Starting phenix.real_space_refine (version: dev) on Wed Feb 22 17:22:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7las_23250/02_2023/7las_23250_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7las_23250/02_2023/7las_23250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7las_23250/02_2023/7las_23250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7las_23250/02_2023/7las_23250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7las_23250/02_2023/7las_23250_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7las_23250/02_2023/7las_23250_trim_updated.pdb" } resolution = 4.4 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= 0.008 sd= 0.157 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 Process input model Symmetric amino acids flipped Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 276": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E ASP 215": "OD1" <-> "OD2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "F PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 210": "OE1" <-> "OE2" Residue "F TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18011 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2901 Classifications: {'peptide': 183} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 170} Chain: "B" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2902 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain: "C" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2901 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain: "D" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2902 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain: "E" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2901 Classifications: {'peptide': 183} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 169} Chain: "F" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2901 Classifications: {'peptide': 183} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 169} Chain: "G" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 284 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "H" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} 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} Time building chain proxies: 8.61, per 1000 atoms: 0.48 Number of scatterers: 18011 At special positions: 0 Unit cell: (104, 98.176, 109.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 18 16.00 P 32 15.00 Mg 4 11.99 O 1803 8.00 N 1579 7.00 C 5951 6.00 H 8624 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 14 sheets defined 29.1% alpha, 9.7% beta 1 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 7.03 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.540A pdb=" N SER A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.671A pdb=" N ALA A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.724A pdb=" N ALA A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 259 through 262 removed outlier: 3.651A pdb=" N TRP A 262 " --> pdb=" O PRO A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.724A pdb=" N CYS B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'C' and resid 122 through 129 removed outlier: 3.625A pdb=" N GLU C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 138 Processing helix chain 'C' and resid 141 through 144 No H-bonds generated for 'chain 'C' and resid 141 through 144' Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 259 through 262 removed outlier: 3.549A pdb=" N TRP C 262 " --> pdb=" O PRO C 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 262' Processing helix chain 'C' and resid 272 through 277 removed outlier: 4.005A pdb=" N ARG C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.559A pdb=" N ALA D 184 " --> pdb=" O LYS D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 271 through 277 removed outlier: 4.575A pdb=" N ARG D 276 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 129 removed outlier: 3.784A pdb=" N GLU E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 138 Processing helix chain 'E' and resid 141 through 144 No H-bonds generated for 'chain 'E' and resid 141 through 144' Processing helix chain 'E' and resid 147 through 156 removed outlier: 3.514A pdb=" N ALA E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 223 through 229 Processing helix chain 'F' and resid 120 through 127 Processing helix chain 'F' and resid 132 through 138 Processing helix chain 'F' and resid 141 through 144 No H-bonds generated for 'chain 'F' and resid 141 through 144' Processing helix chain 'F' and resid 147 through 157 Processing helix chain 'F' and resid 180 through 187 Processing helix chain 'F' and resid 190 through 192 No H-bonds generated for 'chain 'F' and resid 190 through 192' Processing helix chain 'F' and resid 223 through 228 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing sheet with id= A, first strand: chain 'A' and resid 250 through 254 removed outlier: 6.484A pdb=" N ASN A 168 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 253 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS A 170 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER A 280 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 291 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.157A pdb=" N VAL A 211 " --> pdb=" O TYR A 194 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 236 through 239 Processing sheet with id= D, first strand: chain 'B' and resid 250 through 255 removed outlier: 6.020A pdb=" N ASN B 168 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE B 253 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N HIS B 170 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER B 255 " --> pdb=" O HIS B 170 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE B 172 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER B 280 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL B 173 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 282 " --> pdb=" O VAL B 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 193 through 195 removed outlier: 7.146A pdb=" N VAL B 211 " --> pdb=" O TYR B 194 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 236 through 239 removed outlier: 3.554A pdb=" N GLY B 242 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 236 through 239 Processing sheet with id= H, first strand: chain 'C' and resid 289 through 292 removed outlier: 3.953A pdb=" N GLU C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 285 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C 169 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU C 281 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 171 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE C 283 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 173 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS C 285 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 250 through 254 removed outlier: 6.468A pdb=" N ASN D 168 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE D 253 " --> pdb=" O ASN D 168 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS D 170 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER D 280 " --> pdb=" O VAL D 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 236 through 239 Processing sheet with id= K, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.589A pdb=" N VAL E 211 " --> pdb=" O TYR E 194 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 236 through 239 Processing sheet with id= M, first strand: chain 'E' and resid 169 through 172 removed outlier: 7.409A pdb=" N VAL E 171 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 281 " --> pdb=" O VAL E 171 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 170 through 172 removed outlier: 6.736A pdb=" N SER F 280 " --> pdb=" O VAL F 171 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 14.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8612 1.03 - 1.23: 70 1.23 - 1.42: 4120 1.42 - 1.61: 5509 1.61 - 1.81: 24 Bond restraints: 18335 Sorted by residual: bond pdb=" O3' DT G 4 " pdb=" P DT G 5 " ideal model delta sigma weight residual 1.607 1.446 0.161 1.50e-02 4.44e+03 1.16e+02 bond pdb=" CG ASP F 215 " pdb=" OD2 ASP F 215 " ideal model delta sigma weight residual 1.249 1.327 -0.078 1.90e-02 2.77e+03 1.69e+01 bond pdb=" CG ASP C 215 " pdb=" OD1 ASP C 215 " ideal model delta sigma weight residual 1.249 1.326 -0.077 1.90e-02 2.77e+03 1.63e+01 bond pdb=" CG ASP D 215 " pdb=" OD2 ASP D 215 " ideal model delta sigma weight residual 1.249 1.325 -0.076 1.90e-02 2.77e+03 1.60e+01 bond pdb=" CG ASP B 215 " pdb=" OD2 ASP B 215 " ideal model delta sigma weight residual 1.249 1.325 -0.076 1.90e-02 2.77e+03 1.59e+01 ... (remaining 18330 not shown) Histogram of bond angle deviations from ideal: 68.99 - 85.26: 1 85.26 - 101.53: 50 101.53 - 117.80: 23833 117.80 - 134.07: 9060 134.07 - 150.34: 19 Bond angle restraints: 32963 Sorted by residual: angle pdb=" O3' DT G 4 " pdb=" P DT G 5 " pdb=" O5' DT G 5 " ideal model delta sigma weight residual 104.00 68.99 35.01 1.50e+00 4.44e-01 5.45e+02 angle pdb=" C3' DT G 4 " pdb=" O3' DT G 4 " pdb=" P DT G 5 " ideal model delta sigma weight residual 120.20 86.10 34.10 1.50e+00 4.44e-01 5.17e+02 angle pdb=" O3' DT G 4 " pdb=" P DT G 5 " pdb=" OP2 DT G 5 " ideal model delta sigma weight residual 108.00 150.34 -42.34 3.00e+00 1.11e-01 1.99e+02 angle pdb=" C PHE E 217 " pdb=" N TYR E 218 " pdb=" CA TYR E 218 " ideal model delta sigma weight residual 121.98 138.38 -16.40 1.53e+00 4.27e-01 1.15e+02 angle pdb=" C GLU B 209 " pdb=" N GLU B 210 " pdb=" CA GLU B 210 " ideal model delta sigma weight residual 121.54 141.04 -19.50 1.91e+00 2.74e-01 1.04e+02 ... (remaining 32958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 6950 29.56 - 59.12: 386 59.12 - 88.69: 27 88.69 - 118.25: 2 118.25 - 147.81: 4 Dihedral angle restraints: 7369 sinusoidal: 3469 harmonic: 3900 Sorted by residual: dihedral pdb=" CA GLY B 208 " pdb=" C GLY B 208 " pdb=" N GLU B 209 " pdb=" CA GLU B 209 " ideal model delta harmonic sigma weight residual 180.00 78.09 101.91 0 5.00e+00 4.00e-02 4.15e+02 dihedral pdb=" CA GLU B 209 " pdb=" C GLU B 209 " pdb=" N GLU B 210 " pdb=" CA GLU B 210 " ideal model delta harmonic sigma weight residual 180.00 99.48 80.52 0 5.00e+00 4.00e-02 2.59e+02 dihedral pdb=" CA GLY C 208 " pdb=" C GLY C 208 " pdb=" N GLU C 209 " pdb=" CA GLU C 209 " ideal model delta harmonic sigma weight residual 180.00 102.89 77.11 0 5.00e+00 4.00e-02 2.38e+02 ... (remaining 7366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1262 0.086 - 0.172: 213 0.172 - 0.258: 3 0.258 - 0.344: 1 0.344 - 0.429: 1 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CA GLU B 210 " pdb=" N GLU B 210 " pdb=" C GLU B 210 " pdb=" CB GLU B 210 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA GLU A 210 " pdb=" N GLU A 210 " pdb=" C GLU A 210 " pdb=" CB GLU A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CG LEU A 154 " pdb=" CB LEU A 154 " pdb=" CD1 LEU A 154 " pdb=" CD2 LEU A 154 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 1477 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 277 " 0.515 9.50e-02 1.11e+02 1.72e-01 3.13e+01 pdb=" NE ARG D 277 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 277 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 277 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 277 " 0.005 2.00e-02 2.50e+03 pdb="HH11 ARG D 277 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG D 277 " 0.005 2.00e-02 2.50e+03 pdb="HH21 ARG D 277 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 277 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 276 " -0.467 9.50e-02 1.11e+02 1.56e-01 2.57e+01 pdb=" NE ARG C 276 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG C 276 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 276 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 276 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG C 276 " 0.008 2.00e-02 2.50e+03 pdb="HH12 ARG C 276 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG C 276 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 276 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 151 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ALA C 151 " 0.057 2.00e-02 2.50e+03 pdb=" O ALA C 151 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU C 152 " -0.019 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 164 2.03 - 2.67: 25245 2.67 - 3.31: 49779 3.31 - 3.96: 64648 3.96 - 4.60: 100870 Nonbonded interactions: 240706 Sorted by model distance: nonbonded pdb=" CZ2 TRP F 202 " pdb=" OP1 DG G 7 " model vdw 1.386 3.150 nonbonded pdb=" HZ1 LYS E 240 " pdb=" OP1 DC G 6 " model vdw 1.397 1.850 nonbonded pdb=" HZ2 TRP F 202 " pdb=" OP2 DG G 7 " model vdw 1.546 2.450 nonbonded pdb=" HZ1 LYS A 180 " pdb=" O1A ADP A 400 " model vdw 1.591 1.850 nonbonded pdb=" HH TYR D 194 " pdb=" O ASP D 204 " model vdw 1.602 1.850 ... (remaining 240701 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' and (resid 119 through 180 or (resid 181 and (name N or name CA or na \ me C or name O or name CB or name OG or name H or name HA or name HB2 or name HB \ 3)) or resid 182 through 217 or (resid 218 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or n \ ame CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD2 or \ name HE1 or name HE2 or name HH )) or resid 219 through 240 or (resid 241 and (n \ ame N or name CA or name C or name O or name HA2 or name HA3)) or resid 242 thro \ ugh 301)) selection = (chain 'B' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2 or name HH )) or resid 219 through 240 or (r \ esid 241 and (name N or name CA or name C or name O or name HA2 or name HA3)) or \ resid 242 through 301)) selection = (chain 'C' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or resid 181 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HH \ )) or resid 219 through 240 or (resid 241 and (name N or name CA or name C or n \ ame O or name HA2 or name HA3)) or resid 242 through 301)) selection = (chain 'D' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2 or name HH )) or resid 219 through 240 or (r \ esid 241 and (name N or name CA or name C or name O or name HA2 or name HA3)) or \ resid 242 through 301)) selection = (chain 'E' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 240 or (resid 241 and (name N or name CA \ or name C or name O or name HA2 or name HA3)) or resid 242 through 301)) selection = (chain 'F' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2 or name HH )) or resid 219 through 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 32 5.49 5 Mg 4 5.21 5 S 18 5.16 5 C 5951 2.51 5 N 1579 2.21 5 O 1803 1.98 5 H 8624 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.240 Extract box with map and model: 5.290 Check model and map are aligned: 0.260 Process input model: 60.130 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.009 0.161 9711 Z= 0.630 Angle : 1.363 42.339 13393 Z= 0.734 Chirality : 0.060 0.429 1480 Planarity : 0.010 0.223 1576 Dihedral : 18.988 147.811 3476 Min Nonbonded Distance : 1.386 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 7.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.97 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.25), residues: 1086 helix: -0.96 (0.28), residues: 291 sheet: -1.56 (0.44), residues: 141 loop : -2.17 (0.24), residues: 654 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 507 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 435 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 21 residues processed: 472 average time/residue: 0.5845 time to fit residues: 357.8877 Evaluate side-chains 291 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 270 time to evaluate : 1.298 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 3 residues processed: 21 average time/residue: 0.2997 time to fit residues: 11.4865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS D 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9711 Z= 0.222 Angle : 0.760 13.955 13393 Z= 0.372 Chirality : 0.045 0.232 1480 Planarity : 0.005 0.067 1576 Dihedral : 17.609 179.782 1460 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.66 % Favored : 91.16 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.97 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.25), residues: 1086 helix: -0.76 (0.28), residues: 297 sheet: -1.46 (0.41), residues: 166 loop : -2.03 (0.25), residues: 623 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 323 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 322 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 322 average time/residue: 0.5285 time to fit residues: 226.4272 Evaluate side-chains 259 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3334 time to fit residues: 2.3621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN D 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 9711 Z= 0.208 Angle : 0.694 13.122 13393 Z= 0.334 Chirality : 0.043 0.204 1480 Planarity : 0.005 0.080 1576 Dihedral : 17.139 173.065 1460 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.25), residues: 1086 helix: -0.27 (0.29), residues: 296 sheet: -1.43 (0.41), residues: 162 loop : -1.91 (0.25), residues: 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.4953 time to fit residues: 199.3104 Evaluate side-chains 247 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9711 Z= 0.256 Angle : 0.682 13.962 13393 Z= 0.329 Chirality : 0.043 0.206 1480 Planarity : 0.004 0.052 1576 Dihedral : 16.986 176.579 1460 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.67 % Favored : 90.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.25), residues: 1086 helix: -0.17 (0.29), residues: 299 sheet: -1.78 (0.39), residues: 178 loop : -1.84 (0.25), residues: 609 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.5002 time to fit residues: 200.7747 Evaluate side-chains 245 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS D 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 9711 Z= 0.368 Angle : 0.734 12.630 13393 Z= 0.364 Chirality : 0.045 0.252 1480 Planarity : 0.005 0.063 1576 Dihedral : 16.822 164.485 1460 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.31 % Favored : 89.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.25), residues: 1086 helix: -0.45 (0.28), residues: 301 sheet: -1.80 (0.38), residues: 178 loop : -1.98 (0.25), residues: 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.5088 time to fit residues: 198.5102 Evaluate side-chains 240 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 HIS E 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9711 Z= 0.241 Angle : 0.675 13.195 13393 Z= 0.328 Chirality : 0.043 0.161 1480 Planarity : 0.004 0.082 1576 Dihedral : 16.588 143.429 1460 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.21 % Favored : 90.70 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.25), residues: 1086 helix: -0.27 (0.29), residues: 301 sheet: -1.72 (0.42), residues: 158 loop : -1.91 (0.25), residues: 627 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.5106 time to fit residues: 188.6457 Evaluate side-chains 243 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9711 Z= 0.201 Angle : 0.656 12.605 13393 Z= 0.315 Chirality : 0.042 0.156 1480 Planarity : 0.004 0.049 1576 Dihedral : 16.272 131.276 1460 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.85 (0.25), residues: 1086 helix: -0.01 (0.30), residues: 301 sheet: -1.43 (0.42), residues: 163 loop : -1.84 (0.25), residues: 622 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.5179 time to fit residues: 198.7576 Evaluate side-chains 240 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 0.0170 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.6712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9711 Z= 0.177 Angle : 0.649 12.543 13393 Z= 0.309 Chirality : 0.042 0.160 1480 Planarity : 0.004 0.065 1576 Dihedral : 16.096 126.900 1460 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.75 (0.25), residues: 1086 helix: 0.14 (0.30), residues: 304 sheet: -1.36 (0.42), residues: 163 loop : -1.83 (0.25), residues: 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.5067 time to fit residues: 189.9299 Evaluate side-chains 236 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.531 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.6906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9711 Z= 0.213 Angle : 0.658 11.578 13393 Z= 0.315 Chirality : 0.042 0.163 1480 Planarity : 0.004 0.043 1576 Dihedral : 15.982 120.068 1460 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.70 (0.26), residues: 1086 helix: 0.15 (0.30), residues: 304 sheet: -1.22 (0.42), residues: 167 loop : -1.82 (0.25), residues: 615 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.4978 time to fit residues: 177.2628 Evaluate side-chains 227 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9711 Z= 0.260 Angle : 0.667 11.525 13393 Z= 0.323 Chirality : 0.043 0.158 1480 Planarity : 0.004 0.043 1576 Dihedral : 15.966 116.186 1460 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.82 (0.25), residues: 1086 helix: -0.05 (0.30), residues: 307 sheet: -1.27 (0.41), residues: 171 loop : -1.84 (0.25), residues: 608 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.4990 time to fit residues: 176.4666 Evaluate side-chains 223 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.497 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 256 ASN B 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104581 restraints weight = 47503.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108889 restraints weight = 25303.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111793 restraints weight = 16492.955| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.7171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9711 Z= 0.171 Angle : 0.642 12.955 13393 Z= 0.305 Chirality : 0.042 0.155 1480 Planarity : 0.004 0.041 1576 Dihedral : 15.784 110.205 1460 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: -1.60 (0.26), residues: 1086 helix: 0.22 (0.31), residues: 304 sheet: -1.02 (0.42), residues: 167 loop : -1.80 (0.25), residues: 615 =============================================================================== Job complete usr+sys time: 4866.90 seconds wall clock time: 86 minutes 21.73 seconds (5181.73 seconds total)