Starting phenix.real_space_refine on Fri Mar 15 13:45:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kll_0711/03_2024/6kll_0711_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kll_0711/03_2024/6kll_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_0711/03_2024/6kll_0711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kll_0711/03_2024/6kll_0711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kll_0711/03_2024/6kll_0711_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kll_0711/03_2024/6kll_0711_updated.pdb" } resolution = 3.0 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= 0.003 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A 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-5265/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: 6.52, per 1000 atoms: 0.55 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: 4.23 Conformation dependent library (CDL) restraints added in 2.2 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 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: 2.58 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: 3.71 Time building geometry restraints manager: 4.63 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 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: 1.190 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: 4.490 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 33.550 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 % Allowed : 8.28 % Favored : 84.08 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.003 0.001 HIS B 275 PHE 0.011 0.002 PHE B 124 TYR 0.007 0.001 TYR C 69 ARG 0.003 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 78 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8314 (mmt) cc_final: 0.7231 (mmm) REVERT: B 82 MET cc_start: 0.8125 (tpt) cc_final: 0.7872 (tpt) REVERT: C 4 GLU cc_start: 0.5388 (OUTLIER) cc_final: 0.4140 (tm-30) REVERT: C 5 THR cc_start: 0.6181 (OUTLIER) cc_final: 0.5470 (m) REVERT: C 123 MET cc_start: 0.8647 (mmm) cc_final: 0.8398 (mmt) REVERT: C 233 SER cc_start: 0.5856 (OUTLIER) cc_final: 0.5385 (t) REVERT: D 4 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.4748 (tm-30) outliers start: 96 outliers final: 18 residues processed: 167 average time/residue: 1.0814 time to fit residues: 198.0062 Evaluate side-chains 89 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 277 THR 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: 10.0000 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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: 0.8542 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 12004 Z= 0.362 Angle : 0.640 5.876 16292 Z= 0.318 Chirality : 0.049 0.160 1808 Planarity : 0.004 0.031 2084 Dihedral : 8.833 98.342 1702 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.66 % Allowed : 14.49 % Favored : 81.85 % 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: -2.44 (0.20), residues: 1468 helix: -2.33 (0.18), residues: 552 sheet: -1.41 (0.30), residues: 260 loop : -0.81 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.005 0.001 HIS D 275 PHE 0.011 0.001 PHE C 223 TYR 0.013 0.001 TYR D 294 ARG 0.006 0.000 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 115 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 69 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8505 (mmt) cc_final: 0.8203 (mmm) REVERT: B 82 MET cc_start: 0.8134 (tpt) cc_final: 0.7874 (tpt) REVERT: B 325 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7102 (ptm) REVERT: C 50 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7690 (mmtm) REVERT: C 313 MET cc_start: 0.8656 (mmm) cc_final: 0.8426 (mmt) REVERT: D 82 MET cc_start: 0.8584 (tpt) cc_final: 0.8296 (tpt) outliers start: 46 outliers final: 22 residues processed: 106 average time/residue: 1.2052 time to fit residues: 139.6310 Evaluate side-chains 90 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 355 MET 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: 10.0000 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 B 161 HIS C 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 12004 Z= 0.511 Angle : 0.680 7.087 16292 Z= 0.337 Chirality : 0.051 0.140 1808 Planarity : 0.004 0.033 2084 Dihedral : 7.896 98.586 1683 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.34 % Allowed : 16.48 % Favored : 80.18 % 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: -1.93 (0.21), residues: 1468 helix: -1.71 (0.19), residues: 584 sheet: -1.12 (0.32), residues: 260 loop : -0.65 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS D 275 PHE 0.014 0.002 PHE C 223 TYR 0.009 0.001 TYR C 188 ARG 0.004 0.000 ARG C 372 *********************** 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 109 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 67 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8684 (mt) REVERT: B 82 MET cc_start: 0.8132 (tpt) cc_final: 0.7883 (tpt) REVERT: C 50 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7789 (mmtm) REVERT: D 82 MET cc_start: 0.8610 (tpt) cc_final: 0.8350 (tpt) REVERT: D 270 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.3884 (mp0) outliers start: 42 outliers final: 23 residues processed: 102 average time/residue: 1.1985 time to fit residues: 133.9188 Evaluate side-chains 92 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 66 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 355 MET 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: 4.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12004 Z= 0.252 Angle : 0.567 6.388 16292 Z= 0.274 Chirality : 0.046 0.135 1808 Planarity : 0.003 0.030 2084 Dihedral : 7.404 93.742 1678 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.75 % Allowed : 17.75 % Favored : 80.49 % 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: -1.33 (0.22), residues: 1468 helix: -1.12 (0.21), residues: 580 sheet: -1.02 (0.33), residues: 256 loop : -0.32 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 79 HIS 0.003 0.001 HIS D 275 PHE 0.008 0.001 PHE C 255 TYR 0.008 0.001 TYR D 69 ARG 0.008 0.000 ARG A 290 *********************** 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 89 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.8182 (mmm) cc_final: 0.6220 (mpp) REVERT: B 82 MET cc_start: 0.8174 (tpt) cc_final: 0.7938 (tpt) REVERT: C 50 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7737 (mmtm) REVERT: D 82 MET cc_start: 0.8589 (tpt) cc_final: 0.8370 (tpt) REVERT: D 270 GLU cc_start: 0.5774 (OUTLIER) cc_final: 0.3918 (mp0) outliers start: 22 outliers final: 11 residues processed: 81 average time/residue: 1.4106 time to fit residues: 123.4927 Evaluate side-chains 79 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 GLU 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: 6.9990 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 0.0050 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12004 Z= 0.201 Angle : 0.538 7.499 16292 Z= 0.256 Chirality : 0.045 0.134 1808 Planarity : 0.003 0.029 2084 Dihedral : 6.902 85.827 1675 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.99 % Allowed : 17.60 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.22), residues: 1468 helix: -0.69 (0.21), residues: 584 sheet: -0.88 (0.33), residues: 256 loop : -0.01 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 79 HIS 0.003 0.001 HIS D 275 PHE 0.007 0.001 PHE C 255 TYR 0.008 0.001 TYR D 69 ARG 0.003 0.000 ARG C 372 *********************** 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 93 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 68 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8229 (mmm) cc_final: 0.6369 (mpp) REVERT: D 270 GLU cc_start: 0.5821 (OUTLIER) cc_final: 0.3965 (mp0) outliers start: 25 outliers final: 12 residues processed: 88 average time/residue: 1.2823 time to fit residues: 122.5314 Evaluate side-chains 79 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 12004 Z= 0.444 Angle : 0.624 5.967 16292 Z= 0.302 Chirality : 0.049 0.135 1808 Planarity : 0.004 0.032 2084 Dihedral : 7.024 87.293 1673 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.79 % Allowed : 17.52 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.22), residues: 1468 helix: -0.76 (0.21), residues: 596 sheet: -0.82 (0.34), residues: 256 loop : -0.18 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 79 HIS 0.003 0.001 HIS A 40 PHE 0.010 0.001 PHE D 223 TYR 0.009 0.001 TYR A 166 ARG 0.002 0.000 ARG C 28 *********************** 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 101 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 66 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8327 (mmm) cc_final: 0.6484 (mpp) REVERT: D 176 MET cc_start: 0.7756 (mmm) cc_final: 0.7482 (mtt) REVERT: D 270 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.4085 (mp0) outliers start: 35 outliers final: 20 residues processed: 93 average time/residue: 1.2369 time to fit residues: 125.6467 Evaluate side-chains 87 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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: 0.8546 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 : 0.002 0.031 12004 Z= 0.150 Angle : 0.528 9.039 16292 Z= 0.248 Chirality : 0.045 0.131 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.693 83.784 1673 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.51 % Allowed : 18.31 % Favored : 80.18 % 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: -0.60 (0.23), residues: 1468 helix: -0.42 (0.21), residues: 596 sheet: -0.74 (0.34), residues: 256 loop : 0.06 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 356 HIS 0.006 0.001 HIS A 275 PHE 0.007 0.001 PHE A 31 TYR 0.008 0.001 TYR D 69 ARG 0.003 0.000 ARG C 372 *********************** 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 85 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.4965 (OUTLIER) cc_final: 0.4636 (tp30) REVERT: B 44 MET cc_start: 0.8256 (mmm) cc_final: 0.6459 (mpp) REVERT: D 176 MET cc_start: 0.7766 (mmm) cc_final: 0.7536 (mtt) outliers start: 19 outliers final: 12 residues processed: 81 average time/residue: 1.3930 time to fit residues: 122.3412 Evaluate side-chains 79 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8554 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12004 Z= 0.199 Angle : 0.528 5.775 16292 Z= 0.249 Chirality : 0.045 0.132 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.492 81.476 1673 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.35 % Allowed : 19.19 % Favored : 79.46 % 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: -0.47 (0.23), residues: 1468 helix: -0.32 (0.21), residues: 596 sheet: -0.69 (0.34), residues: 256 loop : 0.13 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 356 HIS 0.006 0.001 HIS A 275 PHE 0.007 0.001 PHE A 223 TYR 0.008 0.001 TYR D 69 ARG 0.002 0.000 ARG A 256 *********************** 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 83 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8071 (tpt) cc_final: 0.7801 (tpt) REVERT: B 44 MET cc_start: 0.8257 (mmm) cc_final: 0.6476 (mpp) outliers start: 17 outliers final: 12 residues processed: 80 average time/residue: 1.3664 time to fit residues: 118.7280 Evaluate side-chains 78 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 0.2980 chunk 40 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 125 optimal weight: 0.3980 chunk 87 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12004 Z= 0.150 Angle : 0.508 5.812 16292 Z= 0.238 Chirality : 0.044 0.129 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.167 77.253 1673 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.19 % Allowed : 19.27 % Favored : 79.54 % 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: -0.24 (0.23), residues: 1468 helix: -0.16 (0.22), residues: 596 sheet: -0.30 (0.32), residues: 280 loop : 0.19 (0.28), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 86 HIS 0.005 0.001 HIS A 275 PHE 0.007 0.001 PHE C 255 TYR 0.008 0.001 TYR D 69 ARG 0.003 0.000 ARG C 372 *********************** 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 82 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8173 (mmm) cc_final: 0.6356 (mpp) REVERT: C 82 MET cc_start: 0.8101 (mmm) cc_final: 0.7790 (tpt) outliers start: 15 outliers final: 10 residues processed: 80 average time/residue: 1.4637 time to fit residues: 126.5420 Evaluate side-chains 76 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 147 optimal weight: 0.0770 chunk 135 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 overall best weight: 2.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3005 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= 0.218 Angle : 0.529 5.926 16292 Z= 0.249 Chirality : 0.046 0.171 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.126 77.016 1672 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.04 % Allowed : 19.51 % Favored : 79.46 % 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: -0.12 (0.22), residues: 592 sheet: -0.30 (0.32), residues: 280 loop : 0.17 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 86 HIS 0.005 0.001 HIS A 275 PHE 0.007 0.001 PHE C 255 TYR 0.020 0.001 TYR A 279 ARG 0.002 0.000 ARG C 372 ********************** 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 79 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8235 (mmm) cc_final: 0.6487 (mpp) REVERT: C 82 MET cc_start: 0.8175 (mmm) cc_final: 0.7969 (tpt) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 1.4431 time to fit residues: 120.3372 Evaluate side-chains 76 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.036064 restraints weight = 48418.661| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.18 r_work: 0.2566 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12004 Z= 0.192 Angle : 0.519 5.839 16292 Z= 0.243 Chirality : 0.045 0.184 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.064 76.089 1672 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.88 % Allowed : 19.75 % Favored : 79.38 % 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: -0.20 (0.23), residues: 1468 helix: -0.04 (0.22), residues: 592 sheet: -0.58 (0.34), residues: 256 loop : 0.25 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 86 HIS 0.006 0.001 HIS A 275 PHE 0.008 0.001 PHE C 255 TYR 0.007 0.001 TYR D 69 ARG 0.002 0.000 ARG C 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.96 seconds wall clock time: 53 minutes 53.77 seconds (3233.77 seconds total)