Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 14:13:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lar_23249/04_2023/7lar_23249_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lar_23249/04_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_23249/04_2023/7lar_23249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lar_23249/04_2023/7lar_23249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lar_23249/04_2023/7lar_23249_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lar_23249/04_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 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. 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-1.21rc1-4938/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: 8.01, per 1000 atoms: 0.45 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: 14.35 Conformation dependent library (CDL) restraints added in 1.6 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 14 sheets defined 29.1% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 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: 7.55 Time building geometry restraints manager: 14.70 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 GLY F 205 " pdb=" N TYR F 206 " pdb=" CA TYR F 206 " ideal model delta sigma weight residual 121.70 138.34 -16.64 1.80e+00 3.09e-01 8.54e+01 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 ... (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 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: 0.760 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: 0.260 Extract box with map and model: 5.070 Check model and map are aligned: 0.280 Set scattering table: 0.140 Process input model: 57.570 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 1.202 19.475 12755 Z= 0.642 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 : 5.01 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 : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 34 residues processed: 310 average time/residue: 0.5107 time to fit residues: 213.1410 Evaluate side-chains 213 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.469 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: 0.2841 time to fit residues: 17.2271 ------------------------------------------------------------------------------- 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: 0.8061 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9296 Z= 0.192 Angle : 0.716 9.971 12755 Z= 0.348 Chirality : 0.044 0.228 1408 Planarity : 0.005 0.061 1558 Dihedral : 12.665 134.271 1283 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.36 % 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: -0.43 (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 219 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 213 average time/residue: 0.4413 time to fit residues: 130.7284 Evaluate side-chains 203 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 1.475 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: 0.2084 time to fit residues: 6.5842 ------------------------------------------------------------------------------- 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: 4.9990 chunk 30 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.8111 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 9296 Z= 0.299 Angle : 0.691 9.319 12755 Z= 0.339 Chirality : 0.045 0.214 1408 Planarity : 0.004 0.045 1558 Dihedral : 11.971 138.509 1283 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer Outliers : 2.52 % 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: -2.24 (0.25), residues: 1086 helix: -0.34 (0.29), residues: 290 sheet: -1.53 (0.41), residues: 157 loop : -2.11 (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 216 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 206 average time/residue: 0.4409 time to fit residues: 126.4156 Evaluate side-chains 198 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 1.352 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 18 average time/residue: 0.2000 time to fit residues: 8.2546 ------------------------------------------------------------------------------- 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: 5.9990 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.3143 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= 0.217 Angle : 0.644 9.116 12755 Z= 0.309 Chirality : 0.043 0.196 1408 Planarity : 0.004 0.041 1558 Dihedral : 11.416 140.094 1283 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.92 % Favored : 91.99 % Rotamer Outliers : 1.47 % 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: -2.06 (0.26), residues: 1086 helix: -0.07 (0.30), residues: 291 sheet: -1.41 (0.41), residues: 157 loop : -2.06 (0.25), residues: 638 *********************** 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: 14 poor density : 187 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 194 average time/residue: 0.4478 time to fit residues: 122.3347 Evaluate side-chains 189 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 1.479 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.2192 time to fit residues: 6.1053 ------------------------------------------------------------------------------- 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: 7.9990 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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: 0.8139 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 9296 Z= 0.354 Angle : 0.683 8.859 12755 Z= 0.335 Chirality : 0.045 0.179 1408 Planarity : 0.004 0.038 1558 Dihedral : 11.257 138.151 1283 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.14 % Favored : 88.77 % Rotamer Outliers : 1.99 % 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: -2.35 (0.25), residues: 1086 helix: -0.31 (0.30), residues: 291 sheet: -1.68 (0.41), residues: 157 loop : -2.22 (0.25), residues: 638 *********************** 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 203 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 193 average time/residue: 0.4508 time to fit residues: 122.2614 Evaluate side-chains 188 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 1.493 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.2328 time to fit residues: 5.9062 ------------------------------------------------------------------------------- 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: 10.0000 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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: 0.8116 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9296 Z= 0.231 Angle : 0.642 8.879 12755 Z= 0.309 Chirality : 0.043 0.159 1408 Planarity : 0.003 0.037 1558 Dihedral : 10.997 137.250 1283 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.20 % Favored : 91.71 % Rotamer Outliers : 1.57 % 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: -2.20 (0.26), residues: 1086 helix: -0.13 (0.30), residues: 297 sheet: -1.61 (0.41), residues: 157 loop : -2.16 (0.25), residues: 632 *********************** 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 198 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 189 average time/residue: 0.4386 time to fit residues: 116.5014 Evaluate side-chains 186 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 177 time to evaluate : 1.491 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2275 time to fit residues: 5.4570 ------------------------------------------------------------------------------- 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: 7.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.8102 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9296 Z= 0.200 Angle : 0.627 8.803 12755 Z= 0.300 Chirality : 0.042 0.145 1408 Planarity : 0.003 0.036 1558 Dihedral : 10.781 135.714 1283 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.21 % Favored : 90.70 % 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: -2.06 (0.26), residues: 1086 helix: 0.03 (0.30), residues: 295 sheet: -1.75 (0.45), residues: 137 loop : -2.03 (0.25), residues: 654 *********************** 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 201 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 189 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 193 average time/residue: 0.4314 time to fit residues: 117.8806 Evaluate side-chains 189 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 1.443 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2296 time to fit residues: 5.3733 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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: 0.8129 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 9296 Z= 0.290 Angle : 0.645 8.722 12755 Z= 0.312 Chirality : 0.044 0.141 1408 Planarity : 0.004 0.035 1558 Dihedral : 10.733 135.884 1283 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.77 % Favored : 89.13 % Rotamer Outliers : 0.84 % 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: -2.21 (0.26), residues: 1086 helix: -0.10 (0.30), residues: 295 sheet: -1.90 (0.44), residues: 137 loop : -2.12 (0.25), residues: 654 *********************** 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 191 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 184 average time/residue: 0.4275 time to fit residues: 110.4037 Evaluate side-chains 188 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.510 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2055 time to fit residues: 4.7634 ------------------------------------------------------------------------------- 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: 5.9990 chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8117 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 9296 Z= 0.245 Angle : 0.637 8.745 12755 Z= 0.306 Chirality : 0.043 0.141 1408 Planarity : 0.003 0.038 1558 Dihedral : 10.615 136.326 1283 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.48 % Favored : 90.42 % 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: -2.14 (0.26), residues: 1086 helix: -0.05 (0.30), residues: 298 sheet: -1.89 (0.45), residues: 137 loop : -2.06 (0.25), residues: 651 *********************** 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 196 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 187 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 190 average time/residue: 0.4738 time to fit residues: 125.6782 Evaluate side-chains 188 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.368 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2220 time to fit residues: 4.8513 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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: 0.8108 moved from start: 0.3826 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= 0.216 Angle : 0.628 8.799 12755 Z= 0.300 Chirality : 0.042 0.134 1408 Planarity : 0.003 0.037 1558 Dihedral : 10.522 136.064 1283 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.48 % Favored : 90.42 % Rotamer Outliers : 0.52 % 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: -2.05 (0.26), residues: 1086 helix: 0.04 (0.30), residues: 298 sheet: -1.72 (0.46), residues: 130 loop : -2.06 (0.25), residues: 658 ********************** 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 191 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 186 time to evaluate : 1.389 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: 5 outliers final: 4 residues processed: 188 average time/residue: 0.4301 time to fit residues: 114.4370 Evaluate side-chains 185 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 1.520 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.2342 time to fit residues: 3.3719 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.129925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.106643 restraints weight = 40395.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110876 restraints weight = 21076.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113771 restraints weight = 13559.703| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 9296 Z= 0.162 Angle : 0.608 8.857 12755 Z= 0.287 Chirality : 0.041 0.133 1408 Planarity : 0.003 0.037 1558 Dihedral : 10.180 135.249 1283 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer Outliers : 0.52 % 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: -1.73 (0.26), residues: 1086 helix: 0.42 (0.31), residues: 295 sheet: -1.62 (0.46), residues: 132 loop : -1.88 (0.25), residues: 659 =============================================================================== Job complete usr+sys time: 4189.86 seconds wall clock time: 75 minutes 8.07 seconds (4508.07 seconds total)