Starting phenix.real_space_refine on Fri May 10 03:00:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/05_2024/8v2o_42918_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/05_2024/8v2o_42918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/05_2024/8v2o_42918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/05_2024/8v2o_42918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/05_2024/8v2o_42918_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/05_2024/8v2o_42918_updated.pdb" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.166 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9245 2.51 5 N 2470 2.21 5 O 2825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 107": "OE1" <-> "OE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 286": "OD1" <-> "OD2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E GLU 364": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 14660 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.53, per 1000 atoms: 0.58 Number of scatterers: 14660 At special positions: 0 Unit cell: (81.32, 104.86, 192.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2825 8.00 N 2470 7.00 C 9245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.85 Conformation dependent library (CDL) restraints added in 2.7 seconds 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 20 sheets defined 42.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.285A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.648A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.892A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.995A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.862A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.733A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.940A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 5.019A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 347 removed outlier: 3.670A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 369 through 373 removed outlier: 4.273A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.025A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.623A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.893A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 5.063A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 369 through 373 removed outlier: 4.277A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.019A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.682A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.964A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 5.046A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 347 removed outlier: 3.645A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 369 through 373 removed outlier: 4.223A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 4.225A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.648A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.961A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 5.086A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 347 removed outlier: 3.659A pdb=" N SER E 338 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 369 through 373 removed outlier: 4.300A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.822A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.431A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.776A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.473A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.763A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.407A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.735A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.427A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.707A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.476A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 514 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4770 1.34 - 1.47: 3444 1.47 - 1.59: 6574 1.59 - 1.71: 17 1.71 - 1.84: 180 Bond restraints: 14985 Sorted by residual: bond pdb=" CB PRO B 367 " pdb=" CG PRO B 367 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.65e+00 bond pdb=" CG PRO B 367 " pdb=" CD PRO B 367 " ideal model delta sigma weight residual 1.503 1.404 0.099 3.40e-02 8.65e+02 8.49e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.85e+00 bond pdb=" CB PRO A 367 " pdb=" CG PRO A 367 " ideal model delta sigma weight residual 1.492 1.632 -0.140 5.00e-02 4.00e+02 7.80e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.70e+00 ... (remaining 14980 not shown) Histogram of bond angle deviations from ideal: 95.01 - 103.26: 188 103.26 - 111.51: 6557 111.51 - 119.76: 6634 119.76 - 128.02: 6828 128.02 - 136.27: 133 Bond angle restraints: 20340 Sorted by residual: angle pdb=" CA PRO B 367 " pdb=" N PRO B 367 " pdb=" CD PRO B 367 " ideal model delta sigma weight residual 112.00 95.15 16.85 1.40e+00 5.10e-01 1.45e+02 angle pdb=" CA PRO A 367 " pdb=" N PRO A 367 " pdb=" CD PRO A 367 " ideal model delta sigma weight residual 112.00 96.41 15.59 1.40e+00 5.10e-01 1.24e+02 angle pdb=" CB MET A 305 " pdb=" CG MET A 305 " pdb=" SD MET A 305 " ideal model delta sigma weight residual 112.70 130.45 -17.75 3.00e+00 1.11e-01 3.50e+01 angle pdb=" N PRO B 367 " pdb=" CD PRO B 367 " pdb=" CG PRO B 367 " ideal model delta sigma weight residual 103.20 95.01 8.19 1.50e+00 4.44e-01 2.98e+01 angle pdb=" CA PRO D 367 " pdb=" N PRO D 367 " pdb=" CD PRO D 367 " ideal model delta sigma weight residual 112.00 104.70 7.30 1.40e+00 5.10e-01 2.72e+01 ... (remaining 20335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 8765 34.77 - 69.54: 235 69.54 - 104.31: 10 104.31 - 139.08: 5 139.08 - 173.85: 5 Dihedral angle restraints: 9020 sinusoidal: 3645 harmonic: 5375 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.86 -173.85 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.57 -173.57 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.21 -173.21 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 9017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1661 0.047 - 0.094: 407 0.094 - 0.141: 161 0.141 - 0.188: 17 0.188 - 0.235: 4 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE E 151 " pdb=" CA ILE E 151 " pdb=" CG1 ILE E 151 " pdb=" CG2 ILE E 151 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2247 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 366 " -0.144 5.00e-02 4.00e+02 2.00e-01 6.41e+01 pdb=" N PRO B 367 " 0.345 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.112 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 366 " 0.141 5.00e-02 4.00e+02 1.98e-01 6.26e+01 pdb=" N PRO A 367 " -0.341 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " 0.111 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 366 " -0.115 5.00e-02 4.00e+02 1.71e-01 4.70e+01 pdb=" N PRO D 367 " 0.296 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " -0.097 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " -0.084 5.00e-02 4.00e+02 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3170 2.78 - 3.31: 12501 3.31 - 3.84: 25701 3.84 - 4.37: 31343 4.37 - 4.90: 52309 Nonbonded interactions: 125024 Sorted by model distance: nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.253 2.170 nonbonded pdb=" O GLN D 314 " pdb=" OG1 THR D 318 " model vdw 2.312 2.440 nonbonded pdb=" O GLN A 314 " pdb=" OG1 THR A 318 " model vdw 2.319 2.440 nonbonded pdb=" O GLN E 314 " pdb=" OG1 THR E 318 " model vdw 2.320 2.440 nonbonded pdb=" O GLN B 314 " pdb=" OG1 THR B 318 " model vdw 2.320 2.440 ... (remaining 125019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.000 Extract box with map and model: 4.130 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 42.530 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 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 : 0.004 0.147 14985 Z= 0.289 Angle : 0.800 17.746 20340 Z= 0.411 Chirality : 0.049 0.235 2250 Planarity : 0.009 0.200 2605 Dihedral : 15.842 173.854 5580 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.70 % Allowed : 12.10 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 1835 helix: -1.65 (0.15), residues: 775 sheet: 0.28 (0.27), residues: 375 loop : -0.33 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 356 HIS 0.004 0.001 HIS C 161 PHE 0.014 0.001 PHE C 255 TYR 0.010 0.001 TYR D 306 ARG 0.023 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.714 Fit side-chains REVERT: D 246 GLN cc_start: 0.9107 (mt0) cc_final: 0.8750 (mp10) outliers start: 11 outliers final: 5 residues processed: 126 average time/residue: 1.8497 time to fit residues: 251.0674 Evaluate side-chains 120 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 14985 Z= 0.575 Angle : 0.672 7.496 20340 Z= 0.324 Chirality : 0.050 0.161 2250 Planarity : 0.006 0.108 2605 Dihedral : 9.932 148.081 2095 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.53 % Allowed : 10.06 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.19), residues: 1835 helix: -0.34 (0.18), residues: 765 sheet: 0.59 (0.29), residues: 315 loop : 0.38 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 79 HIS 0.006 0.001 HIS B 161 PHE 0.016 0.002 PHE C 262 TYR 0.011 0.002 TYR A 294 ARG 0.010 0.001 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 1.772 Fit side-chains REVERT: A 176 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8258 (mtt) REVERT: B 227 MET cc_start: 0.8854 (mmm) cc_final: 0.8634 (mmm) REVERT: B 314 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: D 128 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8656 (p0) REVERT: D 246 GLN cc_start: 0.8876 (mt0) cc_final: 0.8478 (mt0) REVERT: D 314 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: E 132 MET cc_start: 0.9345 (tmm) cc_final: 0.9129 (ppp) outliers start: 24 outliers final: 6 residues processed: 124 average time/residue: 1.9787 time to fit residues: 262.6976 Evaluate side-chains 117 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 168 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 162 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14985 Z= 0.161 Angle : 0.524 5.936 20340 Z= 0.242 Chirality : 0.042 0.139 2250 Planarity : 0.004 0.084 2605 Dihedral : 8.633 134.204 2093 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.72 % Allowed : 10.57 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1835 helix: 0.25 (0.19), residues: 755 sheet: 0.53 (0.29), residues: 340 loop : 0.58 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.002 0.000 HIS D 161 PHE 0.009 0.001 PHE B 255 TYR 0.007 0.001 TYR D 69 ARG 0.010 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.736 Fit side-chains REVERT: A 314 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: A 354 GLN cc_start: 0.8660 (pm20) cc_final: 0.8409 (pm20) REVERT: B 227 MET cc_start: 0.8864 (mmm) cc_final: 0.8604 (mmm) REVERT: B 314 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: B 372 ARG cc_start: 0.8759 (mtm110) cc_final: 0.8537 (ptp-110) REVERT: C 246 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: C 314 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8002 (tp40) REVERT: C 354 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8448 (pm20) REVERT: C 372 ARG cc_start: 0.8855 (mtm110) cc_final: 0.8571 (ttp-110) REVERT: D 176 MET cc_start: 0.9149 (mtm) cc_final: 0.8768 (mtm) REVERT: D 246 GLN cc_start: 0.8896 (mt0) cc_final: 0.8510 (mt0) REVERT: E 246 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8536 (mp10) outliers start: 27 outliers final: 3 residues processed: 127 average time/residue: 2.0183 time to fit residues: 274.2221 Evaluate side-chains 121 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 246 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14985 Z= 0.173 Angle : 0.511 5.801 20340 Z= 0.237 Chirality : 0.043 0.133 2250 Planarity : 0.004 0.068 2605 Dihedral : 7.404 114.911 2091 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.66 % Allowed : 10.83 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1835 helix: 0.57 (0.20), residues: 755 sheet: 0.60 (0.29), residues: 340 loop : 0.71 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE B 255 TYR 0.004 0.001 TYR C 69 ARG 0.011 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.660 Fit side-chains REVERT: A 176 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8238 (mtt) REVERT: B 227 MET cc_start: 0.8894 (mmm) cc_final: 0.8542 (mmm) REVERT: B 314 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: B 372 ARG cc_start: 0.8764 (mtm110) cc_final: 0.8539 (ptp-110) REVERT: C 246 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8555 (mt0) REVERT: D 176 MET cc_start: 0.9224 (mtm) cc_final: 0.8843 (mtm) REVERT: D 246 GLN cc_start: 0.8846 (mt0) cc_final: 0.8460 (mt0) REVERT: D 314 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: E 246 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8550 (mp10) outliers start: 26 outliers final: 5 residues processed: 129 average time/residue: 2.0431 time to fit residues: 282.3477 Evaluate side-chains 124 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 152 optimal weight: 0.0050 chunk 123 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 overall best weight: 2.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14985 Z= 0.289 Angle : 0.545 6.177 20340 Z= 0.256 Chirality : 0.045 0.135 2250 Planarity : 0.004 0.060 2605 Dihedral : 6.705 99.103 2090 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.46 % Allowed : 11.40 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1835 helix: 0.62 (0.20), residues: 755 sheet: 0.54 (0.28), residues: 340 loop : 0.68 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE C 262 TYR 0.006 0.001 TYR C 240 ARG 0.010 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.521 Fit side-chains REVERT: A 176 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8276 (mtt) REVERT: A 305 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8836 (mmm) REVERT: B 227 MET cc_start: 0.8909 (mmm) cc_final: 0.8588 (mmm) REVERT: B 314 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: B 372 ARG cc_start: 0.8758 (mtm110) cc_final: 0.8534 (ptp-110) REVERT: C 314 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.7994 (tp40) REVERT: D 176 MET cc_start: 0.9242 (mtm) cc_final: 0.8963 (mtm) REVERT: D 246 GLN cc_start: 0.8826 (mt0) cc_final: 0.8462 (mt0) REVERT: D 314 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8350 (tt0) outliers start: 23 outliers final: 7 residues processed: 122 average time/residue: 2.0132 time to fit residues: 263.1614 Evaluate side-chains 122 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 128 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14985 Z= 0.244 Angle : 0.533 6.090 20340 Z= 0.249 Chirality : 0.044 0.133 2250 Planarity : 0.004 0.053 2605 Dihedral : 6.568 92.804 2090 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.46 % Allowed : 11.46 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1835 helix: 0.69 (0.20), residues: 755 sheet: 0.52 (0.28), residues: 340 loop : 0.71 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.003 0.001 HIS B 161 PHE 0.012 0.001 PHE E 127 TYR 0.005 0.001 TYR C 240 ARG 0.012 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.677 Fit side-chains REVERT: A 176 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8267 (mtt) REVERT: A 305 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8857 (mmm) REVERT: A 314 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: B 176 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8765 (mtm) REVERT: B 227 MET cc_start: 0.8924 (mmm) cc_final: 0.8567 (mmm) REVERT: B 314 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: B 372 ARG cc_start: 0.8757 (mtm110) cc_final: 0.8541 (ptp-110) REVERT: C 246 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8413 (mt0) REVERT: C 314 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.7975 (tp40) REVERT: D 176 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8968 (mtm) REVERT: D 246 GLN cc_start: 0.8797 (mt0) cc_final: 0.8412 (mt0) REVERT: D 314 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8338 (tt0) outliers start: 23 outliers final: 7 residues processed: 124 average time/residue: 2.0045 time to fit residues: 265.9212 Evaluate side-chains 128 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14985 Z= 0.278 Angle : 0.543 6.140 20340 Z= 0.255 Chirality : 0.044 0.133 2250 Planarity : 0.004 0.049 2605 Dihedral : 6.509 90.728 2090 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.46 % Allowed : 11.46 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1835 helix: 0.72 (0.20), residues: 755 sheet: 0.50 (0.28), residues: 340 loop : 0.73 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE C 262 TYR 0.006 0.001 TYR C 240 ARG 0.012 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 1.732 Fit side-chains REVERT: A 176 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8256 (mtt) REVERT: A 305 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8877 (mmm) REVERT: B 176 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8772 (mtm) REVERT: B 227 MET cc_start: 0.8927 (mmm) cc_final: 0.8544 (mmm) REVERT: B 314 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: B 372 ARG cc_start: 0.8757 (mtm110) cc_final: 0.8536 (ptp-110) REVERT: C 246 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8462 (mt0) REVERT: C 314 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7979 (tp40) REVERT: C 354 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: D 246 GLN cc_start: 0.8800 (mt0) cc_final: 0.8470 (mt0) REVERT: D 314 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: E 354 GLN cc_start: 0.8893 (pm20) cc_final: 0.8503 (pm20) outliers start: 23 outliers final: 6 residues processed: 122 average time/residue: 2.0941 time to fit residues: 273.6933 Evaluate side-chains 126 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 113 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14985 Z= 0.307 Angle : 0.554 6.143 20340 Z= 0.261 Chirality : 0.045 0.134 2250 Planarity : 0.004 0.046 2605 Dihedral : 6.548 92.738 2090 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.27 % Allowed : 11.78 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1835 helix: 0.98 (0.20), residues: 730 sheet: 0.48 (0.28), residues: 340 loop : 0.76 (0.25), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.003 0.001 HIS B 161 PHE 0.010 0.001 PHE C 262 TYR 0.006 0.001 TYR C 240 ARG 0.014 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 1.837 Fit side-chains REVERT: A 176 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8251 (mtt) REVERT: A 305 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8936 (mmm) REVERT: A 355 MET cc_start: 0.9287 (mtm) cc_final: 0.9049 (mtp) REVERT: B 176 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8745 (mtm) REVERT: B 227 MET cc_start: 0.8923 (mmm) cc_final: 0.8524 (mmm) REVERT: B 314 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: B 372 ARG cc_start: 0.8758 (mtm110) cc_final: 0.8537 (ptp-110) REVERT: C 246 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8454 (mt0) REVERT: C 314 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.7979 (tp40) REVERT: C 354 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: D 246 GLN cc_start: 0.8803 (mt0) cc_final: 0.8467 (mt0) REVERT: D 314 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: E 44 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8802 (mtt) REVERT: E 354 GLN cc_start: 0.8875 (pm20) cc_final: 0.8505 (pm20) outliers start: 20 outliers final: 6 residues processed: 119 average time/residue: 1.9892 time to fit residues: 253.2517 Evaluate side-chains 126 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 166 optimal weight: 0.4980 chunk 100 optimal weight: 0.0670 chunk 72 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 128 ASN E 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14985 Z= 0.139 Angle : 0.510 6.042 20340 Z= 0.237 Chirality : 0.042 0.138 2250 Planarity : 0.003 0.047 2605 Dihedral : 5.997 80.805 2090 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.34 % Allowed : 11.72 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.21), residues: 1835 helix: 0.88 (0.20), residues: 760 sheet: 0.60 (0.29), residues: 340 loop : 0.88 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE B 255 TYR 0.005 0.001 TYR C 69 ARG 0.016 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.765 Fit side-chains REVERT: A 305 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8911 (mmm) REVERT: A 355 MET cc_start: 0.9243 (mtm) cc_final: 0.8949 (mtp) REVERT: B 176 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8800 (mtm) REVERT: B 227 MET cc_start: 0.8933 (mmm) cc_final: 0.8525 (mmm) REVERT: B 314 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8736 (tp40) REVERT: C 246 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8431 (mt0) REVERT: C 314 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.7941 (tp40) REVERT: C 354 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: D 246 GLN cc_start: 0.8769 (mt0) cc_final: 0.8398 (mt0) REVERT: E 44 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8659 (mtt) outliers start: 21 outliers final: 7 residues processed: 121 average time/residue: 1.9480 time to fit residues: 252.8459 Evaluate side-chains 128 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 0.0030 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 121 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 128 ASN E 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 14985 Z= 0.247 Angle : 0.861 59.183 20340 Z= 0.487 Chirality : 0.047 0.635 2250 Planarity : 0.004 0.081 2605 Dihedral : 5.991 80.868 2090 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 1.02 % Allowed : 12.23 % Favored : 86.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1835 helix: 0.84 (0.20), residues: 760 sheet: 0.62 (0.29), residues: 340 loop : 0.88 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.003 0.001 HIS D 161 PHE 0.009 0.001 PHE B 255 TYR 0.005 0.001 TYR C 69 ARG 0.014 0.000 ARG E 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.747 Fit side-chains REVERT: A 305 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8924 (mmm) REVERT: A 355 MET cc_start: 0.9238 (mtm) cc_final: 0.8948 (mtp) REVERT: B 176 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8802 (mtm) REVERT: B 227 MET cc_start: 0.8935 (mmm) cc_final: 0.8521 (mmm) REVERT: B 314 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8737 (tp40) REVERT: C 246 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8426 (mt0) REVERT: C 314 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.7945 (tp40) REVERT: C 354 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: D 246 GLN cc_start: 0.8770 (mt0) cc_final: 0.8393 (mt0) outliers start: 16 outliers final: 5 residues processed: 120 average time/residue: 2.0922 time to fit residues: 270.5752 Evaluate side-chains 125 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 121 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.059485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.045156 restraints weight = 33575.231| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 2.45 r_work: 0.2485 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 14985 Z= 0.247 Angle : 0.861 59.182 20340 Z= 0.487 Chirality : 0.047 0.635 2250 Planarity : 0.004 0.081 2605 Dihedral : 5.991 80.868 2090 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 0.83 % Allowed : 12.42 % Favored : 86.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1835 helix: 0.84 (0.20), residues: 760 sheet: 0.62 (0.29), residues: 340 loop : 0.88 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.003 0.001 HIS D 161 PHE 0.009 0.001 PHE B 255 TYR 0.005 0.001 TYR C 69 ARG 0.014 0.000 ARG E 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4884.21 seconds wall clock time: 88 minutes 30.54 seconds (5310.54 seconds total)