Starting phenix.real_space_refine on Sun Jul 21 14:51:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/07_2024/8v2o_42918_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/07_2024/8v2o_42918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/07_2024/8v2o_42918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/07_2024/8v2o_42918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/07_2024/8v2o_42918_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2o_42918/07_2024/8v2o_42918_neut.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.166 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9245 2.51 5 N 2470 2.21 5 O 2825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 107": "OE1" <-> "OE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 286": "OD1" <-> "OD2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E GLU 364": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14660 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.21, per 1000 atoms: 0.56 Number of scatterers: 14660 At special positions: 0 Unit cell: (81.32, 104.86, 192.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2825 8.00 N 2470 7.00 C 9245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.5 seconds 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 30 sheets defined 49.5% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.854A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.648A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.597A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.239A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.626A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.850A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.520A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.733A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.637A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.015A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.504A pdb=" N CYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.850A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.544A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.623A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.599A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.727A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.031A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.526A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.501A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.850A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.504A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.682A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.599A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.604A pdb=" N ARG D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.000A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 91 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.501A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.833A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.648A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.638A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 3.612A pdb=" N ARG E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.065A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.533A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.388A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.172A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.517A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.473A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.193A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.578A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.407A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 4.229A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.570A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.289A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.501A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.476A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 727 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.69 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4770 1.34 - 1.47: 3444 1.47 - 1.59: 6574 1.59 - 1.71: 17 1.71 - 1.84: 180 Bond restraints: 14985 Sorted by residual: bond pdb=" CB PRO B 367 " pdb=" CG PRO B 367 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.65e+00 bond pdb=" CG PRO B 367 " pdb=" CD PRO B 367 " ideal model delta sigma weight residual 1.503 1.404 0.099 3.40e-02 8.65e+02 8.49e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.85e+00 bond pdb=" CB PRO A 367 " pdb=" CG PRO A 367 " ideal model delta sigma weight residual 1.492 1.632 -0.140 5.00e-02 4.00e+02 7.80e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.70e+00 ... (remaining 14980 not shown) Histogram of bond angle deviations from ideal: 95.01 - 103.26: 188 103.26 - 111.51: 6557 111.51 - 119.76: 6634 119.76 - 128.02: 6828 128.02 - 136.27: 133 Bond angle restraints: 20340 Sorted by residual: angle pdb=" CA PRO B 367 " pdb=" N PRO B 367 " pdb=" CD PRO B 367 " ideal model delta sigma weight residual 112.00 95.15 16.85 1.40e+00 5.10e-01 1.45e+02 angle pdb=" CA PRO A 367 " pdb=" N PRO A 367 " pdb=" CD PRO A 367 " ideal model delta sigma weight residual 112.00 96.41 15.59 1.40e+00 5.10e-01 1.24e+02 angle pdb=" CB MET A 305 " pdb=" CG MET A 305 " pdb=" SD MET A 305 " ideal model delta sigma weight residual 112.70 130.45 -17.75 3.00e+00 1.11e-01 3.50e+01 angle pdb=" N PRO B 367 " pdb=" CD PRO B 367 " pdb=" CG PRO B 367 " ideal model delta sigma weight residual 103.20 95.01 8.19 1.50e+00 4.44e-01 2.98e+01 angle pdb=" CA PRO D 367 " pdb=" N PRO D 367 " pdb=" CD PRO D 367 " ideal model delta sigma weight residual 112.00 104.70 7.30 1.40e+00 5.10e-01 2.72e+01 ... (remaining 20335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 8765 34.77 - 69.54: 235 69.54 - 104.31: 10 104.31 - 139.08: 5 139.08 - 173.85: 5 Dihedral angle restraints: 9020 sinusoidal: 3645 harmonic: 5375 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.86 -173.85 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.57 -173.57 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.21 -173.21 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 9017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1661 0.047 - 0.094: 407 0.094 - 0.141: 161 0.141 - 0.188: 17 0.188 - 0.235: 4 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE E 151 " pdb=" CA ILE E 151 " pdb=" CG1 ILE E 151 " pdb=" CG2 ILE E 151 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2247 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 366 " -0.144 5.00e-02 4.00e+02 2.00e-01 6.41e+01 pdb=" N PRO B 367 " 0.345 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.112 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 366 " 0.141 5.00e-02 4.00e+02 1.98e-01 6.26e+01 pdb=" N PRO A 367 " -0.341 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " 0.111 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 366 " -0.115 5.00e-02 4.00e+02 1.71e-01 4.70e+01 pdb=" N PRO D 367 " 0.296 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " -0.097 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " -0.084 5.00e-02 4.00e+02 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3151 2.78 - 3.31: 12362 3.31 - 3.84: 25472 3.84 - 4.37: 31011 4.37 - 4.90: 52240 Nonbonded interactions: 124236 Sorted by model distance: nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.253 2.170 nonbonded pdb=" O GLN D 314 " pdb=" OG1 THR D 318 " model vdw 2.312 2.440 nonbonded pdb=" O GLN A 314 " pdb=" OG1 THR A 318 " model vdw 2.319 2.440 nonbonded pdb=" O GLN E 314 " pdb=" OG1 THR E 318 " model vdw 2.320 2.440 nonbonded pdb=" O GLN B 314 " pdb=" OG1 THR B 318 " model vdw 2.320 2.440 ... (remaining 124231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.520 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 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:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 14985 Z= 0.279 Angle : 0.800 17.746 20340 Z= 0.411 Chirality : 0.049 0.235 2250 Planarity : 0.009 0.200 2605 Dihedral : 15.842 173.854 5580 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.70 % Allowed : 12.10 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 1835 helix: -1.65 (0.15), residues: 775 sheet: 0.28 (0.27), residues: 375 loop : -0.33 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 356 HIS 0.004 0.001 HIS C 161 PHE 0.014 0.001 PHE C 255 TYR 0.010 0.001 TYR D 306 ARG 0.023 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.800 Fit side-chains REVERT: D 246 GLN cc_start: 0.9107 (mt0) cc_final: 0.8750 (mp10) outliers start: 11 outliers final: 5 residues processed: 126 average time/residue: 1.8968 time to fit residues: 257.7634 Evaluate side-chains 120 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 140 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 14985 Z= 0.491 Angle : 0.667 7.336 20340 Z= 0.323 Chirality : 0.048 0.150 2250 Planarity : 0.006 0.107 2605 Dihedral : 9.854 146.918 2095 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.21 % Allowed : 10.06 % Favored : 88.73 % 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: 0.28 (0.20), residues: 1835 helix: -0.02 (0.18), residues: 770 sheet: 0.54 (0.29), residues: 325 loop : 0.54 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 340 HIS 0.006 0.001 HIS C 161 PHE 0.017 0.002 PHE C 262 TYR 0.008 0.001 TYR A 306 ARG 0.009 0.001 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.614 Fit side-chains REVERT: A 176 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8276 (mtt) REVERT: B 227 MET cc_start: 0.8834 (mmm) cc_final: 0.8617 (mmm) REVERT: D 246 GLN cc_start: 0.8867 (mt0) cc_final: 0.8493 (mt0) REVERT: D 314 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8388 (tt0) outliers start: 19 outliers final: 4 residues processed: 121 average time/residue: 1.9423 time to fit residues: 251.6240 Evaluate side-chains 113 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 137 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 162 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14985 Z= 0.161 Angle : 0.534 5.967 20340 Z= 0.251 Chirality : 0.043 0.135 2250 Planarity : 0.005 0.088 2605 Dihedral : 8.370 129.598 2091 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.53 % Allowed : 10.25 % Favored : 88.22 % 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 (0.20), residues: 1835 helix: 0.70 (0.19), residues: 765 sheet: 0.58 (0.29), residues: 325 loop : 0.84 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE B 255 TYR 0.006 0.001 TYR D 69 ARG 0.009 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.745 Fit side-chains REVERT: B 227 MET cc_start: 0.8880 (mmm) cc_final: 0.8545 (mmm) REVERT: C 246 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8683 (mt0) REVERT: C 354 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: D 176 MET cc_start: 0.9147 (mtm) cc_final: 0.8745 (mtm) REVERT: D 246 GLN cc_start: 0.8884 (mt0) cc_final: 0.8504 (mt0) REVERT: E 246 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8502 (mp10) outliers start: 24 outliers final: 4 residues processed: 123 average time/residue: 1.8059 time to fit residues: 238.7589 Evaluate side-chains 119 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 246 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 168 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14985 Z= 0.230 Angle : 0.545 5.911 20340 Z= 0.258 Chirality : 0.044 0.130 2250 Planarity : 0.004 0.072 2605 Dihedral : 7.091 107.749 2090 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.40 % Allowed : 10.45 % Favored : 88.15 % 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: 1.06 (0.20), residues: 1835 helix: 0.81 (0.19), residues: 800 sheet: 0.64 (0.29), residues: 325 loop : 0.88 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.004 0.001 HIS B 161 PHE 0.008 0.001 PHE C 262 TYR 0.006 0.001 TYR E 188 ARG 0.010 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.826 Fit side-chains REVERT: A 176 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8279 (mtt) REVERT: B 227 MET cc_start: 0.8916 (mmm) cc_final: 0.8518 (mmm) REVERT: B 314 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: C 246 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8589 (mt0) REVERT: D 128 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8504 (p0) REVERT: D 176 MET cc_start: 0.9239 (mtm) cc_final: 0.8909 (mtm) REVERT: D 246 GLN cc_start: 0.8832 (mt0) cc_final: 0.8442 (mt0) outliers start: 22 outliers final: 9 residues processed: 120 average time/residue: 1.8178 time to fit residues: 234.6051 Evaluate side-chains 124 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 128 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14985 Z= 0.295 Angle : 0.566 6.469 20340 Z= 0.269 Chirality : 0.045 0.136 2250 Planarity : 0.004 0.064 2605 Dihedral : 6.693 95.325 2090 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.17 % Allowed : 9.68 % Favored : 88.15 % 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: 1.26 (0.21), residues: 1835 helix: 1.07 (0.20), residues: 770 sheet: 0.64 (0.28), residues: 325 loop : 0.92 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE C 262 TYR 0.006 0.001 TYR C 240 ARG 0.011 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 1.639 Fit side-chains REVERT: A 176 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8288 (mtt) REVERT: B 314 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: C 246 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8494 (mt0) REVERT: D 95 ARG cc_start: 0.8863 (mtp85) cc_final: 0.8603 (mtt-85) REVERT: D 128 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8607 (p0) REVERT: D 176 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8977 (mtm) REVERT: D 246 GLN cc_start: 0.8804 (mt0) cc_final: 0.8424 (mt0) REVERT: D 314 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: E 354 GLN cc_start: 0.8877 (pm20) cc_final: 0.8468 (pm20) outliers start: 34 outliers final: 10 residues processed: 130 average time/residue: 1.8193 time to fit residues: 253.8399 Evaluate side-chains 128 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 0.0000 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14985 Z= 0.159 Angle : 0.525 6.946 20340 Z= 0.246 Chirality : 0.043 0.131 2250 Planarity : 0.004 0.058 2605 Dihedral : 6.293 84.648 2090 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.08 % Allowed : 11.15 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1835 helix: 1.11 (0.19), residues: 800 sheet: 0.72 (0.29), residues: 325 loop : 0.97 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE B 255 TYR 0.005 0.001 TYR C 69 ARG 0.011 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.567 Fit side-chains REVERT: B 107 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8457 (tm-30) REVERT: B 176 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8817 (mtm) REVERT: C 246 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8572 (mt0) REVERT: C 354 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: D 95 ARG cc_start: 0.8807 (mtp85) cc_final: 0.8545 (mtt-85) REVERT: D 246 GLN cc_start: 0.8784 (mt0) cc_final: 0.8429 (mt0) REVERT: E 354 GLN cc_start: 0.8860 (pm20) cc_final: 0.8471 (pm20) outliers start: 17 outliers final: 7 residues processed: 120 average time/residue: 1.7142 time to fit residues: 221.5053 Evaluate side-chains 125 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 150 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14985 Z= 0.355 Angle : 0.586 8.442 20340 Z= 0.279 Chirality : 0.046 0.167 2250 Planarity : 0.004 0.053 2605 Dihedral : 6.521 92.088 2090 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.34 % Allowed : 10.89 % Favored : 87.77 % 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: 1.39 (0.21), residues: 1835 helix: 1.22 (0.20), residues: 770 sheet: 0.69 (0.28), residues: 325 loop : 0.95 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS C 161 PHE 0.011 0.001 PHE C 262 TYR 0.007 0.001 TYR C 240 ARG 0.012 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 1.674 Fit side-chains REVERT: A 176 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8294 (mtt) REVERT: B 314 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: C 246 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: D 95 ARG cc_start: 0.8847 (mtp85) cc_final: 0.8595 (mtt-85) REVERT: D 246 GLN cc_start: 0.8789 (mt0) cc_final: 0.8434 (mt0) REVERT: D 314 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: E 354 GLN cc_start: 0.8829 (pm20) cc_final: 0.8433 (pm20) outliers start: 21 outliers final: 8 residues processed: 124 average time/residue: 1.7971 time to fit residues: 239.6673 Evaluate side-chains 126 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14985 Z= 0.174 Angle : 0.537 7.759 20340 Z= 0.252 Chirality : 0.043 0.131 2250 Planarity : 0.004 0.053 2605 Dihedral : 6.239 85.045 2090 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.89 % Allowed : 11.40 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.21), residues: 1835 helix: 1.36 (0.20), residues: 770 sheet: 0.76 (0.29), residues: 325 loop : 1.00 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.004 0.001 HIS D 161 PHE 0.007 0.001 PHE D 255 TYR 0.005 0.001 TYR C 69 ARG 0.013 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.814 Fit side-chains REVERT: A 355 MET cc_start: 0.9252 (mtm) cc_final: 0.9043 (mtp) REVERT: B 176 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8821 (mtm) REVERT: C 246 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8550 (mt0) REVERT: C 354 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: D 95 ARG cc_start: 0.8799 (mtp85) cc_final: 0.8552 (mtt-85) REVERT: D 176 MET cc_start: 0.9173 (mtm) cc_final: 0.8820 (mtm) REVERT: D 246 GLN cc_start: 0.8753 (mt0) cc_final: 0.8409 (mt0) REVERT: D 314 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: E 354 GLN cc_start: 0.8816 (pm20) cc_final: 0.8469 (pm20) outliers start: 14 outliers final: 6 residues processed: 120 average time/residue: 1.8277 time to fit residues: 236.1919 Evaluate side-chains 124 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14985 Z= 0.199 Angle : 0.543 8.146 20340 Z= 0.255 Chirality : 0.044 0.130 2250 Planarity : 0.003 0.051 2605 Dihedral : 6.157 83.793 2090 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.96 % Allowed : 11.53 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1835 helix: 1.40 (0.20), residues: 770 sheet: 0.78 (0.29), residues: 325 loop : 1.02 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.003 0.001 HIS A 161 PHE 0.006 0.001 PHE C 262 TYR 0.005 0.001 TYR C 69 ARG 0.017 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.643 Fit side-chains REVERT: A 355 MET cc_start: 0.9264 (mtm) cc_final: 0.9024 (mtp) REVERT: C 246 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8538 (mt0) REVERT: C 354 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8385 (pm20) REVERT: D 95 ARG cc_start: 0.8794 (mtp85) cc_final: 0.8550 (mtt-85) REVERT: D 176 MET cc_start: 0.9193 (mtm) cc_final: 0.8761 (mtm) REVERT: D 246 GLN cc_start: 0.8761 (mt0) cc_final: 0.8416 (mt0) REVERT: D 314 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8328 (tt0) outliers start: 15 outliers final: 9 residues processed: 122 average time/residue: 1.7846 time to fit residues: 234.1792 Evaluate side-chains 126 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 184 optimal weight: 0.0870 chunk 169 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 14985 Z= 0.222 Angle : 0.758 59.199 20340 Z= 0.413 Chirality : 0.045 0.518 2250 Planarity : 0.004 0.050 2605 Dihedral : 6.145 83.779 2090 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 0.96 % Allowed : 11.72 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.21), residues: 1835 helix: 1.41 (0.20), residues: 770 sheet: 0.78 (0.29), residues: 325 loop : 1.02 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS A 161 PHE 0.006 0.001 PHE C 262 TYR 0.004 0.001 TYR C 69 ARG 0.018 0.000 ARG E 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.719 Fit side-chains REVERT: A 355 MET cc_start: 0.9262 (mtm) cc_final: 0.9022 (mtp) REVERT: C 246 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8539 (mt0) REVERT: C 354 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: D 95 ARG cc_start: 0.8794 (mtp85) cc_final: 0.8549 (mtt-85) REVERT: D 176 MET cc_start: 0.9193 (mtm) cc_final: 0.8760 (mtm) REVERT: D 246 GLN cc_start: 0.8760 (mt0) cc_final: 0.8411 (mt0) REVERT: D 314 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8325 (tt0) outliers start: 15 outliers final: 8 residues processed: 122 average time/residue: 1.8339 time to fit residues: 240.9917 Evaluate side-chains 125 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.0070 chunk 44 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.058502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.043599 restraints weight = 32707.986| |-----------------------------------------------------------------------------| r_work (start): 0.2538 rms_B_bonded: 2.52 r_work: 0.2399 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2266 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 14985 Z= 0.222 Angle : 0.758 59.199 20340 Z= 0.413 Chirality : 0.045 0.518 2250 Planarity : 0.004 0.050 2605 Dihedral : 6.145 83.779 2090 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 0.76 % Allowed : 11.91 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.21), residues: 1835 helix: 1.41 (0.20), residues: 770 sheet: 0.78 (0.29), residues: 325 loop : 1.02 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS A 161 PHE 0.006 0.001 PHE C 262 TYR 0.004 0.001 TYR C 69 ARG 0.018 0.000 ARG E 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4593.76 seconds wall clock time: 82 minutes 18.61 seconds (4938.61 seconds total)