Starting phenix.real_space_refine on Sun Mar 17 14:06:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7las_23250/03_2024/7las_23250_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7las_23250/03_2024/7las_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_23250/03_2024/7las_23250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7las_23250/03_2024/7las_23250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7las_23250/03_2024/7las_23250_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7las_23250/03_2024/7las_23250_trim_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.21, per 1000 atoms: 0.51 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: 14.26 Conformation dependent library (CDL) restraints added in 2.0 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: 9.04 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: 5.74 Time building geometry restraints manager: 14.79 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: 8070 29.56 - 59.12: 530 59.12 - 88.69: 29 88.69 - 118.25: 2 118.25 - 147.81: 4 Dihedral angle restraints: 8635 sinusoidal: 4735 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 8632 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 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: 1.090 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: 0.250 Extract box with map and model: 4.530 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 65.420 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 1.366 42.339 13393 Z= 0.740 Chirality : 0.060 0.429 1480 Planarity : 0.010 0.223 1576 Dihedral : 19.048 147.811 3496 Min Nonbonded Distance : 1.386 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 7.55 % Allowed : 10.38 % Favored : 82.08 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 202 HIS 0.005 0.002 HIS D 170 PHE 0.026 0.003 PHE B 217 TYR 0.029 0.003 TYR B 206 ARG 0.009 0.001 ARG C 228 *********************** 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 : 1.330 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 REVERT: A 147 PHE cc_start: 0.9056 (p90) cc_final: 0.8645 (p90) REVERT: A 249 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7791 (mtm-85) REVERT: B 137 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8036 (mt-10) REVERT: B 142 THR cc_start: 0.9280 (m) cc_final: 0.8899 (t) REVERT: B 146 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8254 (p0) REVERT: B 161 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: B 204 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8418 (t70) REVERT: B 225 ASP cc_start: 0.8940 (t0) cc_final: 0.8684 (t0) REVERT: B 275 TYR cc_start: 0.8591 (m-10) cc_final: 0.8335 (m-80) REVERT: C 128 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: C 132 LEU cc_start: 0.8789 (mp) cc_final: 0.8506 (tp) REVERT: C 271 VAL cc_start: 0.9162 (m) cc_final: 0.8958 (p) REVERT: C 283 PHE cc_start: 0.7302 (t80) cc_final: 0.6618 (t80) REVERT: D 161 GLN cc_start: 0.8214 (tt0) cc_final: 0.7901 (tp40) REVERT: D 178 CYS cc_start: 0.9034 (p) cc_final: 0.8538 (p) REVERT: D 180 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8021 (mtmt) REVERT: D 209 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6996 (mm-30) REVERT: D 276 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7665 (mmm160) REVERT: D 278 ILE cc_start: 0.9071 (mm) cc_final: 0.8554 (mm) REVERT: D 285 LYS cc_start: 0.6609 (ptpt) cc_final: 0.6271 (ptpt) REVERT: E 166 LYS cc_start: 0.8101 (tptp) cc_final: 0.7359 (ptpp) REVERT: E 207 HIS cc_start: 0.6774 (t70) cc_final: 0.6124 (t70) REVERT: E 220 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.8543 (p90) REVERT: E 236 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9031 (p) REVERT: E 243 THR cc_start: 0.7730 (p) cc_final: 0.7450 (p) REVERT: E 247 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.8842 (pp) REVERT: E 271 VAL cc_start: 0.7521 (m) cc_final: 0.7046 (t) REVERT: E 275 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: F 137 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8333 (tm-30) REVERT: F 140 PRO cc_start: 0.9326 (Cg_endo) cc_final: 0.9019 (Cg_exo) REVERT: F 201 LYS cc_start: 0.8157 (mppt) cc_final: 0.7599 (tptt) REVERT: F 228 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8216 (ttm110) REVERT: F 232 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6914 (mtm180) REVERT: F 247 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8370 (pt) REVERT: F 258 THR cc_start: 0.8419 (p) cc_final: 0.7823 (t) REVERT: F 276 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7175 (mmm160) outliers start: 72 outliers final: 21 residues processed: 472 average time/residue: 0.5812 time to fit residues: 356.5927 Evaluate side-chains 317 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 284 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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: 0.0870 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 146 ASN B 168 ASN D 168 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9711 Z= 0.227 Angle : 0.771 15.510 13393 Z= 0.386 Chirality : 0.046 0.271 1480 Planarity : 0.005 0.073 1576 Dihedral : 17.713 178.040 1480 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.88 % 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: -0.64 (0.28), residues: 297 sheet: -1.46 (0.41), residues: 166 loop : -1.98 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 202 HIS 0.006 0.001 HIS C 139 PHE 0.018 0.002 PHE F 283 TYR 0.022 0.002 TYR E 275 ARG 0.007 0.001 ARG B 163 *********************** 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 336 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 1.541 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: A 147 PHE cc_start: 0.9000 (p90) cc_final: 0.8424 (p90) REVERT: A 201 LYS cc_start: 0.7700 (pttp) cc_final: 0.7328 (pttp) REVERT: A 218 TYR cc_start: 0.7503 (p90) cc_final: 0.7248 (p90) REVERT: B 161 GLN cc_start: 0.7911 (tp-100) cc_final: 0.7615 (mt0) REVERT: B 168 ASN cc_start: 0.8657 (m-40) cc_final: 0.8290 (m110) REVERT: B 225 ASP cc_start: 0.8893 (t0) cc_final: 0.8659 (t0) REVERT: B 281 LEU cc_start: 0.8697 (tt) cc_final: 0.8489 (tt) REVERT: B 299 VAL cc_start: 0.5504 (m) cc_final: 0.5228 (m) REVERT: D 148 ARG cc_start: 0.8318 (tpt90) cc_final: 0.8058 (mtm-85) REVERT: D 152 GLU cc_start: 0.8938 (tp30) cc_final: 0.8726 (tp30) REVERT: D 161 GLN cc_start: 0.8644 (mt0) cc_final: 0.8086 (tp-100) REVERT: D 178 CYS cc_start: 0.8793 (p) cc_final: 0.8372 (p) REVERT: D 276 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7462 (tpm170) REVERT: D 278 ILE cc_start: 0.9173 (mm) cc_final: 0.8796 (mm) REVERT: E 166 LYS cc_start: 0.8009 (tptp) cc_final: 0.7378 (ptpp) REVERT: E 207 HIS cc_start: 0.6627 (t70) cc_final: 0.6151 (t70) REVERT: E 247 LEU cc_start: 0.8981 (pt) cc_final: 0.8499 (pp) REVERT: F 137 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8306 (tm-30) REVERT: F 140 PRO cc_start: 0.9336 (Cg_endo) cc_final: 0.8910 (Cg_exo) REVERT: F 196 LYS cc_start: 0.8695 (tttp) cc_final: 0.8419 (tttp) REVERT: F 216 ASP cc_start: 0.7785 (t0) cc_final: 0.7131 (p0) REVERT: F 217 PHE cc_start: 0.7917 (t80) cc_final: 0.7678 (t80) REVERT: F 224 ASP cc_start: 0.8617 (p0) cc_final: 0.8312 (p0) REVERT: F 232 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.7029 (mtm180) REVERT: F 276 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7174 (mmm160) REVERT: F 278 ILE cc_start: 0.8680 (mt) cc_final: 0.8477 (mt) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.5597 time to fit residues: 246.4255 Evaluate side-chains 277 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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: 4.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 0.3980 chunk 99 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9711 Z= 0.204 Angle : 0.697 13.866 13393 Z= 0.341 Chirality : 0.044 0.193 1480 Planarity : 0.005 0.050 1576 Dihedral : 17.166 179.303 1480 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: -1.95 (0.25), residues: 1086 helix: -0.18 (0.29), residues: 296 sheet: -1.38 (0.42), residues: 162 loop : -1.87 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 203 HIS 0.005 0.001 HIS B 207 PHE 0.010 0.001 PHE B 217 TYR 0.030 0.002 TYR F 194 ARG 0.006 0.000 ARG A 163 *********************** 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 309 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.459 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: A 134 THR cc_start: 0.8491 (m) cc_final: 0.8250 (p) REVERT: A 147 PHE cc_start: 0.9081 (p90) cc_final: 0.8532 (p90) REVERT: A 201 LYS cc_start: 0.7686 (pttp) cc_final: 0.7323 (ptmm) REVERT: A 207 HIS cc_start: 0.7307 (m90) cc_final: 0.7043 (m90) REVERT: A 227 LEU cc_start: 0.8368 (tp) cc_final: 0.7961 (mm) REVERT: B 161 GLN cc_start: 0.7908 (tp-100) cc_final: 0.7630 (mt0) REVERT: B 168 ASN cc_start: 0.8682 (m-40) cc_final: 0.8309 (m110) REVERT: B 225 ASP cc_start: 0.8929 (t0) cc_final: 0.8705 (t0) REVERT: B 281 LEU cc_start: 0.8701 (tt) cc_final: 0.8453 (tt) REVERT: D 148 ARG cc_start: 0.8405 (tpt90) cc_final: 0.8192 (mtm-85) REVERT: D 161 GLN cc_start: 0.8694 (mt0) cc_final: 0.8074 (tp-100) REVERT: D 178 CYS cc_start: 0.8841 (p) cc_final: 0.8408 (p) REVERT: D 238 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6594 (mt-10) REVERT: D 276 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7442 (tpm170) REVERT: D 278 ILE cc_start: 0.9186 (mm) cc_final: 0.8844 (mm) REVERT: E 166 LYS cc_start: 0.8094 (tptp) cc_final: 0.7343 (ptpp) REVERT: E 207 HIS cc_start: 0.6654 (t70) cc_final: 0.6139 (t70) REVERT: E 227 LEU cc_start: 0.8825 (mt) cc_final: 0.8484 (mt) REVERT: F 137 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8310 (tm-30) REVERT: F 140 PRO cc_start: 0.9289 (Cg_endo) cc_final: 0.8949 (Cg_exo) REVERT: F 142 THR cc_start: 0.8470 (p) cc_final: 0.8190 (p) REVERT: F 196 LYS cc_start: 0.8580 (tttp) cc_final: 0.8299 (tptt) REVERT: F 200 ASN cc_start: 0.7163 (p0) cc_final: 0.6697 (m-40) REVERT: F 224 ASP cc_start: 0.8612 (p0) cc_final: 0.8379 (p0) REVERT: F 276 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7158 (mmm-85) REVERT: F 278 ILE cc_start: 0.8674 (mt) cc_final: 0.8464 (mt) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.5310 time to fit residues: 215.7895 Evaluate side-chains 271 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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: 2.9990 chunk 75 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.7798 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9711 Z= 0.356 Angle : 0.736 13.684 13393 Z= 0.372 Chirality : 0.045 0.227 1480 Planarity : 0.006 0.139 1576 Dihedral : 16.982 174.620 1480 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: -2.19 (0.25), residues: 1086 helix: -0.33 (0.29), residues: 299 sheet: -1.78 (0.39), residues: 175 loop : -1.97 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 202 HIS 0.006 0.001 HIS C 139 PHE 0.022 0.002 PHE C 298 TYR 0.024 0.002 TYR F 206 ARG 0.006 0.001 ARG B 199 *********************** 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 296 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.409 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: A 147 PHE cc_start: 0.9059 (p90) cc_final: 0.8553 (p90) REVERT: A 201 LYS cc_start: 0.7683 (pttp) cc_final: 0.7345 (pttp) REVERT: A 206 TYR cc_start: 0.8656 (t80) cc_final: 0.8368 (t80) REVERT: A 207 HIS cc_start: 0.7360 (m90) cc_final: 0.7072 (m90) REVERT: B 161 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7585 (mt0) REVERT: B 168 ASN cc_start: 0.8757 (m-40) cc_final: 0.8353 (m110) REVERT: B 225 ASP cc_start: 0.9079 (t0) cc_final: 0.8758 (t0) REVERT: C 138 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8616 (mm-40) REVERT: D 137 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7922 (tm-30) REVERT: D 148 ARG cc_start: 0.8554 (tpt90) cc_final: 0.8310 (mtm-85) REVERT: D 161 GLN cc_start: 0.8695 (mt0) cc_final: 0.8113 (tp-100) REVERT: D 178 CYS cc_start: 0.8940 (p) cc_final: 0.8529 (p) REVERT: D 217 PHE cc_start: 0.9319 (t80) cc_final: 0.8560 (t80) REVERT: D 276 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7750 (tpt90) REVERT: E 166 LYS cc_start: 0.8202 (tptp) cc_final: 0.7451 (ptpp) REVERT: E 247 LEU cc_start: 0.8982 (pt) cc_final: 0.8610 (pp) REVERT: F 137 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8282 (tm-30) REVERT: F 140 PRO cc_start: 0.9284 (Cg_endo) cc_final: 0.8951 (Cg_exo) REVERT: F 142 THR cc_start: 0.8347 (p) cc_final: 0.8085 (p) REVERT: F 201 LYS cc_start: 0.7183 (tptt) cc_final: 0.6252 (tptt) REVERT: F 276 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.7177 (mmm160) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.5058 time to fit residues: 198.6260 Evaluate side-chains 249 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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: 8.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9711 Z= 0.307 Angle : 0.696 12.958 13393 Z= 0.350 Chirality : 0.045 0.207 1480 Planarity : 0.005 0.050 1576 Dihedral : 16.716 157.071 1480 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -2.12 (0.25), residues: 1086 helix: -0.17 (0.29), residues: 299 sheet: -1.91 (0.41), residues: 158 loop : -1.95 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 202 HIS 0.004 0.001 HIS C 139 PHE 0.012 0.002 PHE D 147 TYR 0.033 0.002 TYR F 194 ARG 0.008 0.001 ARG B 199 *********************** 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 290 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.437 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: A 147 PHE cc_start: 0.9061 (p90) cc_final: 0.8553 (p90) REVERT: A 168 ASN cc_start: 0.8359 (m110) cc_final: 0.8146 (m110) REVERT: A 200 ASN cc_start: 0.7839 (t0) cc_final: 0.7586 (t0) REVERT: A 201 LYS cc_start: 0.7646 (pttp) cc_final: 0.7272 (pttp) REVERT: A 206 TYR cc_start: 0.8770 (t80) cc_final: 0.8486 (t80) REVERT: B 161 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7653 (mt0) REVERT: B 168 ASN cc_start: 0.8733 (m-40) cc_final: 0.8369 (m110) REVERT: B 183 TRP cc_start: 0.8372 (t60) cc_final: 0.7630 (t-100) REVERT: C 138 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8718 (mm-40) REVERT: D 148 ARG cc_start: 0.8525 (tpt90) cc_final: 0.8183 (ttp-110) REVERT: D 161 GLN cc_start: 0.8549 (mt0) cc_final: 0.7966 (tp-100) REVERT: D 178 CYS cc_start: 0.8984 (p) cc_final: 0.8579 (p) REVERT: D 217 PHE cc_start: 0.9378 (t80) cc_final: 0.8649 (t80) REVERT: D 238 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6625 (mp0) REVERT: D 247 LEU cc_start: 0.9275 (mt) cc_final: 0.9051 (mt) REVERT: D 276 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7704 (tpt90) REVERT: D 278 ILE cc_start: 0.9295 (mm) cc_final: 0.9044 (mm) REVERT: E 166 LYS cc_start: 0.8274 (tptp) cc_final: 0.7459 (ptpp) REVERT: E 247 LEU cc_start: 0.9060 (pt) cc_final: 0.8592 (pp) REVERT: F 137 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8288 (tm-30) REVERT: F 140 PRO cc_start: 0.9258 (Cg_endo) cc_final: 0.8914 (Cg_exo) REVERT: F 142 THR cc_start: 0.8371 (p) cc_final: 0.8112 (p) REVERT: F 189 ASP cc_start: 0.7135 (t0) cc_final: 0.6762 (m-30) REVERT: F 201 LYS cc_start: 0.6944 (tptt) cc_final: 0.6272 (tptt) REVERT: F 276 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7165 (mmm160) REVERT: F 278 ILE cc_start: 0.8775 (mt) cc_final: 0.8526 (mt) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.5196 time to fit residues: 199.1504 Evaluate side-chains 251 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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: 6.9990 chunk 95 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9711 Z= 0.336 Angle : 0.707 11.647 13393 Z= 0.354 Chirality : 0.044 0.191 1480 Planarity : 0.005 0.048 1576 Dihedral : 16.485 134.693 1480 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -2.28 (0.25), residues: 1086 helix: -0.47 (0.28), residues: 302 sheet: -1.88 (0.37), residues: 178 loop : -1.98 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 220 HIS 0.004 0.001 HIS A 207 PHE 0.050 0.002 PHE B 283 TYR 0.015 0.002 TYR F 194 ARG 0.005 0.001 ARG B 199 *********************** 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 286 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.459 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: A 147 PHE cc_start: 0.9075 (p90) cc_final: 0.8584 (p90) REVERT: A 168 ASN cc_start: 0.8356 (m110) cc_final: 0.8125 (m110) REVERT: A 206 TYR cc_start: 0.8855 (t80) cc_final: 0.8479 (t80) REVERT: B 161 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7455 (tt0) REVERT: B 168 ASN cc_start: 0.8755 (m-40) cc_final: 0.8413 (m110) REVERT: B 180 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8212 (mtmt) REVERT: C 138 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8857 (mm-40) REVERT: D 148 ARG cc_start: 0.8553 (tpt90) cc_final: 0.8202 (ttp-110) REVERT: D 161 GLN cc_start: 0.8580 (mt0) cc_final: 0.8015 (tp-100) REVERT: D 178 CYS cc_start: 0.8990 (p) cc_final: 0.8585 (p) REVERT: D 238 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6739 (mp0) REVERT: D 276 ARG cc_start: 0.8196 (ttm110) cc_final: 0.7682 (tpt90) REVERT: E 166 LYS cc_start: 0.8314 (tptp) cc_final: 0.7507 (ptpp) REVERT: E 247 LEU cc_start: 0.9002 (pt) cc_final: 0.8558 (pp) REVERT: F 137 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8263 (tm-30) REVERT: F 142 THR cc_start: 0.8436 (p) cc_final: 0.8169 (p) REVERT: F 196 LYS cc_start: 0.8757 (tttt) cc_final: 0.8531 (tttp) REVERT: F 201 LYS cc_start: 0.6991 (tptt) cc_final: 0.6319 (tptt) REVERT: F 224 ASP cc_start: 0.8736 (p0) cc_final: 0.8516 (p0) REVERT: F 276 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.7118 (mmm160) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.5278 time to fit residues: 199.1741 Evaluate side-chains 243 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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: 4.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 E 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.6476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9711 Z= 0.297 Angle : 0.695 13.903 13393 Z= 0.348 Chirality : 0.044 0.193 1480 Planarity : 0.005 0.051 1576 Dihedral : 16.301 124.396 1480 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.10 % Allowed : 1.26 % Favored : 98.64 % 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: -2.22 (0.25), residues: 1086 helix: -0.39 (0.29), residues: 302 sheet: -1.77 (0.37), residues: 187 loop : -1.98 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 202 HIS 0.006 0.001 HIS A 207 PHE 0.024 0.002 PHE B 283 TYR 0.018 0.002 TYR F 206 ARG 0.006 0.001 ARG A 163 *********************** 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 277 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 1.465 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: A 147 PHE cc_start: 0.9076 (p90) cc_final: 0.8550 (p90) REVERT: A 168 ASN cc_start: 0.8333 (m110) cc_final: 0.8102 (m110) REVERT: A 200 ASN cc_start: 0.7415 (t0) cc_final: 0.7138 (t0) REVERT: A 206 TYR cc_start: 0.8856 (t80) cc_final: 0.8363 (t80) REVERT: B 161 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7465 (tt0) REVERT: B 168 ASN cc_start: 0.8763 (m-40) cc_final: 0.8377 (m110) REVERT: B 216 ASP cc_start: 0.8680 (m-30) cc_final: 0.8423 (m-30) REVERT: D 148 ARG cc_start: 0.8553 (tpt90) cc_final: 0.8224 (ttp-110) REVERT: D 161 GLN cc_start: 0.8582 (mt0) cc_final: 0.8054 (tp-100) REVERT: D 178 CYS cc_start: 0.8983 (p) cc_final: 0.8601 (p) REVERT: D 238 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7069 (mp0) REVERT: D 276 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7599 (mmm160) REVERT: E 166 LYS cc_start: 0.8331 (tptp) cc_final: 0.7526 (ptpp) REVERT: E 247 LEU cc_start: 0.8982 (pt) cc_final: 0.8572 (pp) REVERT: F 137 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8207 (tm-30) REVERT: F 142 THR cc_start: 0.8470 (p) cc_final: 0.8185 (p) REVERT: F 165 TRP cc_start: 0.8453 (p90) cc_final: 0.7945 (p90) REVERT: F 201 LYS cc_start: 0.7066 (tptt) cc_final: 0.6391 (tptt) REVERT: F 224 ASP cc_start: 0.8716 (p0) cc_final: 0.8464 (p0) REVERT: F 276 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7116 (mmm160) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.5185 time to fit residues: 190.1417 Evaluate side-chains 248 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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: 5.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 0.2980 chunk 96 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9711 Z= 0.168 Angle : 0.649 13.016 13393 Z= 0.319 Chirality : 0.043 0.170 1480 Planarity : 0.004 0.045 1576 Dihedral : 16.037 119.635 1480 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 302 sheet: -1.43 (0.42), residues: 163 loop : -1.84 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 203 HIS 0.006 0.001 HIS A 207 PHE 0.031 0.001 PHE E 147 TYR 0.013 0.001 TYR E 233 ARG 0.005 0.001 ARG B 199 *********************** 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 289 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.592 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: A 147 PHE cc_start: 0.9079 (p90) cc_final: 0.8577 (p90) REVERT: A 168 ASN cc_start: 0.8279 (m110) cc_final: 0.8060 (m110) REVERT: A 200 ASN cc_start: 0.7354 (t0) cc_final: 0.7072 (m-40) REVERT: A 206 TYR cc_start: 0.8726 (t80) cc_final: 0.8211 (t80) REVERT: A 216 ASP cc_start: 0.8256 (t70) cc_final: 0.7870 (m-30) REVERT: B 161 GLN cc_start: 0.8056 (tp-100) cc_final: 0.7533 (tt0) REVERT: B 168 ASN cc_start: 0.8800 (m-40) cc_final: 0.8394 (m110) REVERT: D 129 SER cc_start: 0.7857 (p) cc_final: 0.7591 (p) REVERT: D 148 ARG cc_start: 0.8472 (tpt90) cc_final: 0.8144 (ttp-110) REVERT: D 161 GLN cc_start: 0.8520 (mt0) cc_final: 0.7971 (tp-100) REVERT: D 178 CYS cc_start: 0.8989 (p) cc_final: 0.8597 (p) REVERT: D 217 PHE cc_start: 0.9384 (t80) cc_final: 0.8650 (t80) REVERT: D 238 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7073 (mp0) REVERT: D 276 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7513 (mmm160) REVERT: E 166 LYS cc_start: 0.8318 (tptp) cc_final: 0.7488 (ptpp) REVERT: E 193 THR cc_start: 0.9086 (p) cc_final: 0.8865 (p) REVERT: E 247 LEU cc_start: 0.8941 (pt) cc_final: 0.8511 (pp) REVERT: F 142 THR cc_start: 0.8448 (p) cc_final: 0.8128 (p) REVERT: F 165 TRP cc_start: 0.8370 (p90) cc_final: 0.7839 (p90) REVERT: F 201 LYS cc_start: 0.7162 (tptt) cc_final: 0.6485 (tptt) REVERT: F 224 ASP cc_start: 0.8688 (p0) cc_final: 0.8411 (p0) REVERT: F 276 ARG cc_start: 0.7631 (ttm-80) cc_final: 0.7064 (mmm160) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.5220 time to fit residues: 199.0718 Evaluate side-chains 255 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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: 0.8980 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 207 HIS A 256 ASN B 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9711 Z= 0.166 Angle : 0.635 12.707 13393 Z= 0.311 Chirality : 0.042 0.159 1480 Planarity : 0.004 0.046 1576 Dihedral : 15.816 112.350 1480 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.10 % Allowed : 0.94 % Favored : 98.95 % 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: -1.63 (0.26), residues: 1086 helix: 0.22 (0.30), residues: 308 sheet: -1.20 (0.42), residues: 163 loop : -1.78 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 223 HIS 0.006 0.001 HIS B 207 PHE 0.020 0.001 PHE E 147 TYR 0.014 0.002 TYR B 194 ARG 0.005 0.001 ARG B 199 *********************** 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 280 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 279 time to evaluate : 1.500 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: A 147 PHE cc_start: 0.9118 (p90) cc_final: 0.8582 (p90) REVERT: A 206 TYR cc_start: 0.8721 (t80) cc_final: 0.8124 (t80) REVERT: A 216 ASP cc_start: 0.8206 (t70) cc_final: 0.7837 (m-30) REVERT: B 161 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7582 (mt0) REVERT: B 168 ASN cc_start: 0.8833 (m-40) cc_final: 0.8375 (m110) REVERT: B 183 TRP cc_start: 0.8307 (t60) cc_final: 0.8082 (t60) REVERT: D 129 SER cc_start: 0.7802 (p) cc_final: 0.7566 (p) REVERT: D 148 ARG cc_start: 0.8476 (tpt90) cc_final: 0.8179 (ttp-110) REVERT: D 161 GLN cc_start: 0.8518 (mt0) cc_final: 0.7969 (tp-100) REVERT: D 178 CYS cc_start: 0.8950 (p) cc_final: 0.8538 (p) REVERT: D 217 PHE cc_start: 0.9374 (t80) cc_final: 0.8686 (t80) REVERT: D 238 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7090 (mp0) REVERT: D 276 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7453 (mmm160) REVERT: E 166 LYS cc_start: 0.8319 (tptp) cc_final: 0.7479 (ptpp) REVERT: E 247 LEU cc_start: 0.8897 (pt) cc_final: 0.8513 (pp) REVERT: F 137 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8214 (tm-30) REVERT: F 142 THR cc_start: 0.8372 (p) cc_final: 0.8051 (p) REVERT: F 165 TRP cc_start: 0.8348 (p90) cc_final: 0.7809 (p90) REVERT: F 201 LYS cc_start: 0.7199 (tptt) cc_final: 0.6500 (tptt) REVERT: F 224 ASP cc_start: 0.8631 (p0) cc_final: 0.8346 (p0) REVERT: F 276 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.7083 (mmm160) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.5292 time to fit residues: 196.1162 Evaluate side-chains 251 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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: 6.9990 chunk 72 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 207 HIS B 139 HIS B 146 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9711 Z= 0.374 Angle : 0.714 11.840 13393 Z= 0.363 Chirality : 0.045 0.187 1480 Planarity : 0.005 0.069 1576 Dihedral : 16.061 109.700 1480 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.10 % Allowed : 0.63 % Favored : 99.27 % 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: -2.10 (0.25), residues: 1086 helix: -0.49 (0.28), residues: 308 sheet: -1.33 (0.42), residues: 164 loop : -1.93 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 202 HIS 0.006 0.002 HIS B 139 PHE 0.022 0.002 PHE E 147 TYR 0.015 0.002 TYR A 206 ARG 0.006 0.001 ARG B 199 ********************** 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 273 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 1.484 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: A 168 ASN cc_start: 0.8322 (m110) cc_final: 0.8081 (m110) REVERT: A 216 ASP cc_start: 0.8342 (t70) cc_final: 0.7941 (m-30) REVERT: B 161 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7542 (tt0) REVERT: B 168 ASN cc_start: 0.8795 (m-40) cc_final: 0.8400 (m110) REVERT: B 216 ASP cc_start: 0.8651 (m-30) cc_final: 0.8358 (m-30) REVERT: D 128 GLU cc_start: 0.8480 (pp20) cc_final: 0.8108 (pp20) REVERT: D 148 ARG cc_start: 0.8616 (tpt90) cc_final: 0.8287 (ttp-110) REVERT: D 161 GLN cc_start: 0.8528 (mt0) cc_final: 0.7991 (tp-100) REVERT: D 238 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7122 (mp0) REVERT: D 276 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7512 (mmm160) REVERT: E 166 LYS cc_start: 0.8336 (tptp) cc_final: 0.7554 (ptpp) REVERT: E 247 LEU cc_start: 0.8947 (pt) cc_final: 0.8582 (pp) REVERT: F 142 THR cc_start: 0.8403 (p) cc_final: 0.8107 (p) REVERT: F 165 TRP cc_start: 0.8405 (p90) cc_final: 0.7783 (p90) REVERT: F 201 LYS cc_start: 0.7229 (tptt) cc_final: 0.6510 (tptt) REVERT: F 224 ASP cc_start: 0.8688 (p0) cc_final: 0.8416 (p0) REVERT: F 275 TYR cc_start: 0.7328 (m-10) cc_final: 0.7113 (m-10) REVERT: F 276 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7106 (mmm160) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.5544 time to fit residues: 200.9797 Evaluate side-chains 234 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 89 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS E 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.101788 restraints weight = 47403.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.106044 restraints weight = 25456.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.108918 restraints weight = 16673.068| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.7097 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= 0.171 Angle : 0.646 12.148 13393 Z= 0.319 Chirality : 0.043 0.158 1480 Planarity : 0.004 0.048 1576 Dihedral : 15.810 104.829 1480 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.77 (0.25), residues: 1086 helix: -0.05 (0.29), residues: 308 sheet: -1.17 (0.42), residues: 169 loop : -1.82 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 220 HIS 0.006 0.001 HIS E 207 PHE 0.015 0.001 PHE B 283 TYR 0.014 0.001 TYR E 233 ARG 0.008 0.001 ARG C 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5078.34 seconds wall clock time: 89 minutes 50.93 seconds (5390.93 seconds total)