp) REVERT: E 364 GLU cc_start: 0.7614 (pp20) cc_final: 0.7169 (tm-30) REVERT: F 47 MET cc_start: 0.6617 (mtm) cc_final: 0.5890 (mtp) REVERT: F 50 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7094 (mttm) REVERT: F 122 ILE cc_start: 0.8641 (mt) cc_final: 0.8347 (mp) REVERT: F 354 GLN cc_start: 0.7970 (mm110) cc_final: 0.7684 (mm110) outliers start: 34 outliers final: 18 residues processed: 216 average time/residue: 1.6442 time to fit residues: 389.7838 Evaluate side-chains 211 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 41 GLN C 41 GLN D 225 ASN E 225 ASN E 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 17874 Z= 0.304 Angle : 0.584 8.290 24258 Z= 0.282 Chirality : 0.046 0.147 2700 Planarity : 0.005 0.036 3096 Dihedral : 7.059 103.302 2495 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.98 % Allowed : 12.45 % Favored : 85.58 % 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: 0.31 (0.18), residues: 2190 helix: -0.07 (0.17), residues: 888 sheet: 0.46 (0.26), residues: 390 loop : 0.66 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.003 0.001 HIS A 161 PHE 0.009 0.001 PHE F 127 TYR 0.011 0.001 TYR C 188 ARG 0.005 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 2.002 Fit side-chains REVERT: A 224 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7498 (mm-30) REVERT: A 328 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7251 (mtpp) REVERT: A 364 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: B 25 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7067 (p0) REVERT: B 51 ASP cc_start: 0.7805 (p0) cc_final: 0.7583 (p0) REVERT: B 57 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: B 72 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: B 123 MET cc_start: 0.8812 (mmt) cc_final: 0.8103 (mmp) REVERT: B 132 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7985 (ptm) REVERT: B 276 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: C 72 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: C 123 MET cc_start: 0.8884 (mmt) cc_final: 0.8488 (mmt) REVERT: D 72 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: E 57 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: E 132 MET cc_start: 0.8216 (ppp) cc_final: 0.7898 (ppp) REVERT: E 355 MET cc_start: 0.8107 (mtt) cc_final: 0.7817 (mtp) REVERT: E 364 GLU cc_start: 0.7542 (pp20) cc_final: 0.7298 (tt0) REVERT: F 47 MET cc_start: 0.6360 (mtm) cc_final: 0.5971 (mtp) REVERT: F 50 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7110 (mttm) REVERT: F 95 ARG cc_start: 0.7684 (mtt-85) cc_final: 0.7460 (mtm-85) REVERT: F 354 GLN cc_start: 0.8000 (mm110) cc_final: 0.7708 (mm110) outliers start: 37 outliers final: 20 residues processed: 216 average time/residue: 1.6359 time to fit residues: 386.4396 Evaluate side-chains 224 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 193 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 125 optimal weight: 0.0470 chunk 52 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 41 GLN C 41 GLN D 225 ASN D 297 ASN E 225 ASN E 246 GLN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17874 Z= 0.173 Angle : 0.529 8.743 24258 Z= 0.253 Chirality : 0.043 0.132 2700 Planarity : 0.004 0.033 3096 Dihedral : 6.694 101.438 2495 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.60 % Allowed : 13.09 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.18), residues: 2190 helix: 0.09 (0.17), residues: 888 sheet: 0.52 (0.26), residues: 390 loop : 0.75 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 255 TYR 0.009 0.001 TYR D 69 ARG 0.004 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 202 time to evaluate : 2.169 Fit side-chains REVERT: A 338 SER cc_start: 0.8417 (m) cc_final: 0.8078 (m) REVERT: A 364 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: B 25 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.7072 (p0) REVERT: B 51 ASP cc_start: 0.7793 (p0) cc_final: 0.7571 (p0) REVERT: B 123 MET cc_start: 0.8801 (mmt) cc_final: 0.8059 (mmp) REVERT: B 132 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8073 (ptm) REVERT: B 276 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: C 72 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: C 123 MET cc_start: 0.8851 (mmt) cc_final: 0.8520 (mmt) REVERT: D 72 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: E 72 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: E 132 MET cc_start: 0.8186 (ppp) cc_final: 0.7850 (ppp) REVERT: E 355 MET cc_start: 0.8083 (mtt) cc_final: 0.7793 (mtp) REVERT: E 364 GLU cc_start: 0.7498 (pp20) cc_final: 0.7293 (tt0) REVERT: F 47 MET cc_start: 0.6088 (mtm) cc_final: 0.5806 (mtp) REVERT: F 95 ARG cc_start: 0.7656 (mtt-85) cc_final: 0.7443 (mtm-85) REVERT: F 122 ILE cc_start: 0.8568 (mt) cc_final: 0.8299 (mp) REVERT: F 354 GLN cc_start: 0.7979 (mm110) cc_final: 0.7678 (mm110) outliers start: 30 outliers final: 14 residues processed: 219 average time/residue: 1.6738 time to fit residues: 401.4663 Evaluate side-chains 215 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 180 optimal weight: 0.0870 chunk 119 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17874 Z= 0.266 Angle : 0.562 9.903 24258 Z= 0.269 Chirality : 0.045 0.139 2700 Planarity : 0.004 0.034 3096 Dihedral : 6.797 101.614 2495 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.98 % Allowed : 13.03 % Favored : 84.99 % 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: 0.46 (0.18), residues: 2190 helix: 0.04 (0.17), residues: 888 sheet: 0.51 (0.26), residues: 390 loop : 0.77 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 31 TYR 0.010 0.001 TYR C 188 ARG 0.003 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 1.985 Fit side-chains REVERT: A 224 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 328 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7589 (mtpp) REVERT: A 338 SER cc_start: 0.8459 (m) cc_final: 0.8081 (m) REVERT: A 364 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: B 25 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.7101 (p0) REVERT: B 51 ASP cc_start: 0.7780 (p0) cc_final: 0.7567 (p0) REVERT: B 57 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: B 72 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6905 (tp30) REVERT: B 123 MET cc_start: 0.8778 (mmt) cc_final: 0.8048 (mmp) REVERT: B 132 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7933 (ptm) REVERT: B 276 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: C 72 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: C 123 MET cc_start: 0.8859 (mmt) cc_final: 0.8514 (mmt) REVERT: D 72 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: E 72 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: E 132 MET cc_start: 0.8178 (ppp) cc_final: 0.7828 (ppp) REVERT: E 355 MET cc_start: 0.8111 (mtt) cc_final: 0.7836 (mtp) REVERT: F 47 MET cc_start: 0.6156 (mtm) cc_final: 0.5888 (mtp) REVERT: F 95 ARG cc_start: 0.7681 (mtt-85) cc_final: 0.7470 (mtm-85) REVERT: F 314 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: F 354 GLN cc_start: 0.8001 (mm110) cc_final: 0.7686 (mm110) outliers start: 37 outliers final: 26 residues processed: 218 average time/residue: 1.6522 time to fit residues: 393.5372 Evaluate side-chains 236 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 145 optimal weight: 0.0980 chunk 105 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 246 GLN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17874 Z= 0.160 Angle : 0.522 10.482 24258 Z= 0.248 Chirality : 0.043 0.129 2700 Planarity : 0.004 0.033 3096 Dihedral : 6.481 99.835 2495 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.76 % Allowed : 13.51 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2190 helix: 0.19 (0.17), residues: 888 sheet: 0.57 (0.26), residues: 390 loop : 0.87 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.003 0.001 HIS C 161 PHE 0.008 0.001 PHE C 255 TYR 0.009 0.001 TYR D 69 ARG 0.004 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 203 time to evaluate : 2.123 Fit side-chains REVERT: A 338 SER cc_start: 0.8370 (m) cc_final: 0.8044 (m) REVERT: A 364 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: B 51 ASP cc_start: 0.7771 (p0) cc_final: 0.7563 (p0) REVERT: B 132 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8056 (ptm) REVERT: B 276 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: C 72 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6817 (tm-30) REVERT: C 123 MET cc_start: 0.8817 (mmt) cc_final: 0.8509 (mmt) REVERT: D 72 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: E 72 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: E 132 MET cc_start: 0.8165 (ppp) cc_final: 0.7918 (ppp) REVERT: E 355 MET cc_start: 0.8123 (mtt) cc_final: 0.7851 (mtp) REVERT: F 47 MET cc_start: 0.6068 (mtm) cc_final: 0.5766 (mtp) REVERT: F 314 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7810 (tt0) outliers start: 33 outliers final: 18 residues processed: 221 average time/residue: 1.5662 time to fit residues: 379.0424 Evaluate side-chains 218 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 314 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 120 optimal weight: 0.0270 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 0.0040 chunk 61 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 188 optimal weight: 6.9990 chunk 198 optimal weight: 0.7980 overall best weight: 0.5052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 353 GLN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17874 Z= 0.141 Angle : 0.510 10.475 24258 Z= 0.242 Chirality : 0.043 0.129 2700 Planarity : 0.004 0.032 3096 Dihedral : 6.212 96.944 2493 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.28 % Allowed : 14.32 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2190 helix: 0.34 (0.18), residues: 882 sheet: 0.64 (0.26), residues: 390 loop : 0.90 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.003 0.001 HIS D 161 PHE 0.007 0.001 PHE C 31 TYR 0.008 0.001 TYR D 143 ARG 0.008 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 2.096 Fit side-chains REVERT: A 338 SER cc_start: 0.8275 (m) cc_final: 0.8060 (t) REVERT: A 364 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: B 51 ASP cc_start: 0.7768 (p0) cc_final: 0.7559 (p0) REVERT: B 57 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: B 276 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: C 72 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: C 123 MET cc_start: 0.8806 (mmt) cc_final: 0.8504 (mmt) REVERT: D 72 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: E 72 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: E 132 MET cc_start: 0.8171 (ppp) cc_final: 0.7929 (ppp) REVERT: E 355 MET cc_start: 0.8124 (mtt) cc_final: 0.7836 (mtp) REVERT: F 190 MET cc_start: 0.8108 (mtp) cc_final: 0.7602 (ttm) REVERT: F 314 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7823 (tt0) outliers start: 24 outliers final: 16 residues processed: 212 average time/residue: 1.6180 time to fit residues: 376.2384 Evaluate side-chains 215 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 100 optimal weight: 0.0970 chunk 146 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN E 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17874 Z= 0.287 Angle : 0.571 10.931 24258 Z= 0.275 Chirality : 0.046 0.140 2700 Planarity : 0.004 0.033 3096 Dihedral : 6.641 100.532 2493 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.50 % Allowed : 14.21 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2190 helix: 0.13 (0.17), residues: 882 sheet: 0.57 (0.26), residues: 390 loop : 0.83 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.003 0.001 HIS C 161 PHE 0.009 0.001 PHE F 255 TYR 0.011 0.001 TYR C 188 ARG 0.007 0.000 ARG F 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 2.358 Fit side-chains REVERT: A 338 SER cc_start: 0.8394 (m) cc_final: 0.8063 (m) REVERT: A 364 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: B 51 ASP cc_start: 0.7780 (p0) cc_final: 0.7542 (p0) REVERT: B 57 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: B 276 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: C 72 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: C 123 MET cc_start: 0.8855 (mmt) cc_final: 0.8452 (mmt) REVERT: D 72 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: E 72 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: E 132 MET cc_start: 0.8199 (ppp) cc_final: 0.7830 (ppp) REVERT: E 355 MET cc_start: 0.8112 (mtt) cc_final: 0.7823 (mtp) REVERT: F 314 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7811 (tt0) outliers start: 28 outliers final: 20 residues processed: 206 average time/residue: 1.6253 time to fit residues: 366.5498 Evaluate side-chains 215 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.3980 chunk 187 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN E 354 GLN F 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.087721 restraints weight = 20838.686| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.29 r_work: 0.2813 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17874 Z= 0.211 Angle : 0.542 10.130 24258 Z= 0.260 Chirality : 0.044 0.138 2700 Planarity : 0.004 0.033 3096 Dihedral : 6.534 99.704 2493 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.44 % Allowed : 14.16 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2190 helix: 0.15 (0.17), residues: 882 sheet: 0.55 (0.26), residues: 390 loop : 0.86 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 31 TYR 0.009 0.001 TYR D 69 ARG 0.008 0.000 ARG F 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6474.23 seconds wall clock time: 115 minutes 27.77 seconds (6927.77 seconds total)