Starting phenix.real_space_refine on Thu Feb 15 09:14:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djo_7938/02_2024/6djo_7938_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djo_7938/02_2024/6djo_7938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djo_7938/02_2024/6djo_7938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djo_7938/02_2024/6djo_7938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djo_7938/02_2024/6djo_7938_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djo_7938/02_2024/6djo_7938_updated.pdb" } resolution = 3.6 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= 0.000 sd= 0.002 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 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 256": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11748 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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} Time building chain proxies: 7.01, per 1000 atoms: 0.60 Number of scatterers: 11748 At special positions: 0 Unit cell: (100.32, 76.285, 166.155, 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 84 16.00 P 8 15.00 Mg 4 11.99 O 2264 8.00 N 1980 7.00 C 7408 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: 4.77 Conformation dependent library (CDL) restraints added in 2.2 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 16 sheets defined 36.6% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 57 through 60 No H-bonds generated for 'chain 'A' and resid 57 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 removed outlier: 3.534A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) 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 removed outlier: 3.897A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.596A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 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 192 removed outlier: 3.688A pdb=" N TYR A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.569A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.530A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 279 through 282 No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.504A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 292 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 293 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 287 through 294' Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.504A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.725A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 341 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 removed outlier: 3.753A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'B' and resid 57 through 60 No H-bonds generated for 'chain 'B' and resid 57 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 removed outlier: 3.534A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) 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 removed outlier: 3.897A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.596A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 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 192 removed outlier: 3.688A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.569A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.530A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 256 No H-bonds generated for 'chain 'B' and resid 253 through 256' 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 279 through 282 No H-bonds generated for 'chain 'B' and resid 279 through 282' Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.504A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 292 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 293 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 287 through 294' Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 317 removed outlier: 3.503A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 348 removed outlier: 4.725A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 removed outlier: 3.753A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 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 removed outlier: 3.534A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) 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 removed outlier: 3.897A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 removed outlier: 3.596A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 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 192 removed outlier: 3.688A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.569A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.529A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 256 No H-bonds generated for 'chain 'C' and resid 253 through 256' Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 279 through 282 No H-bonds generated for 'chain 'C' and resid 279 through 282' Processing helix chain 'C' and resid 287 through 294 removed outlier: 3.504A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 292 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 293 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 287 through 294' Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 317 removed outlier: 3.503A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.724A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 removed outlier: 3.753A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 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 removed outlier: 3.535A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) 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 removed outlier: 3.897A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.596A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 140 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 192 removed outlier: 3.688A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.568A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.529A pdb=" N ALA D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 No H-bonds generated for 'chain 'D' and resid 253 through 256' 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 279 through 282 No H-bonds generated for 'chain 'D' and resid 279 through 282' Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.504A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP D 292 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU D 293 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR D 294 " --> pdb=" O LYS D 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 287 through 294' Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 317 removed outlier: 3.503A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 4.725A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 346 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 removed outlier: 3.753A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing sheet with id= A, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.539A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N CYS A 10 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 104 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A 12 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 106 " --> pdb=" O ASN A 12 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 107 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 5.809A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (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 29 through 32 removed outlier: 3.539A pdb=" N VAL B 9 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N CYS B 10 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN B 12 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR B 106 " --> pdb=" O ASN B 12 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 107 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 5.809A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (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 29 through 32 removed outlier: 3.540A pdb=" N VAL C 9 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N CYS C 10 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU C 104 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN C 12 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR C 106 " --> pdb=" O ASN C 12 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 107 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 5.810A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (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 29 through 32 removed outlier: 3.539A pdb=" N VAL D 9 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N CYS D 10 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU D 104 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN D 12 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR D 106 " --> pdb=" O ASN D 12 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 107 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 52 through 54 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 5.810A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 272 hydrogen bonds defined for protein. 672 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: 3.56 Time building geometry restraints manager: 4.99 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: 3792 1.34 - 1.46: 2374 1.46 - 1.57: 5678 1.57 - 1.69: 12 1.69 - 1.81: 148 Bond restraints: 12004 Sorted by residual: bond pdb=" C VAL D 370 " pdb=" N HIS D 371 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.46e-02 4.69e+03 1.99e+01 bond pdb=" C VAL B 370 " pdb=" N HIS B 371 " ideal model delta sigma weight residual 1.334 1.387 -0.053 1.46e-02 4.69e+03 1.32e+01 bond pdb=" C VAL C 370 " pdb=" N HIS C 371 " ideal model delta sigma weight residual 1.334 1.382 -0.047 1.46e-02 4.69e+03 1.04e+01 bond pdb=" C VAL A 370 " pdb=" N HIS A 371 " ideal model delta sigma weight residual 1.334 1.381 -0.046 1.46e-02 4.69e+03 1.00e+01 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.90e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.87: 360 105.87 - 113.42: 6666 113.42 - 120.96: 5876 120.96 - 128.51: 3306 128.51 - 136.06: 84 Bond angle restraints: 16292 Sorted by residual: angle pdb=" N HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.50 116.90 -6.40 1.70e+00 3.46e-01 1.42e+01 angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 116.90 -6.40 1.70e+00 3.46e-01 1.42e+01 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 116.88 -6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N HIC A 73 " pdb=" CA HIC A 73 " pdb=" CB HIC A 73 " ideal model delta sigma weight residual 110.50 116.86 -6.36 1.70e+00 3.46e-01 1.40e+01 angle pdb=" C HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.10 103.38 6.72 1.90e+00 2.77e-01 1.25e+01 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 6829 16.77 - 33.54: 297 33.54 - 50.31: 85 50.31 - 67.08: 6 67.08 - 83.85: 3 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" C5' ADP D 802 " pdb=" O5' ADP D 802 " pdb=" PA ADP D 802 " pdb=" O2A ADP D 802 " ideal model delta sinusoidal sigma weight residual -60.00 23.86 -83.85 1 2.00e+01 2.50e-03 2.14e+01 dihedral pdb=" CA MET A 325 " pdb=" C MET A 325 " pdb=" N LYS A 326 " pdb=" CA LYS A 326 " ideal model delta harmonic sigma weight residual 180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA MET D 325 " pdb=" C MET D 325 " pdb=" N LYS D 326 " pdb=" CA LYS D 326 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1126 0.052 - 0.103: 579 0.103 - 0.155: 75 0.155 - 0.206: 12 0.206 - 0.258: 16 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA CYS A 257 " pdb=" N CYS A 257 " pdb=" C CYS A 257 " pdb=" CB CYS A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA CYS D 257 " pdb=" N CYS D 257 " pdb=" C CYS D 257 " pdb=" CB CYS D 257 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 372 " 0.260 9.50e-02 1.11e+02 1.16e-01 8.31e+00 pdb=" NE ARG D 372 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 372 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 372 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 372 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 372 " 0.260 9.50e-02 1.11e+02 1.16e-01 8.30e+00 pdb=" NE ARG C 372 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 372 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 372 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 372 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 372 " 0.259 9.50e-02 1.11e+02 1.16e-01 8.28e+00 pdb=" NE ARG B 372 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 372 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 372 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 372 " 0.009 2.00e-02 2.50e+03 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 163 2.62 - 3.19: 10059 3.19 - 3.76: 17302 3.76 - 4.33: 25593 4.33 - 4.90: 41613 Nonbonded interactions: 94730 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 2.053 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.077 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 2.082 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.092 2.170 nonbonded pdb="MG MG D 801 " pdb=" O3B ADP D 802 " model vdw 2.122 2.170 ... (remaining 94725 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.010 Extract box with map and model: 7.450 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 35.370 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 0.072 12004 Z= 0.591 Angle : 0.943 7.580 16292 Z= 0.502 Chirality : 0.060 0.258 1808 Planarity : 0.008 0.116 2084 Dihedral : 10.850 83.855 4468 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.96 % Allowed : 3.18 % Favored : 95.86 % 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: -4.76 (0.17), residues: 1468 helix: -4.43 (0.10), residues: 556 sheet: -2.45 (0.41), residues: 132 loop : -2.24 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP C 340 HIS 0.008 0.003 HIS D 40 PHE 0.018 0.002 PHE B 31 TYR 0.016 0.002 TYR B 169 ARG 0.012 0.001 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 290 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8798 (ppp) cc_final: 0.8583 (ppp) REVERT: A 283 MET cc_start: 0.7802 (mmt) cc_final: 0.7518 (mmm) REVERT: B 153 LEU cc_start: 0.9050 (tp) cc_final: 0.8796 (tp) REVERT: B 296 ASN cc_start: 0.8378 (m-40) cc_final: 0.8085 (m-40) REVERT: B 367 PRO cc_start: 0.8663 (Cg_endo) cc_final: 0.8430 (Cg_exo) REVERT: C 123 MET cc_start: 0.8833 (mmm) cc_final: 0.8616 (mmt) REVERT: C 244 ASP cc_start: 0.7895 (p0) cc_final: 0.7681 (p0) REVERT: D 10 CYS cc_start: 0.8304 (t) cc_final: 0.8087 (t) REVERT: D 44 MET cc_start: 0.7523 (mmp) cc_final: 0.7092 (mmt) REVERT: D 132 MET cc_start: 0.8660 (ppp) cc_final: 0.8459 (ttp) REVERT: D 154 ASP cc_start: 0.8395 (t0) cc_final: 0.8095 (t0) REVERT: D 162 ASN cc_start: 0.8664 (m110) cc_final: 0.8432 (m110) REVERT: D 191 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8496 (tttm) REVERT: D 326 LYS cc_start: 0.8062 (pmtt) cc_final: 0.7776 (ptmt) outliers start: 12 outliers final: 9 residues processed: 301 average time/residue: 0.2725 time to fit residues: 111.9044 Evaluate side-chains 159 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN B 111 ASN B 162 ASN B 246 GLN C 12 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 137 GLN C 162 ASN D 12 ASN D 78 ASN D 162 ASN D 246 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12004 Z= 0.205 Angle : 0.640 7.082 16292 Z= 0.317 Chirality : 0.047 0.179 1808 Planarity : 0.005 0.038 2084 Dihedral : 8.059 81.719 1702 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.91 % Allowed : 8.20 % Favored : 89.89 % 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: -3.70 (0.18), residues: 1468 helix: -3.51 (0.13), residues: 568 sheet: -2.51 (0.44), residues: 108 loop : -1.52 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.004 0.001 HIS C 40 PHE 0.012 0.001 PHE B 375 TYR 0.009 0.001 TYR A 169 ARG 0.003 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7400 (mmm) cc_final: 0.5825 (mpp) REVERT: A 81 ASP cc_start: 0.7729 (m-30) cc_final: 0.7438 (m-30) REVERT: A 132 MET cc_start: 0.8923 (ppp) cc_final: 0.8683 (ppp) REVERT: A 154 ASP cc_start: 0.8257 (t0) cc_final: 0.8048 (t70) REVERT: A 283 MET cc_start: 0.7758 (mmt) cc_final: 0.7462 (mmm) REVERT: B 41 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: B 367 PRO cc_start: 0.8622 (Cg_endo) cc_final: 0.8392 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6862 (mmtt) cc_final: 0.6255 (mmtt) REVERT: C 123 MET cc_start: 0.8842 (mmm) cc_final: 0.8265 (mmm) REVERT: C 132 MET cc_start: 0.8590 (ppp) cc_final: 0.8368 (ppp) REVERT: D 10 CYS cc_start: 0.8212 (t) cc_final: 0.7949 (t) REVERT: D 132 MET cc_start: 0.8791 (ppp) cc_final: 0.8384 (ttp) REVERT: D 142 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8659 (mt) REVERT: D 154 ASP cc_start: 0.8380 (t0) cc_final: 0.8016 (t0) outliers start: 24 outliers final: 8 residues processed: 188 average time/residue: 0.2038 time to fit residues: 57.0781 Evaluate side-chains 146 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.0770 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 108 optimal weight: 0.3980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 246 GLN B 111 ASN C 12 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 78 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12004 Z= 0.200 Angle : 0.587 6.242 16292 Z= 0.284 Chirality : 0.047 0.199 1808 Planarity : 0.004 0.036 2084 Dihedral : 7.175 78.320 1682 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.99 % Allowed : 10.19 % Favored : 87.82 % 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: -3.09 (0.20), residues: 1468 helix: -2.93 (0.16), residues: 588 sheet: -2.21 (0.44), residues: 124 loop : -1.13 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.004 0.001 HIS C 40 PHE 0.010 0.001 PHE B 375 TYR 0.008 0.001 TYR D 143 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7566 (mmm) cc_final: 0.5875 (mpp) REVERT: A 132 MET cc_start: 0.8874 (ppp) cc_final: 0.8522 (ppp) REVERT: A 137 GLN cc_start: 0.8491 (mt0) cc_final: 0.8249 (mt0) REVERT: A 176 MET cc_start: 0.8226 (mmm) cc_final: 0.7909 (mmt) REVERT: A 283 MET cc_start: 0.7681 (mmt) cc_final: 0.7413 (mmm) REVERT: B 41 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: B 44 MET cc_start: 0.6408 (mmm) cc_final: 0.4341 (mpp) REVERT: B 367 PRO cc_start: 0.8672 (Cg_endo) cc_final: 0.8418 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6887 (mmtt) cc_final: 0.6286 (mmtt) REVERT: C 123 MET cc_start: 0.8822 (mmm) cc_final: 0.8304 (mmm) REVERT: C 132 MET cc_start: 0.8558 (ppp) cc_final: 0.8309 (ppp) REVERT: C 269 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6802 (mtp) REVERT: D 132 MET cc_start: 0.8810 (ppp) cc_final: 0.8339 (ttp) REVERT: D 142 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8666 (mt) REVERT: D 154 ASP cc_start: 0.8404 (t0) cc_final: 0.8065 (t0) outliers start: 25 outliers final: 12 residues processed: 163 average time/residue: 0.2004 time to fit residues: 50.1592 Evaluate side-chains 142 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 121 GLN B 360 GLN C 12 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN D 12 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12004 Z= 0.212 Angle : 0.579 6.231 16292 Z= 0.278 Chirality : 0.046 0.162 1808 Planarity : 0.004 0.035 2084 Dihedral : 6.817 74.982 1678 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.23 % Allowed : 10.51 % Favored : 87.26 % 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: -2.57 (0.21), residues: 1468 helix: -2.48 (0.18), residues: 564 sheet: -2.07 (0.36), residues: 172 loop : -0.77 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 340 HIS 0.007 0.001 HIS A 275 PHE 0.010 0.001 PHE B 375 TYR 0.007 0.001 TYR A 169 ARG 0.002 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7693 (mmm) cc_final: 0.5870 (mpp) REVERT: A 132 MET cc_start: 0.8834 (ppp) cc_final: 0.8512 (ppp) REVERT: A 176 MET cc_start: 0.8288 (mmm) cc_final: 0.7992 (mmt) REVERT: A 283 MET cc_start: 0.7643 (mmt) cc_final: 0.7336 (mmm) REVERT: B 41 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: B 44 MET cc_start: 0.6438 (mmm) cc_final: 0.4371 (mpp) REVERT: B 360 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7991 (pp30) REVERT: B 367 PRO cc_start: 0.8700 (Cg_endo) cc_final: 0.8482 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6881 (mmtt) cc_final: 0.6285 (mmtt) REVERT: C 123 MET cc_start: 0.8768 (mmm) cc_final: 0.8122 (mmm) REVERT: C 132 MET cc_start: 0.8552 (ppp) cc_final: 0.8303 (ppp) REVERT: D 132 MET cc_start: 0.8804 (ppp) cc_final: 0.8355 (ttp) REVERT: D 142 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8645 (mt) REVERT: D 154 ASP cc_start: 0.8424 (t0) cc_final: 0.8084 (t0) outliers start: 28 outliers final: 16 residues processed: 152 average time/residue: 0.1987 time to fit residues: 46.4897 Evaluate side-chains 143 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN B 360 GLN C 12 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN D 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12004 Z= 0.374 Angle : 0.636 6.497 16292 Z= 0.311 Chirality : 0.049 0.154 1808 Planarity : 0.004 0.036 2084 Dihedral : 6.923 77.387 1674 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.31 % Allowed : 10.99 % Favored : 86.70 % 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: -2.37 (0.21), residues: 1468 helix: -2.27 (0.19), residues: 540 sheet: -2.02 (0.37), residues: 172 loop : -0.74 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 340 HIS 0.006 0.002 HIS C 40 PHE 0.012 0.001 PHE B 223 TYR 0.013 0.001 TYR D 143 ARG 0.003 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7515 (mmm) cc_final: 0.5777 (mpp) REVERT: A 132 MET cc_start: 0.8871 (ppp) cc_final: 0.8509 (ppp) REVERT: A 176 MET cc_start: 0.8307 (mmm) cc_final: 0.7998 (mmt) REVERT: A 283 MET cc_start: 0.7732 (mmt) cc_final: 0.7421 (mmm) REVERT: A 325 MET cc_start: 0.8197 (ppp) cc_final: 0.7340 (ppp) REVERT: B 44 MET cc_start: 0.6597 (mmm) cc_final: 0.4602 (mpp) REVERT: B 367 PRO cc_start: 0.8642 (Cg_endo) cc_final: 0.8436 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6979 (mmtt) cc_final: 0.6313 (mmtt) REVERT: C 123 MET cc_start: 0.8783 (mmm) cc_final: 0.8119 (mmm) REVERT: C 132 MET cc_start: 0.8466 (ppp) cc_final: 0.8204 (ppp) REVERT: C 269 MET cc_start: 0.7258 (mtp) cc_final: 0.7032 (mtp) REVERT: D 132 MET cc_start: 0.8906 (ppp) cc_final: 0.8407 (ttp) REVERT: D 142 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8817 (mt) REVERT: D 154 ASP cc_start: 0.8453 (t0) cc_final: 0.8091 (t0) outliers start: 29 outliers final: 17 residues processed: 147 average time/residue: 0.1964 time to fit residues: 45.0666 Evaluate side-chains 137 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN C 12 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12004 Z= 0.191 Angle : 0.568 6.990 16292 Z= 0.271 Chirality : 0.046 0.155 1808 Planarity : 0.003 0.032 2084 Dihedral : 6.634 72.935 1674 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.67 % Allowed : 12.02 % Favored : 86.31 % 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: -2.13 (0.22), residues: 1468 helix: -2.10 (0.20), residues: 544 sheet: -1.86 (0.37), residues: 172 loop : -0.57 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.004 0.001 HIS D 275 PHE 0.011 0.001 PHE B 223 TYR 0.007 0.001 TYR C 306 ARG 0.002 0.000 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7646 (mmm) cc_final: 0.5846 (mpp) REVERT: A 132 MET cc_start: 0.8878 (ppp) cc_final: 0.8539 (ppp) REVERT: A 176 MET cc_start: 0.8275 (mmm) cc_final: 0.7976 (mmt) REVERT: A 283 MET cc_start: 0.7599 (mmt) cc_final: 0.7299 (mmm) REVERT: A 325 MET cc_start: 0.7986 (ppp) cc_final: 0.7124 (ppp) REVERT: B 44 MET cc_start: 0.6383 (mmm) cc_final: 0.4338 (mpp) REVERT: C 113 LYS cc_start: 0.6944 (mmtt) cc_final: 0.6350 (mmtt) REVERT: C 123 MET cc_start: 0.8721 (mmm) cc_final: 0.8193 (mmm) REVERT: C 132 MET cc_start: 0.8478 (ppp) cc_final: 0.8020 (ppp) REVERT: C 205 GLU cc_start: 0.7212 (mp0) cc_final: 0.6849 (mp0) REVERT: C 269 MET cc_start: 0.7096 (mtp) cc_final: 0.6887 (mtp) REVERT: C 325 MET cc_start: 0.8296 (ppp) cc_final: 0.7697 (ppp) REVERT: D 82 MET cc_start: 0.8622 (tpt) cc_final: 0.8289 (tmm) REVERT: D 132 MET cc_start: 0.8874 (ppp) cc_final: 0.8376 (ttp) REVERT: D 142 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8787 (mt) REVERT: D 154 ASP cc_start: 0.8357 (t0) cc_final: 0.8005 (t0) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 0.1788 time to fit residues: 39.4578 Evaluate side-chains 132 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN B 280 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12004 Z= 0.231 Angle : 0.579 9.583 16292 Z= 0.276 Chirality : 0.047 0.154 1808 Planarity : 0.003 0.032 2084 Dihedral : 6.532 70.997 1674 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.67 % Allowed : 11.94 % Favored : 86.39 % 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: -2.00 (0.22), residues: 1468 helix: -2.01 (0.20), residues: 532 sheet: -1.67 (0.37), residues: 172 loop : -0.55 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.004 0.001 HIS C 40 PHE 0.012 0.001 PHE B 223 TYR 0.008 0.001 TYR D 143 ARG 0.002 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7629 (mmm) cc_final: 0.5843 (mpp) REVERT: A 132 MET cc_start: 0.8893 (ppp) cc_final: 0.8562 (ppp) REVERT: A 283 MET cc_start: 0.7704 (mmt) cc_final: 0.7418 (mmm) REVERT: A 313 MET cc_start: 0.7792 (mmm) cc_final: 0.7576 (tpp) REVERT: A 325 MET cc_start: 0.7833 (ppp) cc_final: 0.6929 (ppp) REVERT: B 44 MET cc_start: 0.6285 (mmm) cc_final: 0.4246 (mpp) REVERT: B 292 ASP cc_start: 0.8045 (t0) cc_final: 0.7784 (t0) REVERT: C 113 LYS cc_start: 0.6902 (mmtt) cc_final: 0.6301 (mmtt) REVERT: C 123 MET cc_start: 0.8706 (mmm) cc_final: 0.8210 (mmm) REVERT: C 132 MET cc_start: 0.8466 (ppp) cc_final: 0.8011 (ppp) REVERT: C 202 THR cc_start: 0.8945 (p) cc_final: 0.8634 (p) REVERT: C 205 GLU cc_start: 0.7173 (mp0) cc_final: 0.6947 (mp0) REVERT: C 270 GLU cc_start: 0.7834 (tp30) cc_final: 0.7596 (tm-30) REVERT: C 325 MET cc_start: 0.8250 (ppp) cc_final: 0.7692 (ppp) REVERT: D 82 MET cc_start: 0.8650 (tpt) cc_final: 0.8322 (tmm) REVERT: D 132 MET cc_start: 0.8883 (ppp) cc_final: 0.8392 (ttp) REVERT: D 142 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8812 (mt) REVERT: D 154 ASP cc_start: 0.8335 (t0) cc_final: 0.7980 (t0) outliers start: 21 outliers final: 18 residues processed: 132 average time/residue: 0.1836 time to fit residues: 39.0089 Evaluate side-chains 132 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.0970 chunk 85 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12004 Z= 0.278 Angle : 0.598 7.343 16292 Z= 0.287 Chirality : 0.047 0.152 1808 Planarity : 0.004 0.032 2084 Dihedral : 6.577 71.952 1674 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.99 % Allowed : 12.02 % Favored : 85.99 % 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: -1.93 (0.22), residues: 1468 helix: -1.94 (0.20), residues: 532 sheet: -1.59 (0.38), residues: 172 loop : -0.54 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 340 HIS 0.005 0.001 HIS A 275 PHE 0.011 0.001 PHE D 223 TYR 0.010 0.001 TYR D 143 ARG 0.003 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7552 (mmm) cc_final: 0.5820 (mpp) REVERT: A 132 MET cc_start: 0.8854 (ppp) cc_final: 0.8532 (ppp) REVERT: A 283 MET cc_start: 0.7735 (mmt) cc_final: 0.7450 (mmm) REVERT: A 325 MET cc_start: 0.7835 (ppp) cc_final: 0.6976 (ppp) REVERT: B 44 MET cc_start: 0.6362 (mmm) cc_final: 0.4373 (mpp) REVERT: B 292 ASP cc_start: 0.8046 (t0) cc_final: 0.7788 (t0) REVERT: C 113 LYS cc_start: 0.6916 (mmtt) cc_final: 0.6294 (mmtt) REVERT: C 123 MET cc_start: 0.8737 (mmm) cc_final: 0.8225 (mmm) REVERT: C 132 MET cc_start: 0.8439 (ppp) cc_final: 0.7992 (ppp) REVERT: C 202 THR cc_start: 0.8957 (p) cc_final: 0.8649 (p) REVERT: C 205 GLU cc_start: 0.7193 (mp0) cc_final: 0.6986 (mp0) REVERT: C 325 MET cc_start: 0.8232 (ppp) cc_final: 0.7696 (ppp) REVERT: D 82 MET cc_start: 0.8666 (tpt) cc_final: 0.8361 (tmm) REVERT: D 132 MET cc_start: 0.8904 (ppp) cc_final: 0.8411 (ttp) REVERT: D 142 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8664 (mm) REVERT: D 154 ASP cc_start: 0.8344 (t0) cc_final: 0.7994 (t0) outliers start: 25 outliers final: 21 residues processed: 130 average time/residue: 0.1814 time to fit residues: 37.6980 Evaluate side-chains 131 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 0.0040 chunk 87 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN B 280 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12004 Z= 0.164 Angle : 0.555 6.716 16292 Z= 0.263 Chirality : 0.045 0.151 1808 Planarity : 0.003 0.030 2084 Dihedral : 6.296 69.397 1674 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.35 % Allowed : 13.06 % Favored : 85.59 % 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: -1.74 (0.22), residues: 1468 helix: -1.79 (0.21), residues: 532 sheet: -1.49 (0.38), residues: 172 loop : -0.41 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.003 0.001 HIS A 275 PHE 0.012 0.001 PHE D 223 TYR 0.006 0.001 TYR A 306 ARG 0.001 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.359 Fit side-chains REVERT: A 44 MET cc_start: 0.7513 (mmm) cc_final: 0.5632 (mpp) REVERT: A 132 MET cc_start: 0.8897 (ppp) cc_final: 0.8619 (ppp) REVERT: A 137 GLN cc_start: 0.8295 (mt0) cc_final: 0.8064 (mt0) REVERT: A 269 MET cc_start: 0.7325 (mtp) cc_final: 0.6889 (ttm) REVERT: A 313 MET cc_start: 0.7746 (mmm) cc_final: 0.7509 (tpp) REVERT: A 325 MET cc_start: 0.7704 (ppp) cc_final: 0.7136 (ppp) REVERT: B 44 MET cc_start: 0.6181 (mmm) cc_final: 0.4165 (mpp) REVERT: B 292 ASP cc_start: 0.7946 (t0) cc_final: 0.7699 (t0) REVERT: C 113 LYS cc_start: 0.6900 (mmtt) cc_final: 0.6332 (mmtt) REVERT: C 123 MET cc_start: 0.8638 (mmm) cc_final: 0.8206 (mmm) REVERT: C 132 MET cc_start: 0.8493 (ppp) cc_final: 0.8048 (ppp) REVERT: C 202 THR cc_start: 0.8942 (p) cc_final: 0.8603 (p) REVERT: C 325 MET cc_start: 0.8179 (ppp) cc_final: 0.7641 (ppp) REVERT: D 82 MET cc_start: 0.8619 (tpt) cc_final: 0.8147 (tmm) REVERT: D 132 MET cc_start: 0.8859 (ppp) cc_final: 0.8371 (ttp) REVERT: D 154 ASP cc_start: 0.8328 (t0) cc_final: 0.7977 (t0) outliers start: 17 outliers final: 14 residues processed: 131 average time/residue: 0.2001 time to fit residues: 42.1188 Evaluate side-chains 130 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12004 Z= 0.225 Angle : 0.574 9.260 16292 Z= 0.273 Chirality : 0.046 0.147 1808 Planarity : 0.003 0.030 2084 Dihedral : 6.275 68.315 1674 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.43 % Allowed : 12.90 % Favored : 85.67 % 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: -1.66 (0.22), residues: 1468 helix: -1.71 (0.21), residues: 528 sheet: -1.45 (0.36), residues: 196 loop : -0.34 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 356 HIS 0.004 0.001 HIS C 40 PHE 0.012 0.001 PHE D 223 TYR 0.007 0.001 TYR D 143 ARG 0.002 0.000 ARG C 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.382 Fit side-chains REVERT: A 44 MET cc_start: 0.7566 (mmm) cc_final: 0.5705 (mpp) REVERT: A 132 MET cc_start: 0.8839 (ppp) cc_final: 0.8556 (ppp) REVERT: A 137 GLN cc_start: 0.8305 (mt0) cc_final: 0.8083 (mt0) REVERT: A 269 MET cc_start: 0.7346 (mtp) cc_final: 0.6910 (ttm) REVERT: A 313 MET cc_start: 0.7812 (mmm) cc_final: 0.7557 (tpp) REVERT: A 325 MET cc_start: 0.7750 (ppp) cc_final: 0.6956 (ppp) REVERT: B 44 MET cc_start: 0.6194 (mmm) cc_final: 0.4187 (mpp) REVERT: B 292 ASP cc_start: 0.7976 (t0) cc_final: 0.7731 (t0) REVERT: C 113 LYS cc_start: 0.6892 (mmtt) cc_final: 0.6306 (mmtt) REVERT: C 123 MET cc_start: 0.8667 (mmm) cc_final: 0.8216 (mmm) REVERT: C 132 MET cc_start: 0.8504 (ppp) cc_final: 0.8059 (ppp) REVERT: C 291 LYS cc_start: 0.6774 (mptt) cc_final: 0.6486 (mptt) REVERT: C 325 MET cc_start: 0.8181 (ppp) cc_final: 0.7651 (ppp) REVERT: D 82 MET cc_start: 0.8657 (tpt) cc_final: 0.8194 (tmm) REVERT: D 132 MET cc_start: 0.8883 (ppp) cc_final: 0.8392 (ttp) REVERT: D 154 ASP cc_start: 0.8314 (t0) cc_final: 0.7958 (t0) outliers start: 18 outliers final: 16 residues processed: 129 average time/residue: 0.1841 time to fit residues: 37.8390 Evaluate side-chains 128 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 120 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.0570 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.075978 restraints weight = 23802.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.078782 restraints weight = 12376.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.080699 restraints weight = 7728.557| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12004 Z= 0.146 Angle : 0.550 9.972 16292 Z= 0.258 Chirality : 0.045 0.148 1808 Planarity : 0.003 0.030 2084 Dihedral : 5.989 63.254 1674 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.27 % Allowed : 13.22 % Favored : 85.51 % 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: -1.49 (0.22), residues: 1468 helix: -1.56 (0.21), residues: 528 sheet: -1.40 (0.36), residues: 196 loop : -0.23 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.003 0.001 HIS A 275 PHE 0.012 0.001 PHE D 223 TYR 0.007 0.001 TYR C 306 ARG 0.002 0.000 ARG C 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2196.63 seconds wall clock time: 41 minutes 18.73 seconds (2478.73 seconds total)