Starting phenix.real_space_refine on Thu Feb 15 09:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djn_7937/02_2024/6djn_7937_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djn_7937/02_2024/6djn_7937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djn_7937/02_2024/6djn_7937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djn_7937/02_2024/6djn_7937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djn_7937/02_2024/6djn_7937_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djn_7937/02_2024/6djn_7937_updated.pdb" } resolution = 3.1 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 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2280 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 "A ARG 372": "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 "B ARG 372": "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 "C ARG 372": "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" Residue "D ARG 372": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11768 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.75, per 1000 atoms: 0.57 Number of scatterers: 11768 At special positions: 0 Unit cell: (100.32, 76.285, 165.11, 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 12 15.00 Mg 4 11.99 O 2280 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: 5.01 Conformation dependent library (CDL) restraints added in 2.6 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 37.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.902A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.785A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 192 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: 3.879A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.923A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.724A pdb=" N LEU A 293 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) 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 310 through 317 removed outlier: 3.514A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.533A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.522A pdb=" N ILE A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 370' Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.901A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.785A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 192 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: 3.879A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.922A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.725A pdb=" N LEU B 293 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) 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 310 through 317 removed outlier: 3.513A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.533A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.522A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 370' Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.901A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.785A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 192 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: 3.879A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.922A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 276 through 282 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.725A pdb=" N LEU C 293 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) 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 310 through 317 removed outlier: 3.514A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.533A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.522A pdb=" N ILE C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 370' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.901A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 144 removed outlier: 3.785A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 192 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: 3.880A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.922A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 276 through 282 Processing helix chain 'D' and resid 289 through 294 removed outlier: 3.724A pdb=" N LEU D 293 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR D 294 " --> pdb=" O LYS D 291 " (cutoff:3.500A) 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 310 through 317 removed outlier: 3.513A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 removed outlier: 3.533A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 366 through 370 removed outlier: 3.523A pdb=" N ILE D 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 366 through 370' Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.762A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.534A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.423A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.761A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 removed outlier: 3.535A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.424A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.761A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.535A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.423A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.761A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 removed outlier: 3.534A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.422A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 312 hydrogen bonds defined for protein. 828 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: 3.76 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3420 1.33 - 1.45: 1833 1.45 - 1.57: 6607 1.57 - 1.68: 12 1.68 - 1.80: 148 Bond restraints: 12020 Sorted by residual: bond pdb=" O3 PO4 B 803 " pdb=" P PO4 B 803 " ideal model delta sigma weight residual 1.569 1.494 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O3 PO4 D 803 " pdb=" P PO4 D 803 " ideal model delta sigma weight residual 1.569 1.496 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O2 PO4 A 803 " pdb=" P PO4 A 803 " ideal model delta sigma weight residual 1.567 1.496 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O3 PO4 C 803 " pdb=" P PO4 C 803 " ideal model delta sigma weight residual 1.569 1.498 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O3 PO4 A 803 " pdb=" P PO4 A 803 " ideal model delta sigma weight residual 1.569 1.501 0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 12015 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.48: 335 105.48 - 113.13: 6511 113.13 - 120.77: 5698 120.77 - 128.42: 3683 128.42 - 136.06: 89 Bond angle restraints: 16316 Sorted by residual: angle pdb=" C GLY A 46 " pdb=" N MET A 47 " pdb=" CA MET A 47 " ideal model delta sigma weight residual 122.08 127.89 -5.81 1.47e+00 4.63e-01 1.56e+01 angle pdb=" C GLY C 46 " pdb=" N MET C 47 " pdb=" CA MET C 47 " ideal model delta sigma weight residual 122.08 127.85 -5.77 1.47e+00 4.63e-01 1.54e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 122.08 127.84 -5.76 1.47e+00 4.63e-01 1.54e+01 angle pdb=" C GLY B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 122.08 127.84 -5.76 1.47e+00 4.63e-01 1.53e+01 angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 116.45 -5.95 1.70e+00 3.46e-01 1.23e+01 ... (remaining 16311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 7035 23.63 - 47.26: 177 47.26 - 70.89: 0 70.89 - 94.53: 4 94.53 - 118.16: 4 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" C5' ADP B 802 " pdb=" O5' ADP B 802 " pdb=" PA ADP B 802 " pdb=" O2A ADP B 802 " ideal model delta sinusoidal sigma weight residual -60.00 58.16 -118.16 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" C5' ADP A 802 " pdb=" O5' ADP A 802 " pdb=" PA ADP A 802 " pdb=" O2A ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 53.64 -113.63 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" C5' ADP C 802 " pdb=" O5' ADP C 802 " pdb=" PA ADP C 802 " pdb=" O2A ADP C 802 " ideal model delta sinusoidal sigma weight residual -60.00 48.00 -108.00 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1193 0.057 - 0.114: 530 0.114 - 0.171: 61 0.171 - 0.228: 12 0.228 - 0.285: 12 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 332 " 0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO A 333 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 332 " -0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO D 333 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 333 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 333 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 332 " 0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO C 333 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.048 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 240 2.66 - 3.22: 10590 3.22 - 3.78: 18417 3.78 - 4.34: 26480 4.34 - 4.90: 43435 Nonbonded interactions: 99162 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.117 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 2.131 2.170 nonbonded pdb="MG MG A 801 " pdb=" O4 PO4 A 803 " model vdw 2.146 2.170 ... (remaining 99157 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 8.570 Check model and map are aligned: 0.170 Set scattering table: 0.130 Process input model: 36.320 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.011 0.075 12020 Z= 0.689 Angle : 0.950 9.577 16316 Z= 0.495 Chirality : 0.062 0.285 1808 Planarity : 0.008 0.087 2084 Dihedral : 10.671 118.157 4468 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: -4.61 (0.16), residues: 1468 helix: -4.20 (0.10), residues: 600 sheet: -2.19 (0.29), residues: 244 loop : -1.95 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP C 340 HIS 0.011 0.003 HIS A 40 PHE 0.019 0.003 PHE A 31 TYR 0.015 0.002 TYR B 169 ARG 0.013 0.002 ARG D 147 *********************** 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 246 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.421 Fit side-chains REVERT: A 157 ASP cc_start: 0.7962 (t0) cc_final: 0.7665 (t0) REVERT: A 202 THR cc_start: 0.9037 (p) cc_final: 0.8632 (p) REVERT: A 205 GLU cc_start: 0.8141 (mp0) cc_final: 0.7771 (mp0) REVERT: B 51 ASP cc_start: 0.7591 (t70) cc_final: 0.7312 (p0) REVERT: B 82 MET cc_start: 0.9160 (tpt) cc_final: 0.8746 (tpt) REVERT: B 184 ASP cc_start: 0.8012 (m-30) cc_final: 0.7804 (m-30) REVERT: B 191 LYS cc_start: 0.8445 (ttpt) cc_final: 0.7875 (tttm) REVERT: B 194 THR cc_start: 0.8884 (m) cc_final: 0.8615 (p) REVERT: B 314 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8049 (tt0) REVERT: C 92 ASN cc_start: 0.8420 (m110) cc_final: 0.8160 (m-40) REVERT: C 191 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7972 (tttm) REVERT: D 92 ASN cc_start: 0.8298 (m110) cc_final: 0.8060 (m-40) REVERT: D 191 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8122 (ttmm) REVERT: D 225 ASN cc_start: 0.8181 (m-40) cc_final: 0.7796 (m-40) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2976 time to fit residues: 98.1623 Evaluate side-chains 114 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 161 HIS A 162 ASN A 263 GLN B 12 ASN B 59 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS B 162 ASN C 161 HIS C 162 ASN C 246 GLN D 12 ASN D 161 HIS D 162 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12020 Z= 0.205 Angle : 0.591 6.575 16316 Z= 0.291 Chirality : 0.045 0.139 1808 Planarity : 0.006 0.063 2084 Dihedral : 7.625 104.028 1672 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.27 % Allowed : 6.77 % Favored : 91.96 % 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: -3.00 (0.19), residues: 1468 helix: -2.69 (0.17), residues: 604 sheet: -1.64 (0.29), residues: 236 loop : -1.12 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 340 HIS 0.004 0.001 HIS C 40 PHE 0.010 0.001 PHE B 255 TYR 0.011 0.001 TYR C 143 ARG 0.006 0.001 ARG D 372 *********************** 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 149 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.521 Fit side-chains REVERT: A 157 ASP cc_start: 0.7825 (t0) cc_final: 0.7415 (t0) REVERT: A 191 LYS cc_start: 0.8536 (ttpt) cc_final: 0.8165 (ttmt) REVERT: B 82 MET cc_start: 0.9045 (tpt) cc_final: 0.8503 (tpt) REVERT: B 157 ASP cc_start: 0.7944 (t0) cc_final: 0.7585 (t0) REVERT: B 191 LYS cc_start: 0.8269 (ttpt) cc_final: 0.7981 (tttm) REVERT: B 305 MET cc_start: 0.7997 (mmt) cc_final: 0.7656 (mmt) outliers start: 16 outliers final: 10 residues processed: 144 average time/residue: 0.2793 time to fit residues: 57.8771 Evaluate side-chains 113 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 134 optimal weight: 0.3980 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS C 59 GLN C 121 GLN D 173 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 12020 Z= 0.469 Angle : 0.679 6.582 16316 Z= 0.336 Chirality : 0.050 0.153 1808 Planarity : 0.006 0.060 2084 Dihedral : 8.087 116.536 1672 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.35 % Allowed : 8.36 % Favored : 90.29 % 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: -2.31 (0.21), residues: 1468 helix: -2.07 (0.18), residues: 632 sheet: -1.32 (0.32), residues: 236 loop : -0.69 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 340 HIS 0.007 0.002 HIS C 40 PHE 0.015 0.002 PHE D 262 TYR 0.012 0.002 TYR B 69 ARG 0.004 0.001 ARG A 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 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.414 Fit side-chains REVERT: A 12 ASN cc_start: 0.8241 (p0) cc_final: 0.8013 (p0) REVERT: A 157 ASP cc_start: 0.7763 (t0) cc_final: 0.7358 (t0) REVERT: A 205 GLU cc_start: 0.7978 (mp0) cc_final: 0.7732 (mp0) REVERT: A 305 MET cc_start: 0.8627 (mmm) cc_final: 0.8374 (mmt) REVERT: B 82 MET cc_start: 0.9082 (tpt) cc_final: 0.8563 (tpt) REVERT: C 84 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8942 (mttt) REVERT: C 355 MET cc_start: 0.8058 (mtm) cc_final: 0.7806 (mtm) outliers start: 17 outliers final: 11 residues processed: 117 average time/residue: 0.2150 time to fit residues: 38.4009 Evaluate side-chains 104 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12020 Z= 0.171 Angle : 0.537 6.294 16316 Z= 0.257 Chirality : 0.044 0.137 1808 Planarity : 0.004 0.053 2084 Dihedral : 7.125 99.188 1672 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.19 % Allowed : 9.47 % Favored : 89.33 % 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: -1.55 (0.22), residues: 1468 helix: -1.40 (0.20), residues: 632 sheet: -0.94 (0.32), residues: 236 loop : -0.33 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.004 0.001 HIS C 40 PHE 0.008 0.001 PHE B 255 TYR 0.007 0.001 TYR B 169 ARG 0.005 0.000 ARG D 206 *********************** 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 124 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.447 Fit side-chains REVERT: A 157 ASP cc_start: 0.7762 (t0) cc_final: 0.7506 (t0) REVERT: A 305 MET cc_start: 0.8625 (mmm) cc_final: 0.8353 (mmt) REVERT: A 325 MET cc_start: 0.7905 (ppp) cc_final: 0.7359 (ppp) REVERT: B 157 ASP cc_start: 0.7959 (t0) cc_final: 0.7539 (t0) REVERT: B 325 MET cc_start: 0.7846 (ppp) cc_final: 0.7108 (ppp) REVERT: C 79 TRP cc_start: 0.8317 (m100) cc_final: 0.8060 (m100) REVERT: C 84 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8766 (mttt) outliers start: 15 outliers final: 12 residues processed: 122 average time/residue: 0.2031 time to fit residues: 38.5050 Evaluate side-chains 118 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 12020 Z= 0.439 Angle : 0.644 6.583 16316 Z= 0.315 Chirality : 0.049 0.149 1808 Planarity : 0.005 0.055 2084 Dihedral : 7.826 115.057 1672 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.39 % Allowed : 9.63 % Favored : 87.98 % 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: -1.59 (0.21), residues: 1468 helix: -1.33 (0.20), residues: 640 sheet: -0.76 (0.33), residues: 236 loop : -0.56 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 79 HIS 0.007 0.002 HIS B 40 PHE 0.013 0.002 PHE D 262 TYR 0.012 0.001 TYR B 69 ARG 0.004 0.001 ARG A 256 *********************** 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 136 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 1.553 Fit side-chains REVERT: A 12 ASN cc_start: 0.8189 (p0) cc_final: 0.7909 (p0) REVERT: A 157 ASP cc_start: 0.7751 (t0) cc_final: 0.7492 (t0) REVERT: A 305 MET cc_start: 0.8647 (mmm) cc_final: 0.8443 (mmt) REVERT: A 325 MET cc_start: 0.8131 (ppp) cc_final: 0.7548 (ppp) REVERT: B 84 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8776 (mtpp) REVERT: B 325 MET cc_start: 0.7912 (ppp) cc_final: 0.6998 (ppp) REVERT: C 84 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8928 (mttt) outliers start: 30 outliers final: 21 residues processed: 129 average time/residue: 0.2181 time to fit residues: 42.7473 Evaluate side-chains 127 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 75 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN A 246 GLN A 360 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12020 Z= 0.267 Angle : 0.569 6.337 16316 Z= 0.274 Chirality : 0.046 0.147 1808 Planarity : 0.004 0.051 2084 Dihedral : 7.415 107.781 1672 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.23 % Allowed : 10.35 % Favored : 87.42 % 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: -1.21 (0.22), residues: 1468 helix: -1.00 (0.21), residues: 640 sheet: -0.61 (0.34), residues: 236 loop : -0.37 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS B 40 PHE 0.009 0.001 PHE B 255 TYR 0.007 0.001 TYR B 169 ARG 0.008 0.000 ARG C 335 *********************** 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 137 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.549 Fit side-chains REVERT: A 12 ASN cc_start: 0.8263 (p0) cc_final: 0.8001 (p0) REVERT: A 157 ASP cc_start: 0.7743 (t0) cc_final: 0.7486 (t0) REVERT: A 325 MET cc_start: 0.8066 (ppp) cc_final: 0.7599 (ppp) REVERT: B 84 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8758 (mtpp) REVERT: B 325 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.6967 (ppp) REVERT: C 84 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8892 (mttt) REVERT: C 242 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8737 (mp) outliers start: 28 outliers final: 20 residues processed: 128 average time/residue: 0.2140 time to fit residues: 42.3731 Evaluate side-chains 126 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 chunk 120 optimal weight: 0.0770 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 0.0040 overall best weight: 0.4550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS A 246 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12020 Z= 0.143 Angle : 0.518 6.199 16316 Z= 0.244 Chirality : 0.043 0.148 1808 Planarity : 0.004 0.050 2084 Dihedral : 6.490 88.125 1672 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.99 % Allowed : 10.75 % 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: -0.78 (0.23), residues: 1468 helix: -0.65 (0.22), residues: 640 sheet: -0.47 (0.33), residues: 236 loop : -0.10 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 356 HIS 0.003 0.001 HIS A 161 PHE 0.008 0.001 PHE B 255 TYR 0.005 0.001 TYR B 169 ARG 0.008 0.000 ARG C 335 *********************** 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 137 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 1.460 Fit side-chains REVERT: A 12 ASN cc_start: 0.8267 (p0) cc_final: 0.8024 (p0) REVERT: A 157 ASP cc_start: 0.7725 (t0) cc_final: 0.7494 (t0) REVERT: A 325 MET cc_start: 0.7982 (ppp) cc_final: 0.7641 (ppp) REVERT: B 157 ASP cc_start: 0.7943 (t0) cc_final: 0.7573 (t0) REVERT: B 325 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.6953 (ppp) REVERT: C 79 TRP cc_start: 0.8267 (m100) cc_final: 0.8046 (m100) REVERT: C 84 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8573 (mtmt) outliers start: 25 outliers final: 17 residues processed: 133 average time/residue: 0.2023 time to fit residues: 42.0354 Evaluate side-chains 126 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 355 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.0570 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN A 121 GLN A 246 GLN A 353 GLN A 360 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 12020 Z= 0.241 Angle : 0.552 6.244 16316 Z= 0.263 Chirality : 0.045 0.150 1808 Planarity : 0.004 0.047 2084 Dihedral : 6.820 95.673 1672 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.15 % Allowed : 10.67 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1468 helix: -0.59 (0.22), residues: 640 sheet: -0.44 (0.34), residues: 236 loop : -0.07 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.004 0.001 HIS B 40 PHE 0.008 0.001 PHE B 255 TYR 0.008 0.001 TYR B 69 ARG 0.006 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 131 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.357 Fit side-chains REVERT: A 47 MET cc_start: 0.7418 (ppp) cc_final: 0.6009 (ppp) REVERT: A 103 THR cc_start: 0.9218 (m) cc_final: 0.8955 (p) REVERT: A 157 ASP cc_start: 0.7739 (t0) cc_final: 0.7371 (t0) REVERT: A 325 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7696 (ppp) REVERT: B 157 ASP cc_start: 0.7943 (t0) cc_final: 0.7559 (t0) REVERT: B 325 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7081 (ppp) REVERT: C 84 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8722 (mtmt) outliers start: 27 outliers final: 19 residues processed: 123 average time/residue: 0.1902 time to fit residues: 37.1454 Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 355 MET 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: 0.7980 chunk 132 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12020 Z= 0.266 Angle : 0.565 6.315 16316 Z= 0.272 Chirality : 0.046 0.158 1808 Planarity : 0.004 0.047 2084 Dihedral : 6.972 98.929 1672 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.75 % Allowed : 11.23 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1468 helix: -0.42 (0.22), residues: 616 sheet: -0.43 (0.34), residues: 236 loop : -0.02 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 79 HIS 0.004 0.001 HIS A 40 PHE 0.007 0.001 PHE A 127 TYR 0.008 0.001 TYR B 69 ARG 0.006 0.000 ARG C 335 *********************** 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 124 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 2.177 Fit side-chains REVERT: A 12 ASN cc_start: 0.8046 (p0) cc_final: 0.7822 (p0) REVERT: A 47 MET cc_start: 0.7317 (ppp) cc_final: 0.5970 (ppp) REVERT: A 157 ASP cc_start: 0.7772 (t0) cc_final: 0.7378 (t0) REVERT: A 325 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7685 (ppp) REVERT: B 132 MET cc_start: 0.8223 (ppp) cc_final: 0.8003 (ptm) REVERT: B 325 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7063 (ppp) REVERT: C 84 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8769 (mttt) outliers start: 22 outliers final: 18 residues processed: 119 average time/residue: 0.1978 time to fit residues: 37.5141 Evaluate side-chains 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 147 optimal weight: 0.0870 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 0.0370 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 0.0030 chunk 125 optimal weight: 1.9990 overall best weight: 0.6248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 360 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12020 Z= 0.175 Angle : 0.531 6.280 16316 Z= 0.253 Chirality : 0.044 0.151 1808 Planarity : 0.004 0.047 2084 Dihedral : 6.469 87.650 1672 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.59 % Allowed : 11.46 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.23), residues: 1468 helix: -0.42 (0.22), residues: 640 sheet: -0.38 (0.34), residues: 236 loop : 0.11 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE B 255 TYR 0.006 0.001 TYR B 169 ARG 0.005 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 127 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.439 Fit side-chains REVERT: A 12 ASN cc_start: 0.8026 (p0) cc_final: 0.7762 (p0) REVERT: A 157 ASP cc_start: 0.7759 (t0) cc_final: 0.7377 (t0) REVERT: A 325 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7689 (ppp) REVERT: B 157 ASP cc_start: 0.7944 (t0) cc_final: 0.7645 (t0) REVERT: B 325 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7104 (ppp) REVERT: C 84 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8702 (mtmt) outliers start: 20 outliers final: 17 residues processed: 123 average time/residue: 0.1982 time to fit residues: 38.2965 Evaluate side-chains 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 117 optimal weight: 0.0570 chunk 49 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 246 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.094865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.081393 restraints weight = 18940.998| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.95 r_work: 0.2888 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12020 Z= 0.211 Angle : 0.545 6.259 16316 Z= 0.260 Chirality : 0.045 0.152 1808 Planarity : 0.004 0.047 2084 Dihedral : 6.568 91.229 1672 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.75 % Allowed : 11.46 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.23), residues: 1468 helix: -0.40 (0.22), residues: 640 sheet: -0.37 (0.34), residues: 236 loop : 0.12 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.003 0.001 HIS B 40 PHE 0.007 0.001 PHE A 127 TYR 0.006 0.001 TYR B 69 ARG 0.006 0.000 ARG C 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.99 seconds wall clock time: 45 minutes 6.16 seconds (2706.16 seconds total)