Starting phenix.real_space_refine on Fri Feb 16 09:43:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t1y_10363/02_2024/6t1y_10363_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t1y_10363/02_2024/6t1y_10363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t1y_10363/02_2024/6t1y_10363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t1y_10363/02_2024/6t1y_10363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t1y_10363/02_2024/6t1y_10363_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t1y_10363/02_2024/6t1y_10363_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 10 5.49 5 Mg 5 5.21 5 S 110 5.16 5 C 9410 2.51 5 N 2510 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14915 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 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} Time building chain proxies: 8.67, per 1000 atoms: 0.58 Number of scatterers: 14915 At special positions: 0 Unit cell: (94.62, 90.06, 192.66, 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 110 16.00 P 10 15.00 Mg 5 11.99 O 2870 8.00 N 2510 7.00 C 9410 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: 6.71 Conformation dependent library (CDL) restraints added in 2.9 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH F 4 " pdb=" CB DTH G 4 " pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 3490 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 20 sheets defined 41.4% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 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 92 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 123 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.109A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 290 through 294 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 347 removed outlier: 5.355A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 56 through 60 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 92 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 123 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.110A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 347 removed outlier: 5.355A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 56 through 60 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 92 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 123 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.111A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 290 through 294 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 347 removed outlier: 5.356A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 355 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 56 through 60 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 92 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 123 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.110A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 347 removed outlier: 5.355A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 355 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 56 through 60 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 92 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 123 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 182 through 196 removed outlier: 4.110A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 231 Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 347 removed outlier: 5.355A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 355 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.678A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.047A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.993A 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: 6.678A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.046A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.993A 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: 6.679A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.046A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.993A 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: 6.679A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 52 through 54 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.045A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.994A 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: 6.679A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 52 through 54 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.045A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.993A 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 241 540 hydrogen bonds defined for protein. 1305 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: 5.08 Time building geometry restraints manager: 7.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3772 1.32 - 1.44: 3422 1.44 - 1.56: 7856 1.56 - 1.68: 5 1.68 - 1.81: 190 Bond restraints: 15245 Sorted by residual: bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" CA EEP G 2 " pdb=" C EEP G 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" CA EEP F 2 " pdb=" C EEP F 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 15240 not shown) Histogram of bond angle deviations from ideal: 94.02 - 102.36: 84 102.36 - 110.71: 5575 110.71 - 119.05: 7062 119.05 - 127.40: 7816 127.40 - 135.75: 168 Bond angle restraints: 20705 Sorted by residual: angle pdb=" C ALA A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta sigma weight residual 119.66 128.66 -9.00 7.30e-01 1.88e+00 1.52e+02 angle pdb=" C ALA E 331 " pdb=" N PRO E 332 " pdb=" CA PRO E 332 " ideal model delta sigma weight residual 119.66 128.64 -8.98 7.30e-01 1.88e+00 1.51e+02 angle pdb=" C ALA C 331 " pdb=" N PRO C 332 " pdb=" CA PRO C 332 " ideal model delta sigma weight residual 119.66 128.64 -8.98 7.30e-01 1.88e+00 1.51e+02 angle pdb=" C ALA D 331 " pdb=" N PRO D 332 " pdb=" CA PRO D 332 " ideal model delta sigma weight residual 119.66 128.63 -8.97 7.30e-01 1.88e+00 1.51e+02 angle pdb=" C ALA B 331 " pdb=" N PRO B 332 " pdb=" CA PRO B 332 " ideal model delta sigma weight residual 119.66 128.56 -8.90 7.30e-01 1.88e+00 1.49e+02 ... (remaining 20700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.95: 9014 29.95 - 59.90: 91 59.90 - 89.86: 45 89.86 - 119.81: 0 119.81 - 149.76: 10 Dihedral angle restraints: 9160 sinusoidal: 3710 harmonic: 5450 Sorted by residual: dihedral pdb=" O1B ADP C 376 " pdb=" O3A ADP C 376 " pdb=" PB ADP C 376 " pdb=" PA ADP C 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.76 -149.76 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP D 376 " pdb=" O3A ADP D 376 " pdb=" PB ADP D 376 " pdb=" PA ADP D 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.74 -149.74 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP A 376 " pdb=" O3A ADP A 376 " pdb=" PB ADP A 376 " pdb=" PA ADP A 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.73 -149.73 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 9157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 855 0.043 - 0.087: 764 0.087 - 0.130: 390 0.130 - 0.174: 223 0.174 - 0.217: 73 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CA TYR B 91 " pdb=" N TYR B 91 " pdb=" C TYR B 91 " pdb=" CB TYR B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TYR D 91 " pdb=" N TYR D 91 " pdb=" C TYR D 91 " pdb=" CB TYR D 91 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA TYR C 91 " pdb=" N TYR C 91 " pdb=" C TYR C 91 " pdb=" CB TYR C 91 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2302 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 375 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C PHE B 375 " -0.062 2.00e-02 2.50e+03 pdb=" O PHE B 375 " 0.022 2.00e-02 2.50e+03 pdb=" OXT PHE B 375 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 375 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C PHE E 375 " 0.062 2.00e-02 2.50e+03 pdb=" O PHE E 375 " -0.022 2.00e-02 2.50e+03 pdb=" OXT PHE E 375 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 375 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C PHE C 375 " 0.062 2.00e-02 2.50e+03 pdb=" O PHE C 375 " -0.022 2.00e-02 2.50e+03 pdb=" OXT PHE C 375 " -0.022 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 10 2.05 - 2.76: 3127 2.76 - 3.47: 21170 3.47 - 4.19: 37895 4.19 - 4.90: 64508 Nonbonded interactions: 126710 Sorted by model distance: nonbonded pdb=" N TRP J 1 " pdb=" C ALA J 7 " model vdw 1.332 3.350 nonbonded pdb=" N TRP F 1 " pdb=" C ALA F 7 " model vdw 1.332 3.350 nonbonded pdb=" N TRP G 1 " pdb=" C ALA G 7 " model vdw 1.332 3.350 nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.333 3.350 nonbonded pdb=" N TRP I 1 " pdb=" C ALA I 7 " model vdw 1.333 3.350 ... (remaining 126705 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' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.870 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: 4.170 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 44.970 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 0.017 0.100 15245 Z= 1.144 Angle : 1.604 10.897 20705 Z= 1.082 Chirality : 0.082 0.217 2305 Planarity : 0.006 0.060 2630 Dihedral : 12.477 149.759 5670 Min Nonbonded Distance : 1.332 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.32 % Allowed : 0.00 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1830 helix: -1.01 (0.17), residues: 770 sheet: -0.88 (0.30), residues: 240 loop : -0.05 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.006 TRP B 340 HIS 0.008 0.002 HIS E 88 PHE 0.021 0.004 PHE A 124 TYR 0.038 0.005 TYR D 294 ARG 0.005 0.001 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 460 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLU cc_start: 0.8209 (tp30) cc_final: 0.7930 (tp30) REVERT: A 370 VAL cc_start: 0.8452 (m) cc_final: 0.8140 (m) REVERT: C 78 ASN cc_start: 0.8592 (t0) cc_final: 0.8130 (t0) REVERT: C 157 ASP cc_start: 0.8345 (t70) cc_final: 0.8072 (t70) REVERT: C 187 ASP cc_start: 0.8366 (t70) cc_final: 0.8045 (t0) REVERT: C 305 MET cc_start: 0.8235 (mmm) cc_final: 0.7953 (mmt) REVERT: D 206 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7876 (ttm170) REVERT: E 40 HIS cc_start: 0.7922 (m-70) cc_final: 0.7641 (m-70) outliers start: 5 outliers final: 5 residues processed: 465 average time/residue: 0.2945 time to fit residues: 193.9029 Evaluate side-chains 232 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 227 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain G residue 5 CYS Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 162 ASN A 354 GLN A 360 GLN B 92 ASN C 173 HIS D 12 ASN D 40 HIS D 354 GLN E 173 HIS ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15245 Z= 0.212 Angle : 0.674 8.253 20705 Z= 0.333 Chirality : 0.047 0.209 2305 Planarity : 0.005 0.035 2630 Dihedral : 12.680 159.865 2180 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.48 % Allowed : 8.00 % Favored : 89.52 % 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: 0.15 (0.19), residues: 1830 helix: 0.18 (0.19), residues: 765 sheet: -0.38 (0.30), residues: 280 loop : 0.47 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 1 HIS 0.003 0.001 HIS D 173 PHE 0.016 0.001 PHE C 375 TYR 0.011 0.001 TYR A 337 ARG 0.006 0.001 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 287 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8432 (mtp) cc_final: 0.8009 (mtt) REVERT: B 47 MET cc_start: 0.7752 (mtt) cc_final: 0.7074 (mtm) REVERT: B 296 ASN cc_start: 0.7684 (m-40) cc_final: 0.7441 (m-40) REVERT: B 375 PHE cc_start: 0.4220 (OUTLIER) cc_final: 0.3609 (t80) REVERT: C 119 MET cc_start: 0.7747 (ttp) cc_final: 0.7452 (ttp) REVERT: C 187 ASP cc_start: 0.8222 (t70) cc_final: 0.7949 (t0) REVERT: C 286 ASP cc_start: 0.7198 (t0) cc_final: 0.6885 (m-30) REVERT: C 314 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7977 (tm-30) REVERT: D 47 MET cc_start: 0.5038 (mtp) cc_final: 0.4291 (ttm) REVERT: D 123 MET cc_start: 0.7609 (mmt) cc_final: 0.7374 (mmt) REVERT: D 206 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7573 (ttm170) REVERT: E 40 HIS cc_start: 0.7838 (m-70) cc_final: 0.7505 (m-70) REVERT: E 44 MET cc_start: 0.2496 (tpt) cc_final: 0.2178 (mtp) REVERT: E 191 LYS cc_start: 0.8788 (tttt) cc_final: 0.8482 (tttt) outliers start: 39 outliers final: 25 residues processed: 312 average time/residue: 0.2546 time to fit residues: 118.3912 Evaluate side-chains 242 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 354 GLN D 12 ASN D 40 HIS D 173 HIS D 354 GLN ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15245 Z= 0.427 Angle : 0.706 6.793 20705 Z= 0.345 Chirality : 0.049 0.230 2305 Planarity : 0.005 0.052 2630 Dihedral : 12.181 179.172 2179 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.86 % Allowed : 10.16 % Favored : 86.98 % 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: 0.11 (0.19), residues: 1830 helix: 0.06 (0.18), residues: 790 sheet: -0.48 (0.28), residues: 315 loop : 0.68 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 1 HIS 0.005 0.001 HIS C 40 PHE 0.026 0.002 PHE A 223 TYR 0.014 0.002 TYR D 143 ARG 0.004 0.001 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 220 time to evaluate : 1.781 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 345 ILE cc_start: 0.9283 (mm) cc_final: 0.9078 (mt) REVERT: B 296 ASN cc_start: 0.8052 (m-40) cc_final: 0.7838 (m110) REVERT: B 375 PHE cc_start: 0.3882 (OUTLIER) cc_final: 0.3484 (t80) REVERT: C 82 MET cc_start: 0.7972 (tpt) cc_final: 0.7288 (tpt) REVERT: C 119 MET cc_start: 0.7756 (ttp) cc_final: 0.7497 (ttp) REVERT: C 227 MET cc_start: 0.8133 (mmm) cc_final: 0.7590 (mmm) REVERT: D 123 MET cc_start: 0.7938 (mmt) cc_final: 0.7723 (mmt) REVERT: D 206 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7619 (ttm170) REVERT: E 40 HIS cc_start: 0.7984 (m-70) cc_final: 0.7633 (m-70) REVERT: E 143 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7836 (t80) outliers start: 45 outliers final: 34 residues processed: 248 average time/residue: 0.2679 time to fit residues: 100.4679 Evaluate side-chains 228 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 40 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15245 Z= 0.183 Angle : 0.591 6.684 20705 Z= 0.278 Chirality : 0.045 0.238 2305 Planarity : 0.004 0.041 2630 Dihedral : 11.713 178.715 2176 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.16 % Allowed : 12.00 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1830 helix: 0.62 (0.19), residues: 730 sheet: -0.46 (0.28), residues: 310 loop : 0.93 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 1 HIS 0.003 0.001 HIS C 161 PHE 0.023 0.001 PHE A 223 TYR 0.013 0.001 TYR E 53 ARG 0.004 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 223 time to evaluate : 2.222 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 176 MET cc_start: 0.8512 (mtp) cc_final: 0.8000 (mtt) REVERT: A 313 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7726 (ttt) REVERT: B 47 MET cc_start: 0.7657 (mtt) cc_final: 0.7089 (mtm) REVERT: B 296 ASN cc_start: 0.7941 (m-40) cc_final: 0.7696 (m110) REVERT: B 314 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: C 190 MET cc_start: 0.8608 (ttp) cc_final: 0.8267 (mtm) REVERT: C 227 MET cc_start: 0.8038 (mmm) cc_final: 0.7586 (mmm) REVERT: C 276 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: E 40 HIS cc_start: 0.7861 (m-70) cc_final: 0.7545 (m-70) REVERT: E 143 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7779 (t80) outliers start: 34 outliers final: 23 residues processed: 245 average time/residue: 0.2458 time to fit residues: 92.8052 Evaluate side-chains 229 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 41 GLN D 12 ASN D 40 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15245 Z= 0.382 Angle : 0.657 6.711 20705 Z= 0.315 Chirality : 0.047 0.238 2305 Planarity : 0.005 0.042 2630 Dihedral : 11.351 176.210 2176 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.43 % Allowed : 11.56 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1830 helix: 0.14 (0.18), residues: 790 sheet: -0.41 (0.28), residues: 320 loop : 0.75 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 79 HIS 0.004 0.001 HIS C 40 PHE 0.020 0.002 PHE C 124 TYR 0.015 0.001 TYR B 337 ARG 0.003 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 203 time to evaluate : 1.820 Fit side-chains REVERT: A 83 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 176 MET cc_start: 0.8596 (mtp) cc_final: 0.8339 (mtt) REVERT: B 44 MET cc_start: 0.7852 (mtt) cc_final: 0.7575 (mtt) REVERT: B 314 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: C 190 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8353 (mtm) REVERT: C 227 MET cc_start: 0.8086 (mmm) cc_final: 0.7641 (mmm) REVERT: C 276 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: E 143 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7854 (t80) REVERT: E 314 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7633 (tt0) outliers start: 54 outliers final: 36 residues processed: 235 average time/residue: 0.2459 time to fit residues: 88.3043 Evaluate side-chains 229 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 178 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN D 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15245 Z= 0.175 Angle : 0.581 6.738 20705 Z= 0.271 Chirality : 0.044 0.229 2305 Planarity : 0.004 0.039 2630 Dihedral : 10.790 178.205 2175 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.73 % Allowed : 12.76 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1830 helix: 0.45 (0.19), residues: 760 sheet: -0.30 (0.28), residues: 320 loop : 1.02 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.003 0.001 HIS D 161 PHE 0.014 0.001 PHE C 124 TYR 0.009 0.001 TYR B 337 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 201 time to evaluate : 1.707 Fit side-chains REVERT: A 83 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 270 GLU cc_start: 0.4849 (mm-30) cc_final: 0.4518 (mm-30) REVERT: B 184 ASP cc_start: 0.7761 (m-30) cc_final: 0.7559 (m-30) REVERT: B 314 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: C 190 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8353 (mtm) REVERT: C 227 MET cc_start: 0.8034 (mmm) cc_final: 0.7705 (mmm) REVERT: C 276 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: D 206 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7566 (ttm170) REVERT: E 139 VAL cc_start: 0.8982 (t) cc_final: 0.8767 (m) REVERT: E 314 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: E 372 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6887 (mtm-85) outliers start: 43 outliers final: 29 residues processed: 226 average time/residue: 0.2504 time to fit residues: 85.9084 Evaluate side-chains 227 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 0.0060 chunk 99 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15245 Z= 0.267 Angle : 0.603 8.139 20705 Z= 0.283 Chirality : 0.045 0.223 2305 Planarity : 0.004 0.036 2630 Dihedral : 10.321 172.420 2175 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.86 % Allowed : 13.08 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1830 helix: 0.43 (0.19), residues: 760 sheet: -0.28 (0.29), residues: 320 loop : 0.85 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 86 HIS 0.003 0.001 HIS D 161 PHE 0.016 0.001 PHE C 124 TYR 0.011 0.001 TYR B 337 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 199 time to evaluate : 1.555 Fit side-chains REVERT: A 83 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 270 GLU cc_start: 0.4836 (mm-30) cc_final: 0.4310 (mm-30) REVERT: B 314 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: C 190 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8394 (mtm) REVERT: C 227 MET cc_start: 0.8026 (mmm) cc_final: 0.7683 (mmm) REVERT: C 276 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: D 44 MET cc_start: 0.4115 (ttt) cc_final: 0.3746 (ttt) REVERT: D 206 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7602 (ttm170) REVERT: E 139 VAL cc_start: 0.8999 (t) cc_final: 0.8795 (m) REVERT: E 314 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: E 372 ARG cc_start: 0.7104 (mtm-85) cc_final: 0.6814 (mtm-85) outliers start: 45 outliers final: 34 residues processed: 227 average time/residue: 0.2491 time to fit residues: 85.7685 Evaluate side-chains 223 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 0.1980 chunk 53 optimal weight: 0.0870 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15245 Z= 0.151 Angle : 0.569 9.392 20705 Z= 0.262 Chirality : 0.043 0.219 2305 Planarity : 0.004 0.040 2630 Dihedral : 10.004 177.295 2175 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.97 % Allowed : 14.10 % Favored : 83.94 % 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: 0.73 (0.20), residues: 1830 helix: 0.55 (0.19), residues: 760 sheet: -0.12 (0.29), residues: 315 loop : 0.99 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.003 0.001 HIS D 161 PHE 0.022 0.001 PHE D 375 TYR 0.007 0.001 TYR B 337 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 1.578 Fit side-chains REVERT: A 83 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 176 MET cc_start: 0.8540 (mtp) cc_final: 0.8287 (mtt) REVERT: A 270 GLU cc_start: 0.4923 (mm-30) cc_final: 0.4226 (mm-30) REVERT: B 314 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: C 47 MET cc_start: 0.5121 (mpp) cc_final: 0.4847 (mpp) REVERT: C 190 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8374 (mtm) REVERT: C 227 MET cc_start: 0.7971 (mmm) cc_final: 0.7616 (mmm) REVERT: C 276 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: D 206 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7545 (ttm170) REVERT: D 375 PHE cc_start: 0.5576 (t80) cc_final: 0.4659 (t80) REVERT: E 139 VAL cc_start: 0.8942 (t) cc_final: 0.8739 (m) REVERT: E 314 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7596 (tt0) outliers start: 31 outliers final: 22 residues processed: 229 average time/residue: 0.2585 time to fit residues: 89.7273 Evaluate side-chains 220 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15245 Z= 0.243 Angle : 0.605 11.501 20705 Z= 0.281 Chirality : 0.044 0.215 2305 Planarity : 0.004 0.036 2630 Dihedral : 9.841 170.290 2175 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.60 % Allowed : 13.78 % Favored : 83.62 % 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: 0.60 (0.20), residues: 1830 helix: 0.52 (0.19), residues: 760 sheet: -0.18 (0.29), residues: 320 loop : 0.84 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 86 HIS 0.003 0.001 HIS D 161 PHE 0.018 0.001 PHE D 375 TYR 0.010 0.001 TYR B 337 ARG 0.003 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 1.741 Fit side-chains REVERT: A 83 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 176 MET cc_start: 0.8572 (mtp) cc_final: 0.8317 (mtt) REVERT: A 270 GLU cc_start: 0.4895 (mm-30) cc_final: 0.4150 (mm-30) REVERT: B 314 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: C 190 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8418 (mtm) REVERT: C 227 MET cc_start: 0.8044 (mmm) cc_final: 0.7704 (mmm) REVERT: C 276 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: D 44 MET cc_start: 0.3626 (ttt) cc_final: 0.3415 (ttt) REVERT: D 206 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7571 (ttm170) REVERT: E 314 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7639 (tt0) outliers start: 41 outliers final: 32 residues processed: 221 average time/residue: 0.2630 time to fit residues: 88.4011 Evaluate side-chains 220 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15245 Z= 0.267 Angle : 0.619 11.536 20705 Z= 0.287 Chirality : 0.045 0.215 2305 Planarity : 0.004 0.038 2630 Dihedral : 9.747 159.521 2175 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.67 % Allowed : 14.03 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1830 helix: 0.28 (0.19), residues: 790 sheet: -0.18 (0.29), residues: 320 loop : 0.61 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 86 HIS 0.003 0.001 HIS C 161 PHE 0.014 0.001 PHE E 375 TYR 0.011 0.001 TYR B 337 ARG 0.005 0.000 ARG E 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 185 time to evaluate : 1.793 Fit side-chains REVERT: A 83 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 176 MET cc_start: 0.8574 (mtp) cc_final: 0.8320 (mtt) REVERT: A 270 GLU cc_start: 0.4932 (mm-30) cc_final: 0.4484 (mm-30) REVERT: B 283 MET cc_start: 0.7952 (mmm) cc_final: 0.7742 (mmm) REVERT: B 314 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: C 47 MET cc_start: 0.4928 (mpp) cc_final: 0.4399 (mpp) REVERT: C 190 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8424 (mtm) REVERT: C 227 MET cc_start: 0.7995 (mmm) cc_final: 0.7638 (mmm) REVERT: C 276 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: E 314 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7643 (tt0) outliers start: 42 outliers final: 32 residues processed: 213 average time/residue: 0.2494 time to fit residues: 81.4781 Evaluate side-chains 217 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN D 354 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.089441 restraints weight = 22240.965| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.31 r_work: 0.2902 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15245 Z= 0.179 Angle : 0.582 10.410 20705 Z= 0.268 Chirality : 0.044 0.211 2305 Planarity : 0.004 0.037 2630 Dihedral : 9.456 147.576 2175 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.29 % Allowed : 14.67 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1830 helix: 0.55 (0.19), residues: 760 sheet: -0.05 (0.30), residues: 315 loop : 0.83 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 356 HIS 0.003 0.001 HIS E 161 PHE 0.011 0.001 PHE A 31 TYR 0.010 0.001 TYR B 133 ARG 0.003 0.000 ARG E 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3171.08 seconds wall clock time: 58 minutes 35.25 seconds (3515.25 seconds total)