Starting phenix.real_space_refine (version: dev) on Wed Feb 22 14:56:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lar_23249/02_2023/7lar_23249_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lar_23249/02_2023/7lar_23249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lar_23249/02_2023/7lar_23249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lar_23249/02_2023/7lar_23249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lar_23249/02_2023/7lar_23249_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lar_23249/02_2023/7lar_23249_trim_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.177 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 276": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E ASP 215": "OD1" <-> "OD2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "F PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 210": "OE1" <-> "OE2" Residue "F TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 17714 Number of models: 1 Model: "" Number of chains: 11 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: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 194 Classifications: {'DNA': 6} Modifications used: {'3*END': 1, 'p5*END': 1} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.91, per 1000 atoms: 0.50 Number of scatterers: 17714 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 14 15.00 Mg 4 11.99 O 1697 8.00 N 1508 7.00 C 5776 6.00 H 8697 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: 14.24 Conformation dependent library (CDL) restraints added in 1.5 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 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 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: 4.576A 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: 6.857A pdb=" N SER A 280 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.770A 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: 6.158A 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: 6.019A 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: 6.735A 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: 3.952A pdb=" N GLU C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS C 285 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 6.747A 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: 6.746A 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: 6.599A 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: 7.284A 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: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 14.86 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: 8685 1.03 - 1.23: 78 1.23 - 1.42: 3928 1.42 - 1.62: 5278 1.62 - 1.81: 24 Bond restraints: 17993 Sorted by residual: 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 1.67e+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 1.65e+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 1.61e+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 E 215 " pdb=" OD1 ASP E 215 " ideal model delta sigma weight residual 1.249 1.322 -0.073 1.90e-02 2.77e+03 1.49e+01 ... (remaining 17988 not shown) Histogram of bond angle deviations from ideal: 99.77 - 108.02: 3466 108.02 - 116.27: 19356 116.27 - 124.52: 8498 124.52 - 132.77: 1113 132.77 - 141.01: 67 Bond angle restraints: 32500 Sorted by residual: angle pdb=" C PHE E 217 " pdb=" N TYR E 218 " pdb=" CA TYR E 218 " ideal model delta sigma weight residual 121.98 138.41 -16.43 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 121.54 141.01 -19.47 1.91e+00 2.74e-01 1.04e+02 angle pdb=" C GLU A 209 " pdb=" N GLU A 210 " pdb=" CA GLU A 210 " ideal model delta sigma weight residual 121.54 140.75 -19.21 1.91e+00 2.74e-01 1.01e+02 angle pdb=" C LYS F 240 " pdb=" N GLY F 241 " pdb=" CA GLY F 241 " ideal model delta sigma weight residual 121.51 134.99 -13.48 1.52e+00 4.33e-01 7.86e+01 angle pdb=" N GLU B 210 " pdb=" CA GLU B 210 " pdb=" C GLU B 210 " ideal model delta sigma weight residual 110.80 127.68 -16.88 2.13e+00 2.20e-01 6.28e+01 ... (remaining 32495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 6890 29.56 - 59.12: 276 59.12 - 88.67: 27 88.67 - 118.23: 2 118.23 - 147.79: 4 Dihedral angle restraints: 7199 sinusoidal: 3299 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 99.46 80.54 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 180.00 102.92 77.08 0 5.00e+00 4.00e-02 2.38e+02 ... (remaining 7196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1215 0.086 - 0.172: 188 0.172 - 0.258: 3 0.258 - 0.345: 1 0.345 - 0.431: 1 Chirality restraints: 1408 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 4.64e+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 2.57e+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 8.82e-01 ... (remaining 1405 not shown) Planarity restraints: 2582 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 " -0.004 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 3.32e-02 1.10e+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 " -0.020 2.00e-02 2.50e+03 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1221 2.20 - 2.80: 35591 2.80 - 3.40: 46048 3.40 - 4.00: 62617 4.00 - 4.60: 95101 Nonbonded interactions: 240578 Sorted by model distance: nonbonded pdb=" HH TYR D 194 " pdb=" O ASP D 204 " model vdw 1.602 1.850 nonbonded pdb=" HH TYR C 194 " pdb=" O ASP C 204 " model vdw 1.612 1.850 nonbonded pdb=" HZ1 LYS E 240 " pdb=" OP1 DT G 6 " model vdw 1.617 1.850 nonbonded pdb=" OD1 ASP A 231 " pdb=" HE ARG A 277 " model vdw 1.630 1.850 nonbonded pdb=" O SER E 131 " pdb=" HG1 THR E 134 " model vdw 1.663 1.850 ... (remaining 240573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 119 through 180 or (resid 181 and (name N or name CA or na \ me C or name O or name CB or name OG or name H or name HA or name HB2 or name HB \ 3)) or resid 182 through 217 or (resid 218 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or n \ ame CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD2 or \ name HE1 or name HE2 or name HH )) or resid 219 through 240 or (resid 241 and (n \ ame N or name CA or name C or name O or name HA2 or name HA3)) or resid 242 thro \ ugh 301)) selection = (chain 'B' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2 or name HH )) or resid 219 through 240 or (r \ esid 241 and (name N or name CA or name C or name O or name HA2 or name HA3)) or \ resid 242 through 301)) selection = (chain 'C' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or resid 181 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HH \ )) or resid 219 through 240 or (resid 241 and (name N or name CA or name C or n \ ame O or name HA2 or name HA3)) or resid 242 through 301)) selection = (chain 'D' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2 or name HH )) or resid 219 through 240 or (r \ esid 241 and (name N or name CA or name C or name O or name HA2 or name HA3)) or \ resid 242 through 301)) selection = (chain 'E' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 240 or (resid 241 and (name N or name CA \ or name C or name O or name HA2 or name HA3)) or resid 242 through 301)) selection = (chain 'F' and (resid 119 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 181 and (name N o \ r name CA or name C or name O or name CB or name OG or name H or name HA or name \ HB2 or name HB3)) or resid 182 through 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2 or name HH )) or resid 219 through 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 14 5.49 5 Mg 4 5.21 5 S 18 5.16 5 C 5776 2.51 5 N 1508 2.21 5 O 1697 1.98 5 H 8697 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.280 Extract box with map and model: 5.500 Check model and map are aligned: 0.270 Process input model: 55.580 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.850 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 0.090 9296 Z= 0.631 Angle : 1.198 19.475 12755 Z= 0.635 Chirality : 0.059 0.431 1408 Planarity : 0.010 0.223 1558 Dihedral : 17.513 147.790 3299 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 7.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.97 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.25), residues: 1086 helix: -0.96 (0.28), residues: 291 sheet: -1.56 (0.44), residues: 141 loop : -2.17 (0.24), residues: 654 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 263 time to evaluate : 1.513 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 outliers start: 71 outliers final: 34 residues processed: 310 average time/residue: 0.5062 time to fit residues: 210.0666 Evaluate side-chains 213 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.492 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 3 residues processed: 34 average time/residue: 0.2705 time to fit residues: 16.4237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 257 GLN F 146 ASN F 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9296 Z= 0.189 Angle : 0.723 14.276 12755 Z= 0.343 Chirality : 0.044 0.229 1408 Planarity : 0.005 0.059 1558 Dihedral : 12.655 133.320 1283 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.46 % Favored : 92.45 % Rotamer Outliers : 1.89 % 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: -2.16 (0.25), residues: 1086 helix: -0.44 (0.29), residues: 291 sheet: -1.34 (0.41), residues: 157 loop : -2.01 (0.25), residues: 638 *********************** 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 221 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 215 average time/residue: 0.4412 time to fit residues: 132.0282 Evaluate side-chains 204 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.519 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 13 average time/residue: 0.2095 time to fit residues: 6.7158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 78 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: D 257 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 9296 Z= 0.376 Angle : 0.724 13.757 12755 Z= 0.353 Chirality : 0.047 0.217 1408 Planarity : 0.004 0.046 1558 Dihedral : 12.079 140.183 1283 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer Outliers : 2.73 % 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: -2.43 (0.25), residues: 1086 helix: -0.52 (0.29), residues: 290 sheet: -1.65 (0.40), residues: 157 loop : -2.22 (0.25), residues: 639 *********************** 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 215 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 20 residues processed: 204 average time/residue: 0.4457 time to fit residues: 126.4050 Evaluate side-chains 196 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 1.409 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.1978 time to fit residues: 8.8440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 9296 Z= 0.164 Angle : 0.654 14.100 12755 Z= 0.305 Chirality : 0.042 0.194 1408 Planarity : 0.004 0.043 1558 Dihedral : 11.498 139.229 1283 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 1.05 % 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: -2.02 (0.26), residues: 1086 helix: 0.06 (0.31), residues: 284 sheet: -1.46 (0.45), residues: 137 loop : -2.05 (0.25), residues: 665 *********************** 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 201 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 197 average time/residue: 0.4398 time to fit residues: 121.0031 Evaluate side-chains 188 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 182 time to evaluate : 1.652 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.2134 time to fit residues: 4.1360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9296 Z= 0.227 Angle : 0.650 13.846 12755 Z= 0.304 Chirality : 0.043 0.171 1408 Planarity : 0.003 0.038 1558 Dihedral : 11.186 136.935 1283 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.26), residues: 1086 helix: 0.10 (0.31), residues: 290 sheet: -1.40 (0.41), residues: 157 loop : -2.05 (0.25), residues: 639 *********************** 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 199 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 192 average time/residue: 0.4250 time to fit residues: 114.8457 Evaluate side-chains 190 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 181 time to evaluate : 1.652 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2069 time to fit residues: 5.2218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 0.0170 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 9296 Z= 0.180 Angle : 0.635 13.897 12755 Z= 0.294 Chirality : 0.042 0.157 1408 Planarity : 0.003 0.036 1558 Dihedral : 10.871 134.974 1283 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.27 % Favored : 92.63 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.26), residues: 1086 helix: 0.23 (0.31), residues: 294 sheet: -1.47 (0.45), residues: 137 loop : -1.91 (0.25), residues: 655 *********************** 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 196 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.646 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 outliers start: 12 outliers final: 7 residues processed: 191 average time/residue: 0.4269 time to fit residues: 115.2094 Evaluate side-chains 188 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 181 time to evaluate : 1.594 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.2503 time to fit residues: 4.8782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9296 Z= 0.186 Angle : 0.625 13.687 12755 Z= 0.289 Chirality : 0.042 0.147 1408 Planarity : 0.003 0.035 1558 Dihedral : 10.685 133.818 1283 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.76 (0.26), residues: 1086 helix: 0.35 (0.31), residues: 297 sheet: -1.50 (0.45), residues: 137 loop : -1.90 (0.25), residues: 652 *********************** 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 197 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 185 average time/residue: 0.4330 time to fit residues: 112.3862 Evaluate side-chains 188 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 1.769 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.2284 time to fit residues: 6.0663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.1980 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9296 Z= 0.171 Angle : 0.623 13.692 12755 Z= 0.286 Chirality : 0.042 0.130 1408 Planarity : 0.003 0.034 1558 Dihedral : 10.495 133.199 1283 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.26), residues: 1086 helix: 0.55 (0.31), residues: 297 sheet: -1.47 (0.45), residues: 137 loop : -1.82 (0.25), residues: 652 *********************** 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 195 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 190 average time/residue: 0.4355 time to fit residues: 116.2935 Evaluate side-chains 185 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 1.572 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.2228 time to fit residues: 3.7671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9296 Z= 0.263 Angle : 0.642 13.397 12755 Z= 0.301 Chirality : 0.043 0.140 1408 Planarity : 0.003 0.033 1558 Dihedral : 10.490 134.016 1283 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.26), residues: 1086 helix: 0.33 (0.31), residues: 297 sheet: -1.62 (0.45), residues: 137 loop : -1.87 (0.25), residues: 652 *********************** 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 188 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 179 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 182 average time/residue: 0.4359 time to fit residues: 112.9289 Evaluate side-chains 183 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 1.539 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.2285 time to fit residues: 4.7702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 68 optimal weight: 0.0060 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 9296 Z= 0.162 Angle : 0.615 13.670 12755 Z= 0.282 Chirality : 0.041 0.132 1408 Planarity : 0.003 0.036 1558 Dihedral : 10.233 134.241 1283 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 0.31 % 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: -1.54 (0.26), residues: 1086 helix: 0.64 (0.31), residues: 297 sheet: -1.57 (0.45), residues: 139 loop : -1.77 (0.25), residues: 650 ********************** 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 189 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 187 average time/residue: 0.4625 time to fit residues: 121.0068 Evaluate side-chains 181 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 1.426 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2610 time to fit residues: 2.6424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106392 restraints weight = 40458.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110620 restraints weight = 21132.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113515 restraints weight = 13609.621| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9296 Z= 0.198 Angle : 0.619 13.472 12755 Z= 0.285 Chirality : 0.042 0.131 1408 Planarity : 0.003 0.034 1558 Dihedral : 10.069 134.050 1283 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer Outliers : 0.42 % 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: -1.53 (0.26), residues: 1086 helix: 0.65 (0.31), residues: 297 sheet: -1.57 (0.45), residues: 139 loop : -1.77 (0.25), residues: 650 =============================================================================== Job complete usr+sys time: 4176.72 seconds wall clock time: 74 minutes 20.87 seconds (4460.87 seconds total)