Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 12:19:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t1y_10363/04_2023/6t1y_10363_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t1y_10363/04_2023/6t1y_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_10363/04_2023/6t1y_10363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t1y_10363/04_2023/6t1y_10363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t1y_10363/04_2023/6t1y_10363_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t1y_10363/04_2023/6t1y_10363_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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: 8.54, per 1000 atoms: 0.57 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: 6.10 Conformation dependent library (CDL) restraints added in 2.3 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: 1.59 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: 4.74 Time building geometry restraints manager: 6.55 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: 8964 29.95 - 59.90: 91 59.90 - 89.86: 45 89.86 - 119.81: 0 119.81 - 149.76: 10 Dihedral angle restraints: 9110 sinusoidal: 3660 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 9107 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.800 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 40.400 Find NCS groups from input model: 0.990 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.600 ------------------------------------------------------------------------------- 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 : 12.351 149.759 5620 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 % 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 *********************** 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 : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 465 average time/residue: 0.3107 time to fit residues: 204.8506 Evaluate side-chains 228 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 223 time to evaluate : 1.880 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 5 average time/residue: 0.1316 time to fit residues: 3.7059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 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: 0.7980 chunk 168 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8144 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 15245 Z= 0.211 Angle : 0.669 8.166 20705 Z= 0.327 Chirality : 0.047 0.210 2305 Planarity : 0.005 0.036 2630 Dihedral : 12.430 159.294 2125 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1830 helix: 0.20 (0.19), residues: 760 sheet: -0.58 (0.28), residues: 310 loop : 0.52 (0.22), residues: 760 *********************** 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 322 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 285 time to evaluate : 1.950 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 308 average time/residue: 0.2605 time to fit residues: 120.4774 Evaluate side-chains 233 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 208 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1597 time to fit residues: 9.4959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 149 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 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 354 GLN B 40 HIS 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.049 15245 Z= 0.432 Angle : 0.723 7.388 20705 Z= 0.354 Chirality : 0.049 0.243 2305 Planarity : 0.005 0.059 2630 Dihedral : 12.178 178.369 2125 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 1.71 % 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: 0.08 (0.19), residues: 1830 helix: 0.04 (0.18), residues: 790 sheet: -0.47 (0.28), residues: 315 loop : 0.64 (0.23), residues: 725 *********************** 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 261 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 1.962 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 249 average time/residue: 0.2603 time to fit residues: 97.6722 Evaluate side-chains 204 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 2.116 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1721 time to fit residues: 7.8883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 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 ** C 354 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15245 Z= 0.179 Angle : 0.592 6.633 20705 Z= 0.279 Chirality : 0.045 0.238 2305 Planarity : 0.004 0.041 2630 Dihedral : 11.448 176.992 2125 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 1.27 % 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: 0.68 (0.19), residues: 1830 helix: 0.62 (0.19), residues: 730 sheet: -0.45 (0.28), residues: 320 loop : 0.99 (0.22), residues: 780 *********************** 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 232 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 212 time to evaluate : 1.838 Fit side-chains outliers start: 20 outliers final: 6 residues processed: 224 average time/residue: 0.2505 time to fit residues: 85.7445 Evaluate side-chains 201 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 195 time to evaluate : 1.673 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1492 time to fit residues: 3.9182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 0.0670 chunk 73 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.061 15245 Z= 0.585 Angle : 0.749 7.266 20705 Z= 0.366 Chirality : 0.051 0.249 2305 Planarity : 0.005 0.062 2630 Dihedral : 11.090 163.761 2125 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.78 % 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: -0.07 (0.19), residues: 1830 helix: -0.08 (0.18), residues: 795 sheet: -0.50 (0.28), residues: 320 loop : 0.54 (0.23), residues: 715 *********************** 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 221 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 1.981 Fit side-chains outliers start: 28 outliers final: 18 residues processed: 208 average time/residue: 0.2492 time to fit residues: 79.8097 Evaluate side-chains 188 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.824 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1581 time to fit residues: 7.3208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 35 optimal weight: 0.0370 chunk 104 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 162 ASN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 15245 Z= 0.163 Angle : 0.584 6.553 20705 Z= 0.273 Chirality : 0.044 0.232 2305 Planarity : 0.004 0.042 2630 Dihedral : 10.442 167.784 2125 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 0.76 % 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: 0.29 (0.20), residues: 1830 helix: 0.24 (0.18), residues: 790 sheet: -0.27 (0.29), residues: 315 loop : 0.66 (0.23), residues: 725 *********************** 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 207 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 1.885 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 201 average time/residue: 0.2490 time to fit residues: 77.1475 Evaluate side-chains 193 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1428 time to fit residues: 5.1415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 15245 Z= 0.411 Angle : 0.673 6.894 20705 Z= 0.321 Chirality : 0.048 0.228 2305 Planarity : 0.005 0.046 2630 Dihedral : 10.358 148.976 2125 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.21 % 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: 0.09 (0.20), residues: 1830 helix: 0.10 (0.18), residues: 790 sheet: -0.40 (0.29), residues: 320 loop : 0.55 (0.23), residues: 720 *********************** 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 195 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 1.895 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 181 average time/residue: 0.2527 time to fit residues: 71.0315 Evaluate side-chains 178 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 1.907 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1406 time to fit residues: 4.5267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8303 moved from start: 0.4574 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= 0.213 Angle : 0.599 7.000 20705 Z= 0.280 Chirality : 0.045 0.226 2305 Planarity : 0.004 0.039 2630 Dihedral : 10.026 147.767 2125 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.51 % 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: 0.16 (0.20), residues: 1830 helix: 0.22 (0.19), residues: 790 sheet: -0.37 (0.29), residues: 320 loop : 0.50 (0.23), residues: 720 *********************** 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 192 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 1.861 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 188 average time/residue: 0.2542 time to fit residues: 73.6537 Evaluate side-chains 181 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 2.060 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1568 time to fit residues: 4.6393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 100 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 165 optimal weight: 0.0870 chunk 109 optimal weight: 5.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 354 GLN ** 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: 0.8292 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 15245 Z= 0.203 Angle : 0.590 7.997 20705 Z= 0.274 Chirality : 0.044 0.219 2305 Planarity : 0.004 0.039 2630 Dihedral : 9.648 142.364 2125 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.32 % 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: 0.25 (0.20), residues: 1830 helix: 0.34 (0.19), residues: 785 sheet: -0.26 (0.29), residues: 320 loop : 0.45 (0.23), residues: 725 *********************** 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 195 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 1.937 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 192 average time/residue: 0.2526 time to fit residues: 75.4512 Evaluate side-chains 175 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 2.024 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1341 time to fit residues: 3.2332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 354 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 15245 Z= 0.252 Angle : 0.616 11.487 20705 Z= 0.287 Chirality : 0.045 0.217 2305 Planarity : 0.004 0.039 2630 Dihedral : 9.615 141.628 2125 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1830 helix: 0.30 (0.19), residues: 785 sheet: -0.24 (0.30), residues: 320 loop : 0.43 (0.23), residues: 725 ********************** 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 180 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.821 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 180 average time/residue: 0.2469 time to fit residues: 69.0656 Evaluate side-chains 175 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 1.817 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1441 time to fit residues: 3.1704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.089786 restraints weight = 22359.132| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.30 r_work: 0.2918 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15245 Z= 0.181 Angle : 0.590 10.468 20705 Z= 0.272 Chirality : 0.044 0.212 2305 Planarity : 0.004 0.040 2630 Dihedral : 9.332 136.584 2125 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1830 helix: 0.39 (0.19), residues: 785 sheet: -0.10 (0.30), residues: 315 loop : 0.47 (0.23), residues: 730 =============================================================================== Job complete usr+sys time: 2985.19 seconds wall clock time: 55 minutes 27.58 seconds (3327.58 seconds total)