Starting phenix.real_space_refine (version: dev) on Mon Dec 12 19:27:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kll_0711/12_2022/6kll_0711_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kll_0711/12_2022/6kll_0711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kll_0711/12_2022/6kll_0711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kll_0711/12_2022/6kll_0711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kll_0711/12_2022/6kll_0711_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kll_0711/12_2022/6kll_0711_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 286": "OD1" <-> "OD2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 286": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 6.93, per 1000 atoms: 0.59 Number of scatterers: 11748 At special positions: 0 Unit cell: (87.74, 96.3, 165.85, 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: 4.80 Conformation dependent library (CDL) restraints added in 1.9 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: 88 helices and 16 sheets defined 41.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 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 92 removed outlier: 3.563A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.542A 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 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.637A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) 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 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: 3.662A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.665A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 282 Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.893A pdb=" N LEU A 293 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.604A 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 309 through 318 removed outlier: 3.518A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 346 removed outlier: 5.117A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 341 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.890A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 372 " --> pdb=" O ILE A 369 " (cutoff:3.500A) 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 92 removed outlier: 3.563A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.543A 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 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.637A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) 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 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: 3.662A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.665A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.894A pdb=" N LEU B 293 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.605A 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 309 through 318 removed outlier: 3.518A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 346 removed outlier: 5.117A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.889A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 372 " --> pdb=" O ILE B 369 " (cutoff:3.500A) 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 92 removed outlier: 3.563A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.542A 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 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.637A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) 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 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: 3.661A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.664A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 256' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 282 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.893A pdb=" N LEU C 293 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.605A 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 309 through 318 removed outlier: 3.518A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 346 removed outlier: 5.117A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.890A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 372 " --> pdb=" O ILE C 369 " (cutoff:3.500A) 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 92 removed outlier: 3.563A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.542A 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 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.638A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) 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 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: 3.662A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.666A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 256' Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 282 Processing helix chain 'D' and resid 289 through 294 removed outlier: 3.893A pdb=" N LEU D 293 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.605A 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 309 through 318 removed outlier: 3.518A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 346 removed outlier: 5.117A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D 346 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.889A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 372 " --> pdb=" O ILE D 369 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.694A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.131A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.731A 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: 6.694A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.131A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.731A 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: 6.694A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.130A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.731A 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: 6.694A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.131A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.730A 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 241 340 hydrogen bonds defined for protein. 840 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: 3.45 Time building geometry restraints manager: 5.21 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: 3832 1.34 - 1.46: 2526 1.46 - 1.58: 5482 1.58 - 1.69: 16 1.69 - 1.81: 148 Bond restraints: 12004 Sorted by residual: bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.04e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" CA LEU A 104 " pdb=" CB LEU A 104 " ideal model delta sigma weight residual 1.528 1.496 0.033 1.51e-02 4.39e+03 4.66e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 98.82 - 106.26: 414 106.26 - 113.70: 6730 113.70 - 121.13: 5903 121.13 - 128.57: 3168 128.57 - 136.00: 77 Bond angle restraints: 16292 Sorted by residual: angle pdb=" CB GLU C 4 " pdb=" CG GLU C 4 " pdb=" CD GLU C 4 " ideal model delta sigma weight residual 112.60 119.71 -7.11 1.70e+00 3.46e-01 1.75e+01 angle pdb=" CB GLU A 4 " pdb=" CG GLU A 4 " pdb=" CD GLU A 4 " ideal model delta sigma weight residual 112.60 119.71 -7.11 1.70e+00 3.46e-01 1.75e+01 angle pdb=" CB GLU D 4 " pdb=" CG GLU D 4 " pdb=" CD GLU D 4 " ideal model delta sigma weight residual 112.60 119.68 -7.08 1.70e+00 3.46e-01 1.73e+01 angle pdb=" CB GLU B 4 " pdb=" CG GLU B 4 " pdb=" CD GLU B 4 " ideal model delta sigma weight residual 112.60 119.66 -7.06 1.70e+00 3.46e-01 1.73e+01 angle pdb=" CA GLU D 4 " pdb=" CB GLU D 4 " pdb=" CG GLU D 4 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.51e+01 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.69: 6531 20.69 - 41.39: 597 41.39 - 62.08: 80 62.08 - 82.77: 4 82.77 - 103.47: 8 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 43.47 -103.47 1 2.00e+01 2.50e-03 2.96e+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 43.47 -103.46 1 2.00e+01 2.50e-03 2.96e+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 43.44 -103.43 1 2.00e+01 2.50e-03 2.96e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1008 0.042 - 0.084: 597 0.084 - 0.126: 183 0.126 - 0.168: 16 0.168 - 0.210: 4 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB VAL C 370 " pdb=" CA VAL C 370 " pdb=" CG1 VAL C 370 " pdb=" CG2 VAL C 370 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB VAL D 370 " pdb=" CA VAL D 370 " pdb=" CG1 VAL D 370 " pdb=" CG2 VAL D 370 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB VAL A 370 " pdb=" CA VAL A 370 " pdb=" CG1 VAL A 370 " pdb=" CG2 VAL A 370 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO D 243 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO B 243 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO C 243 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.021 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 96 2.53 - 3.13: 8784 3.13 - 3.72: 17657 3.72 - 4.31: 27182 4.31 - 4.90: 44383 Nonbonded interactions: 98102 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 1.944 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 1.944 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 1.944 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 1.945 2.170 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.173 2.440 ... (remaining 98097 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 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. 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: 1.430 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: 5.010 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.100 Process input model: 33.580 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 : 0.007 0.060 12004 Z= 0.466 Angle : 0.776 7.763 16292 Z= 0.445 Chirality : 0.052 0.210 1808 Planarity : 0.004 0.038 2084 Dihedral : 15.546 103.465 4468 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 7.64 % 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: -3.74 (0.18), residues: 1468 helix: -3.54 (0.13), residues: 568 sheet: -1.95 (0.30), residues: 244 loop : -1.44 (0.22), residues: 656 *********************** 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 174 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 78 time to evaluate : 1.501 Fit side-chains revert: symmetry clash outliers start: 96 outliers final: 18 residues processed: 167 average time/residue: 1.0784 time to fit residues: 198.1404 Evaluate side-chains 85 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 1.8334 ------------------------------------------------------------------------------- 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: 0.8980 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 59 GLN A 101 HIS A 161 HIS A 162 ASN D 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 12004 Z= 0.333 Angle : 0.627 5.773 16292 Z= 0.311 Chirality : 0.048 0.162 1808 Planarity : 0.004 0.032 2084 Dihedral : 7.369 97.840 1672 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 3.50 % 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: -2.39 (0.20), residues: 1468 helix: -2.29 (0.18), residues: 552 sheet: -1.43 (0.30), residues: 260 loop : -0.75 (0.23), residues: 656 *********************** 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 114 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 70 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 26 residues processed: 105 average time/residue: 1.1835 time to fit residues: 136.2222 Evaluate side-chains 92 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 66 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 1.1673 time to fit residues: 4.4490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 chunk 108 optimal weight: 9.9990 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 12 ASN B 101 HIS C 101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.033 12004 Z= 0.435 Angle : 0.643 6.392 16292 Z= 0.318 Chirality : 0.050 0.140 1808 Planarity : 0.004 0.033 2084 Dihedral : 7.240 96.632 1672 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 3.74 % 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: -1.79 (0.21), residues: 1468 helix: -1.62 (0.19), residues: 584 sheet: -1.13 (0.32), residues: 260 loop : -0.49 (0.24), residues: 624 *********************** 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 114 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 67 time to evaluate : 1.446 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 29 residues processed: 106 average time/residue: 1.1087 time to fit residues: 129.6208 Evaluate side-chains 95 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 66 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 1 average time/residue: 1.1191 time to fit residues: 3.1425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 0.0050 chunk 64 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2370 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= 0.176 Angle : 0.534 5.726 16292 Z= 0.256 Chirality : 0.045 0.135 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.866 88.923 1672 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 2.55 % 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: -1.09 (0.22), residues: 1468 helix: -0.99 (0.21), residues: 584 sheet: -0.98 (0.33), residues: 256 loop : -0.06 (0.26), residues: 628 *********************** 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 101 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 69 time to evaluate : 1.388 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 22 residues processed: 96 average time/residue: 1.1687 time to fit residues: 123.0903 Evaluate side-chains 88 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 1.7557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.032 12004 Z= 0.414 Angle : 0.614 7.040 16292 Z= 0.297 Chirality : 0.049 0.135 1808 Planarity : 0.004 0.031 2084 Dihedral : 6.895 87.916 1672 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 3.42 % 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: -0.95 (0.22), residues: 1468 helix: -0.82 (0.21), residues: 584 sheet: -0.87 (0.33), residues: 260 loop : -0.05 (0.26), residues: 624 *********************** 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 109 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 66 time to evaluate : 1.579 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 32 residues processed: 105 average time/residue: 1.1011 time to fit residues: 128.0891 Evaluate side-chains 98 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 66 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 1.9942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 12004 Z= 0.152 Angle : 0.519 5.648 16292 Z= 0.244 Chirality : 0.045 0.132 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.572 83.624 1672 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1468 helix: -0.53 (0.21), residues: 596 sheet: -0.78 (0.33), residues: 260 loop : 0.15 (0.27), residues: 612 *********************** 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 100 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 66 time to evaluate : 1.515 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 26 residues processed: 97 average time/residue: 1.1560 time to fit residues: 123.5092 Evaluate side-chains 92 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 66 time to evaluate : 1.374 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 26 residues processed: 0 time to fit residues: 1.8577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12004 Z= 0.169 Angle : 0.515 5.679 16292 Z= 0.242 Chirality : 0.045 0.131 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.318 79.491 1672 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 2.87 % 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: -0.35 (0.23), residues: 1468 helix: -0.32 (0.22), residues: 596 sheet: -0.37 (0.32), residues: 284 loop : 0.24 (0.28), residues: 588 *********************** 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 102 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 66 time to evaluate : 1.404 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 30 residues processed: 98 average time/residue: 1.1986 time to fit residues: 129.1118 Evaluate side-chains 96 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 66 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 1.3782 time to fit residues: 3.6686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12004 Z= 0.169 Angle : 0.507 5.788 16292 Z= 0.237 Chirality : 0.045 0.134 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.164 77.342 1672 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 3.11 % 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: -0.22 (0.23), residues: 1468 helix: -0.21 (0.22), residues: 596 sheet: -0.31 (0.32), residues: 284 loop : 0.30 (0.28), residues: 588 *********************** 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 105 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 66 time to evaluate : 1.278 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 29 residues processed: 102 average time/residue: 1.1719 time to fit residues: 131.3604 Evaluate side-chains 95 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 66 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 1.8820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 132 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 40 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 12004 Z= 0.130 Angle : 0.501 5.747 16292 Z= 0.234 Chirality : 0.044 0.149 1808 Planarity : 0.003 0.026 2084 Dihedral : 5.943 72.845 1672 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.55 % 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: 0.01 (0.23), residues: 1468 helix: 0.01 (0.22), residues: 580 sheet: -0.22 (0.32), residues: 284 loop : 0.40 (0.28), residues: 604 *********************** 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 98 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 66 time to evaluate : 1.509 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 29 residues processed: 96 average time/residue: 1.1545 time to fit residues: 122.4356 Evaluate side-chains 95 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 66 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 1 average time/residue: 1.1273 time to fit residues: 3.1468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 125 optimal weight: 0.0980 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 12004 Z= 0.301 Angle : 0.559 9.248 16292 Z= 0.264 Chirality : 0.047 0.165 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.128 76.710 1672 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 2.39 % 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: -0.23 (0.23), residues: 1468 helix: -0.10 (0.22), residues: 592 sheet: -0.55 (0.33), residues: 260 loop : 0.26 (0.27), residues: 616 ********************** 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 96 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 66 time to evaluate : 1.613 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 27 residues processed: 94 average time/residue: 1.1321 time to fit residues: 117.2204 Evaluate side-chains 93 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 26 residues processed: 1 average time/residue: 1.0417 time to fit residues: 2.8506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 14 optimal weight: 0.0010 chunk 21 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.043777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.035846 restraints weight = 48570.786| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 3.25 r_work: 0.2558 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2989 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= 0.218 Angle : 0.526 5.845 16292 Z= 0.247 Chirality : 0.046 0.166 1808 Planarity : 0.003 0.026 2084 Dihedral : 6.097 76.801 1672 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 2.39 % 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: -0.17 (0.23), residues: 1468 helix: -0.06 (0.22), residues: 592 sheet: -0.52 (0.34), residues: 260 loop : 0.29 (0.27), residues: 616 =============================================================================== Job complete usr+sys time: 2948.29 seconds wall clock time: 53 minutes 49.72 seconds (3229.72 seconds total)